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biotinylated peanut agglutinin (pna)  (Vector Laboratories)


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    Structured Review

    Vector Laboratories biotinylated peanut agglutinin (pna)
    Biotinylated Peanut Agglutinin (Pna), supplied by Vector Laboratories, used in various techniques. Bioz Stars score: 95/100, based on 911 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/peanut+agglutinin+pna/Biotinylated+Peanut+Agglutinin+(PNA)/custom%40b-1075%4042414656
    Average 95 stars, based on 911 article reviews
    biotinylated peanut agglutinin (pna) - by Bioz Stars, 2026-09
    95/100 stars

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    Related Articles

    Staining:

    Article Title: Characterization of Metabolic Patterns in Mouse Spermatogenesis and Its Clinical Implications in Humans.
    Article Snippet: .. The sperm acrosomes were stained using Peanut Agglutinin (PNA) (RL-1072, Vector laboratories, Newark, CA, USA) for 60 min at a 1:500 dilution. .. The photographs were visualized using the Zeiss LSM800 laser-scanning microscope(Carl Zeiss, Oberkochen, Baden-Württemberg, Germany).

    Article Title: Bmal1 Deletion Alters Mitochondrial Microstructure and Function in Mouse Cone Photoreceptors
    Article Snippet: Primaries antibodies were labeled using Proteintech FlexAble Antibody labeling Kit (KFA001, KFA002) prior to incubate samples. .. Cones inner segments were stained using Peanut Agglutinin (PNA), Rhodamine (RL-1072, Vector Labs 1:1000) After washing with PBS, slides were mounted with ProLong TM Gold Antifade Mountant with DAPI (Invitrogen TM ) and retinal sections were visualized with a fluorescence microscope (Zeiss LSM700). .. HEK293Cells were seeded in 24 well dishes, 24 hours later, were transfected with 10 ng of Mic60 promoter-GL4.13 or Mutated Mic60 promoter-GL4.13, 1 ng of pRL-CMV Vector (Promega E226A), along with 150 ng of Bmal1-CMV-pcDNA3.1, CLOCK-CMVpcDNA3.1.

    Article Title: Characterization of Metabolic Patterns in Mouse Spermatogenesis and Its Clinical Implications in Humans
    Article Snippet: .. The sperm acrosomes were stained using Peanut Agglutinin (PNA) (RL-1072, Vector laboratories, Newark, CA, USA) for 60 min at a 1:500 dilution. .. The photographs were visualized using the Zeiss LSM800 laser-scanning microscope(Carl Zeiss, Oberkochen, Baden-Württemberg, Germany).

    Fluorescence:

    Article Title: Bmal1 Deletion Alters Mitochondrial Microstructure and Function in Mouse Cone Photoreceptors
    Article Snippet: Primaries antibodies were labeled using Proteintech FlexAble Antibody labeling Kit (KFA001, KFA002) prior to incubate samples. .. Cones inner segments were stained using Peanut Agglutinin (PNA), Rhodamine (RL-1072, Vector Labs 1:1000) After washing with PBS, slides were mounted with ProLong TM Gold Antifade Mountant with DAPI (Invitrogen TM ) and retinal sections were visualized with a fluorescence microscope (Zeiss LSM700). .. HEK293Cells were seeded in 24 well dishes, 24 hours later, were transfected with 10 ng of Mic60 promoter-GL4.13 or Mutated Mic60 promoter-GL4.13, 1 ng of pRL-CMV Vector (Promega E226A), along with 150 ng of Bmal1-CMV-pcDNA3.1, CLOCK-CMVpcDNA3.1.

    Microscopy:

    Article Title: Bmal1 Deletion Alters Mitochondrial Microstructure and Function in Mouse Cone Photoreceptors
    Article Snippet: Primaries antibodies were labeled using Proteintech FlexAble Antibody labeling Kit (KFA001, KFA002) prior to incubate samples. .. Cones inner segments were stained using Peanut Agglutinin (PNA), Rhodamine (RL-1072, Vector Labs 1:1000) After washing with PBS, slides were mounted with ProLong TM Gold Antifade Mountant with DAPI (Invitrogen TM ) and retinal sections were visualized with a fluorescence microscope (Zeiss LSM700). .. HEK293Cells were seeded in 24 well dishes, 24 hours later, were transfected with 10 ng of Mic60 promoter-GL4.13 or Mutated Mic60 promoter-GL4.13, 1 ng of pRL-CMV Vector (Promega E226A), along with 150 ng of Bmal1-CMV-pcDNA3.1, CLOCK-CMVpcDNA3.1.

    Whole Genome Amplification:

    Article Title: Single-cell mapping of the glycocalyx in the adult human and mouse ocular surface
    Article Snippet: .. Unconjugated lectins—including Aleuria aurantia lectin (AAL), Maclura pomifera agglutinin 17 (MPA), Maackia amurensis agglutinin I (MAA I), Concanavalin A (ConA), Datura stramonium 18 agglutinin (DSA), wheat germ agglutinin (WGA), peanut agglutinin (PNA), and Erythrina cristagalli 19 agglutinin (ECA)—as well as biotinylated Sambucus nigra agglutinin I (SNA I), were obtained from 20 Vector Laboratories (Newark, CA, USA). .. DNA oligonucleotides for lectin conjugation were 21 synthesized by Integrated DNA Technologies (Coralville, IA, USA).

    Article Title: Single-cell mapping of the glycocalyx in the adult human and mouse ocular surface
    Article Snippet: Lectins were conjugated to DNA oligonucleotides, each carrying a unique barcode sequence for precise identification and a capture sequence compatible with the 10x Genomics Next GEM kit. .. Unconjugated lectins—including AAL, Maclura pomifera agglutinin (MPA), Maackia amurensis agglutinin I (MAA I), Concanavalin A (ConA), Datura stramonium agglutinin (DSA), wheat germ agglutinin (WGA), peanut agglutinin (PNA), and Erythrina cristagalli agglutinin (ECA)—as well as biotinylated Sambucus nigra agglutinin I (SNA I), were obtained from Vector Laboratories (Newark, CA, USA). .. DNA oligonucleotides for lectin conjugation were synthesized by Integrated DNA Technologies (Coralville, IA, USA).

    Reverse Transcription:

    Article Title: Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-ELOF1 Abclonal custom-ordered Rabbit Anti-AID Abclonal Cat#A16217; RRID: AB_2763671 Rabbit Anti-RPB1 S2-p Abcam Cat#ab5095; RRID: AB_304749 Rat Anti-RPB1 S5-p Abcam Cat#ab252852 Rabbit Anti-pan-RPB1 Bethyl Cat#A304-405A; RRID: AB_2620600 Rabbit Anti-RPB1 NTD Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit Anti-SPT5 Santa Cruz Cat#sc-28678; RRID: AB_668824 Mouse Anti-Flag-Tag Abmart Cat#M20008; RRID: AB_2713960 Rabbit Anti-HA-Tag Cell Signaling Technology Cat#3724; RRID: AB_1549585 Rabbit Anti-Histone H3 (acetyl K27) Abcam Cat#ab4729; RRID: AB_2118291 Mouse Anti-cyclobutane pyrimidine dimers (CPDs) Cosmo Bio Cat#NMDND001 Rat Anti-CD40 ThermoFisher Cat#16-0401-82; RRID: AB_468941 Goat Anti-IgM, APC SouthernBiotech Cat#1020-11S; RRID: AB_2794210 Rat Anti-IgA, PE eBioscience Cat#12-4204-83; RRID: AB_465918 Rat Anti-IgG1, FITC BD Bioscience Cat#553443; RRID: AB_394862 Rat Anti-IgG1, PE BD Bioscience Cat#550083; RRID: AB_393553 Rat Anti-IgE, FITC SouthernBiotech Cat#1130-02; RRID: AB_2794616 Rat Anti-IgG3, FITC BD Bioscience Cat#553403; RRID: AB_394840 Rat Anti-CD45R (B220), APC eBioscience Cat#47-0452-82; RRID: AB_1518810 Bacterial and virus strains BL21(DE3) Competent Cells NEW ENGLAND BioLabs Cat#C2527H DH5a Competent Cells TIANGEN Cat#CB101 Stbl3 Competent Cells Exinbio Cat#CC104-01 Chemicals, peptides, and recombinant proteins Recombinant Human TGF-beta 1 Novoprotein Cat#CA59 Recombinant Mouse IL-4 Novoprotein Cat#CK15 Blasticidin S Selleck Cat#S7419 Puromycin GIBCO Cat#1767008 Lipopolysaccharide (LPS) Sigma Aldrich Cat#L2630 Zeocin InvivoGen Cat#11006-33-0 Cisplatin MedChemExpress Cat#HY-17393 Biotin-11-ATP Perkinelmer Cat#NEL544001EA Biotin-11-CTP Perkinelmer Cat#NEL542001EA Biotin-11-UTP Perkinelmer Cat#NEL543001EA Biotin-11-GTP Perkinelmer Cat#NEL545001EA 5,6-Dichlorobenzimidazole riboside (DRB) MedChemExpress Cat#HY-14392 NVP-2 MedChemExpress Cat#HY-12214A dTAG-13 ligand Tocris Cat#6605 4-Hydroxytamoxifen Sigma Aldrich Cat#H7904 N-Ethylmaleimide Sangon Cat#A600450 BeyoZonase Super Nuclease Beyotime Cat#D7126 Q5 High-Fidelity DNA polymerase NEW ENGLAND BioLabs Cat#M0491L Q5U Hot Start High-Fidelity DNA Polymerase NEW ENGLAND BioLabs Cat#M0515S (Continued on next page) e1 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 RNA Ligase 1 (ssRNA Ligase) NEW ENGLAND BioLabs Cat#M0204L SuperScript II reverse transcriptase Invitrogen Cat#18064071 TransStart FastPfu DNA Polymerase TransGen Cat#AP221-03 Peanut Agglutinin (PNA), Fluorescein Vector Laboratories Cat#FL-1071 Critical commercial assays Protein A Magnetic Beads ThermoFisher Cat#88846 Anti-Mouse IgM MicroBeads Miltenyi Biotec Cat#130-047-301 Dynabeads MyOne Streptavidin C1 ThermoFisher Cat#65001 Pierce Glutathione Magnetic Agarose Beads ThermoFisher Cat#78601 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7760S NEBNext rRNA Depletion Kit (Human/Mouse/Rat) NEW ENGLAND BioLabs Cat#E6310L NEBNext Ultra II DNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7645S CellTrace CFSE Cell Proliferation Kit Invitrogen Cat#C34554 cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693159001 Cell Counting Kit-8 APExBIO Cat#K1018 EasySep mouse B cell isolation kit STEMCELL Cat#19854 4-15% BeyoGel Plus Precast PAGE Gel Beyotime Cat#P0466 Micro Bio-Spin P-30 Columns BioRad Cat#732-6250 Deposited data CRISPR screening This paper SRA: PRJNA1124255 Amplicon-seq This paper SRA: PRJNA1124255 RNA-seq This paper GEO: GSE284306 ChIP-seq This paper GEO: GSE284303 PRO-seq This paper GEO: GSE284305 HTGTS This paper SRA: PRJNA1124255 Damage-seq This paper GEO: GSE284303 PADD-seq This paper GEO: GSE284303 PRO-seq of SPT5-dTAG DLD1 cells Hu et al.14 GEO: GSE180845 GRO-seq of SPT5 depleted MEF Fitz et al.17 GEO: GSE106313 ChIP-seq of RPB1 S2-p in RPE1-iCas9 cells van der Weegen et al.30 GEO: GSE149760 All the unprocessed and uncompressed imaging data This paper Mendeley Data doi: https://doi.org/10.17632/ 3hxdrzfvsw.1 Experimental models: Cell lines CH12F3 Nakamura et al.65 N/A CH12F3-mcherry (1 clone) Yang et al.44 N/A CH12F3 Elof1-/- (5 clones, #1 and #2 were used in most experiments) This paper N/A CH12F3 Ung-/- Msh2-/- (2 clones) Yang et al.44 N/A CH12F3 Ung-/- Msh2-/- Elof1-/- (2 clones) This paper N/A CH12F3 Ung-/- Msh2-/- Aicda-/- (1 clone) Xie et al.45 N/A CH12F3 Aicda-/- (1 clone) Han et al.66 N/A CH12F3 Elof1-/- Aicda-/- (2 clones) This paper N/A CH12F3 Csb (Ercc6)-/- (5 clones, #1 were used in most experiments) This paper N/A CH12F3 Csb-/-Elof1-/- (1 clone) This paper N/A CH12F3 RPB1K1268R (8 clones, #1 were used in most experiments) This paper N/A CH12F3 Sa-invert (2 clones) This paper N/A (Continued on next page) Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER K-562 ATCC Cat#CCL-243 Drosophila S2 ATCC Cat#CRL-1963 Experimental models: Organisms/strains CD21-Cre Kraus et al.42 JAX stock #006368 Elof1flox/ko This paper, Shanghai Model Organisms Center N/A Aicda-/- Muramatsu et al.67 N/A See Table S3 for the information of each mouse used in this paper This paper N/A Oligonucleotides See Table S3 This paper N/A Recombinant DNA lentiCRISPRv2 Sanjana et al.68 Addgene #52961 pX330-Sm-Cas9 Liu et al.41 N/A pX330-Sg1-Cas9 Liu et al.41 N/A lenti_dcas9_3xflag_blast Liu et al.69 Addgene #112133 pX330-Sm-MS2-MCP-hA3a This paper N/A pX330-Sg1-MS2-MCP-hA3a This paper N/A pGEX6P1-GST-Dsk2 This paper N/A pMX-ELOF1-3xHA-puro This paper N/A pMX-ELOF1-DN-3xHA-puro This paper N/A pMX-ELOF1-SDK-3xHA-puro This paper N/A pMX-ELOF1-ZF-3xHA-puro This paper N/A pMX-ELOF1-Dock-3xHA-puro This paper N/A pMX-3xHA-puro This paper N/A pMX-ELOF1-GFP-3xHA-puro This paper N/A pMX-GFP-3xHA-puro This paper N/A pMX-AID-3xFlag-ER-puro This paper N/A pMX-3xFlag-ER-puro This paper N/A Software and algorithms MAGeCK (v0.5.6) Li et al.70 https://sourceforge.net/projects/mageck/ STAR (v2.7.3a) Dobin et al.71 https://github.com/alexdobin/STAR Bowtie2 (v2.3.1) Langmead and Salzberg72 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml featureCounts (v1.6.4) Liao et al.73 https://github.com/ShiLab-Bioinformatics/subread DESeq2 (v1.38.3) Love et al.74 https://bioconductor.org/packages/release/bioc/html/ DESeq2.html cutadapt (v2.3) Martin75 https://cutadapt.readthedocs.io/en/stable/ deepTools (v3.2.1) Ramı́rez et al.76 https://github.com/deeptools/deepTools SAMtools (v1.9) Li et al.77 https://www.htslib.org/ picard (v2.21.1) Broad Institute https://broadinstitute.github.io/picard/ transloc_pipeline Hu et al.78 https://github.com/robinmeyers/transloc_pipeline BEDTools (v2.29.2) Quinlan and Hall79 https://bedtools.readthedocs.io/en/latest/index.html IGV (v2.3.98) Robinson et al.80 https://software.broadinstitute.org/software/igv/ landmarc Chen et al.47 https://bitbucket.org/Fred_Alt_Lab/landmarc/src/master/ Alphafold2 (ColabFold, v1.5.2) Mirdita et al.49 https://colab.research.google.com/github/sokrypton/ ColabFold/blob/main/AlphaFold2.ipynb Tidyverse (v2.0.0) Wickham et al.81 https://www.tidyverse.org/ R (4.2.3) R Core Team https://www.r-project.org/ Python (v3.8.8) Python Software Foundation https://www.python.org/ ImageJ (v2.14.0/1.54f) Schneider et al.82 https://imagej.nih.gov/ij/download.html e3 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025

    Magnetic Beads:

    Article Title: Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-ELOF1 Abclonal custom-ordered Rabbit Anti-AID Abclonal Cat#A16217; RRID: AB_2763671 Rabbit Anti-RPB1 S2-p Abcam Cat#ab5095; RRID: AB_304749 Rat Anti-RPB1 S5-p Abcam Cat#ab252852 Rabbit Anti-pan-RPB1 Bethyl Cat#A304-405A; RRID: AB_2620600 Rabbit Anti-RPB1 NTD Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit Anti-SPT5 Santa Cruz Cat#sc-28678; RRID: AB_668824 Mouse Anti-Flag-Tag Abmart Cat#M20008; RRID: AB_2713960 Rabbit Anti-HA-Tag Cell Signaling Technology Cat#3724; RRID: AB_1549585 Rabbit Anti-Histone H3 (acetyl K27) Abcam Cat#ab4729; RRID: AB_2118291 Mouse Anti-cyclobutane pyrimidine dimers (CPDs) Cosmo Bio Cat#NMDND001 Rat Anti-CD40 ThermoFisher Cat#16-0401-82; RRID: AB_468941 Goat Anti-IgM, APC SouthernBiotech Cat#1020-11S; RRID: AB_2794210 Rat Anti-IgA, PE eBioscience Cat#12-4204-83; RRID: AB_465918 Rat Anti-IgG1, FITC BD Bioscience Cat#553443; RRID: AB_394862 Rat Anti-IgG1, PE BD Bioscience Cat#550083; RRID: AB_393553 Rat Anti-IgE, FITC SouthernBiotech Cat#1130-02; RRID: AB_2794616 Rat Anti-IgG3, FITC BD Bioscience Cat#553403; RRID: AB_394840 Rat Anti-CD45R (B220), APC eBioscience Cat#47-0452-82; RRID: AB_1518810 Bacterial and virus strains BL21(DE3) Competent Cells NEW ENGLAND BioLabs Cat#C2527H DH5a Competent Cells TIANGEN Cat#CB101 Stbl3 Competent Cells Exinbio Cat#CC104-01 Chemicals, peptides, and recombinant proteins Recombinant Human TGF-beta 1 Novoprotein Cat#CA59 Recombinant Mouse IL-4 Novoprotein Cat#CK15 Blasticidin S Selleck Cat#S7419 Puromycin GIBCO Cat#1767008 Lipopolysaccharide (LPS) Sigma Aldrich Cat#L2630 Zeocin InvivoGen Cat#11006-33-0 Cisplatin MedChemExpress Cat#HY-17393 Biotin-11-ATP Perkinelmer Cat#NEL544001EA Biotin-11-CTP Perkinelmer Cat#NEL542001EA Biotin-11-UTP Perkinelmer Cat#NEL543001EA Biotin-11-GTP Perkinelmer Cat#NEL545001EA 5,6-Dichlorobenzimidazole riboside (DRB) MedChemExpress Cat#HY-14392 NVP-2 MedChemExpress Cat#HY-12214A dTAG-13 ligand Tocris Cat#6605 4-Hydroxytamoxifen Sigma Aldrich Cat#H7904 N-Ethylmaleimide Sangon Cat#A600450 BeyoZonase Super Nuclease Beyotime Cat#D7126 Q5 High-Fidelity DNA polymerase NEW ENGLAND BioLabs Cat#M0491L Q5U Hot Start High-Fidelity DNA Polymerase NEW ENGLAND BioLabs Cat#M0515S (Continued on next page) e1 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 RNA Ligase 1 (ssRNA Ligase) NEW ENGLAND BioLabs Cat#M0204L SuperScript II reverse transcriptase Invitrogen Cat#18064071 TransStart FastPfu DNA Polymerase TransGen Cat#AP221-03 Peanut Agglutinin (PNA), Fluorescein Vector Laboratories Cat#FL-1071 Critical commercial assays Protein A Magnetic Beads ThermoFisher Cat#88846 Anti-Mouse IgM MicroBeads Miltenyi Biotec Cat#130-047-301 Dynabeads MyOne Streptavidin C1 ThermoFisher Cat#65001 Pierce Glutathione Magnetic Agarose Beads ThermoFisher Cat#78601 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7760S NEBNext rRNA Depletion Kit (Human/Mouse/Rat) NEW ENGLAND BioLabs Cat#E6310L NEBNext Ultra II DNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7645S CellTrace CFSE Cell Proliferation Kit Invitrogen Cat#C34554 cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693159001 Cell Counting Kit-8 APExBIO Cat#K1018 EasySep mouse B cell isolation kit STEMCELL Cat#19854 4-15% BeyoGel Plus Precast PAGE Gel Beyotime Cat#P0466 Micro Bio-Spin P-30 Columns BioRad Cat#732-6250 Deposited data CRISPR screening This paper SRA: PRJNA1124255 Amplicon-seq This paper SRA: PRJNA1124255 RNA-seq This paper GEO: GSE284306 ChIP-seq This paper GEO: GSE284303 PRO-seq This paper GEO: GSE284305 HTGTS This paper SRA: PRJNA1124255 Damage-seq This paper GEO: GSE284303 PADD-seq This paper GEO: GSE284303 PRO-seq of SPT5-dTAG DLD1 cells Hu et al.14 GEO: GSE180845 GRO-seq of SPT5 depleted MEF Fitz et al.17 GEO: GSE106313 ChIP-seq of RPB1 S2-p in RPE1-iCas9 cells van der Weegen et al.30 GEO: GSE149760 All the unprocessed and uncompressed imaging data This paper Mendeley Data doi: https://doi.org/10.17632/ 3hxdrzfvsw.1 Experimental models: Cell lines CH12F3 Nakamura et al.65 N/A CH12F3-mcherry (1 clone) Yang et al.44 N/A CH12F3 Elof1-/- (5 clones, #1 and #2 were used in most experiments) This paper N/A CH12F3 Ung-/- Msh2-/- (2 clones) Yang et al.44 N/A CH12F3 Ung-/- Msh2-/- Elof1-/- (2 clones) This paper N/A CH12F3 Ung-/- Msh2-/- Aicda-/- (1 clone) Xie et al.45 N/A CH12F3 Aicda-/- (1 clone) Han et al.66 N/A CH12F3 Elof1-/- Aicda-/- (2 clones) This paper N/A CH12F3 Csb (Ercc6)-/- (5 clones, #1 were used in most experiments) This paper N/A CH12F3 Csb-/-Elof1-/- (1 clone) This paper N/A CH12F3 RPB1K1268R (8 clones, #1 were used in most experiments) This paper N/A CH12F3 Sa-invert (2 clones) This paper N/A (Continued on next page) Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER K-562 ATCC Cat#CCL-243 Drosophila S2 ATCC Cat#CRL-1963 Experimental models: Organisms/strains CD21-Cre Kraus et al.42 JAX stock #006368 Elof1flox/ko This paper, Shanghai Model Organisms Center N/A Aicda-/- Muramatsu et al.67 N/A See Table S3 for the information of each mouse used in this paper This paper N/A Oligonucleotides See Table S3 This paper N/A Recombinant DNA lentiCRISPRv2 Sanjana et al.68 Addgene #52961 pX330-Sm-Cas9 Liu et al.41 N/A pX330-Sg1-Cas9 Liu et al.41 N/A lenti_dcas9_3xflag_blast Liu et al.69 Addgene #112133 pX330-Sm-MS2-MCP-hA3a This paper N/A pX330-Sg1-MS2-MCP-hA3a This paper N/A pGEX6P1-GST-Dsk2 This paper N/A pMX-ELOF1-3xHA-puro This paper N/A pMX-ELOF1-DN-3xHA-puro This paper N/A pMX-ELOF1-SDK-3xHA-puro This paper N/A pMX-ELOF1-ZF-3xHA-puro This paper N/A pMX-ELOF1-Dock-3xHA-puro This paper N/A pMX-3xHA-puro This paper N/A pMX-ELOF1-GFP-3xHA-puro This paper N/A pMX-GFP-3xHA-puro This paper N/A pMX-AID-3xFlag-ER-puro This paper N/A pMX-3xFlag-ER-puro This paper N/A Software and algorithms MAGeCK (v0.5.6) Li et al.70 https://sourceforge.net/projects/mageck/ STAR (v2.7.3a) Dobin et al.71 https://github.com/alexdobin/STAR Bowtie2 (v2.3.1) Langmead and Salzberg72 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml featureCounts (v1.6.4) Liao et al.73 https://github.com/ShiLab-Bioinformatics/subread DESeq2 (v1.38.3) Love et al.74 https://bioconductor.org/packages/release/bioc/html/ DESeq2.html cutadapt (v2.3) Martin75 https://cutadapt.readthedocs.io/en/stable/ deepTools (v3.2.1) Ramı́rez et al.76 https://github.com/deeptools/deepTools SAMtools (v1.9) Li et al.77 https://www.htslib.org/ picard (v2.21.1) Broad Institute https://broadinstitute.github.io/picard/ transloc_pipeline Hu et al.78 https://github.com/robinmeyers/transloc_pipeline BEDTools (v2.29.2) Quinlan and Hall79 https://bedtools.readthedocs.io/en/latest/index.html IGV (v2.3.98) Robinson et al.80 https://software.broadinstitute.org/software/igv/ landmarc Chen et al.47 https://bitbucket.org/Fred_Alt_Lab/landmarc/src/master/ Alphafold2 (ColabFold, v1.5.2) Mirdita et al.49 https://colab.research.google.com/github/sokrypton/ ColabFold/blob/main/AlphaFold2.ipynb Tidyverse (v2.0.0) Wickham et al.81 https://www.tidyverse.org/ R (4.2.3) R Core Team https://www.r-project.org/ Python (v3.8.8) Python Software Foundation https://www.python.org/ ImageJ (v2.14.0/1.54f) Schneider et al.82 https://imagej.nih.gov/ij/download.html e3 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025

    Protease Inhibitor:

    Article Title: Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-ELOF1 Abclonal custom-ordered Rabbit Anti-AID Abclonal Cat#A16217; RRID: AB_2763671 Rabbit Anti-RPB1 S2-p Abcam Cat#ab5095; RRID: AB_304749 Rat Anti-RPB1 S5-p Abcam Cat#ab252852 Rabbit Anti-pan-RPB1 Bethyl Cat#A304-405A; RRID: AB_2620600 Rabbit Anti-RPB1 NTD Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit Anti-SPT5 Santa Cruz Cat#sc-28678; RRID: AB_668824 Mouse Anti-Flag-Tag Abmart Cat#M20008; RRID: AB_2713960 Rabbit Anti-HA-Tag Cell Signaling Technology Cat#3724; RRID: AB_1549585 Rabbit Anti-Histone H3 (acetyl K27) Abcam Cat#ab4729; RRID: AB_2118291 Mouse Anti-cyclobutane pyrimidine dimers (CPDs) Cosmo Bio Cat#NMDND001 Rat Anti-CD40 ThermoFisher Cat#16-0401-82; RRID: AB_468941 Goat Anti-IgM, APC SouthernBiotech Cat#1020-11S; RRID: AB_2794210 Rat Anti-IgA, PE eBioscience Cat#12-4204-83; RRID: AB_465918 Rat Anti-IgG1, FITC BD Bioscience Cat#553443; RRID: AB_394862 Rat Anti-IgG1, PE BD Bioscience Cat#550083; RRID: AB_393553 Rat Anti-IgE, FITC SouthernBiotech Cat#1130-02; RRID: AB_2794616 Rat Anti-IgG3, FITC BD Bioscience Cat#553403; RRID: AB_394840 Rat Anti-CD45R (B220), APC eBioscience Cat#47-0452-82; RRID: AB_1518810 Bacterial and virus strains BL21(DE3) Competent Cells NEW ENGLAND BioLabs Cat#C2527H DH5a Competent Cells TIANGEN Cat#CB101 Stbl3 Competent Cells Exinbio Cat#CC104-01 Chemicals, peptides, and recombinant proteins Recombinant Human TGF-beta 1 Novoprotein Cat#CA59 Recombinant Mouse IL-4 Novoprotein Cat#CK15 Blasticidin S Selleck Cat#S7419 Puromycin GIBCO Cat#1767008 Lipopolysaccharide (LPS) Sigma Aldrich Cat#L2630 Zeocin InvivoGen Cat#11006-33-0 Cisplatin MedChemExpress Cat#HY-17393 Biotin-11-ATP Perkinelmer Cat#NEL544001EA Biotin-11-CTP Perkinelmer Cat#NEL542001EA Biotin-11-UTP Perkinelmer Cat#NEL543001EA Biotin-11-GTP Perkinelmer Cat#NEL545001EA 5,6-Dichlorobenzimidazole riboside (DRB) MedChemExpress Cat#HY-14392 NVP-2 MedChemExpress Cat#HY-12214A dTAG-13 ligand Tocris Cat#6605 4-Hydroxytamoxifen Sigma Aldrich Cat#H7904 N-Ethylmaleimide Sangon Cat#A600450 BeyoZonase Super Nuclease Beyotime Cat#D7126 Q5 High-Fidelity DNA polymerase NEW ENGLAND BioLabs Cat#M0491L Q5U Hot Start High-Fidelity DNA Polymerase NEW ENGLAND BioLabs Cat#M0515S (Continued on next page) e1 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 RNA Ligase 1 (ssRNA Ligase) NEW ENGLAND BioLabs Cat#M0204L SuperScript II reverse transcriptase Invitrogen Cat#18064071 TransStart FastPfu DNA Polymerase TransGen Cat#AP221-03 Peanut Agglutinin (PNA), Fluorescein Vector Laboratories Cat#FL-1071 Critical commercial assays Protein A Magnetic Beads ThermoFisher Cat#88846 Anti-Mouse IgM MicroBeads Miltenyi Biotec Cat#130-047-301 Dynabeads MyOne Streptavidin C1 ThermoFisher Cat#65001 Pierce Glutathione Magnetic Agarose Beads ThermoFisher Cat#78601 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7760S NEBNext rRNA Depletion Kit (Human/Mouse/Rat) NEW ENGLAND BioLabs Cat#E6310L NEBNext Ultra II DNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7645S CellTrace CFSE Cell Proliferation Kit Invitrogen Cat#C34554 cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693159001 Cell Counting Kit-8 APExBIO Cat#K1018 EasySep mouse B cell isolation kit STEMCELL Cat#19854 4-15% BeyoGel Plus Precast PAGE Gel Beyotime Cat#P0466 Micro Bio-Spin P-30 Columns BioRad Cat#732-6250 Deposited data CRISPR screening This paper SRA: PRJNA1124255 Amplicon-seq This paper SRA: PRJNA1124255 RNA-seq This paper GEO: GSE284306 ChIP-seq This paper GEO: GSE284303 PRO-seq This paper GEO: GSE284305 HTGTS This paper SRA: PRJNA1124255 Damage-seq This paper GEO: GSE284303 PADD-seq This paper GEO: GSE284303 PRO-seq of SPT5-dTAG DLD1 cells Hu et al.14 GEO: GSE180845 GRO-seq of SPT5 depleted MEF Fitz et al.17 GEO: GSE106313 ChIP-seq of RPB1 S2-p in RPE1-iCas9 cells van der Weegen et al.30 GEO: GSE149760 All the unprocessed and uncompressed imaging data This paper Mendeley Data doi: https://doi.org/10.17632/ 3hxdrzfvsw.1 Experimental models: Cell lines CH12F3 Nakamura et al.65 N/A CH12F3-mcherry (1 clone) Yang et al.44 N/A CH12F3 Elof1-/- (5 clones, #1 and #2 were used in most experiments) This paper N/A CH12F3 Ung-/- Msh2-/- (2 clones) Yang et al.44 N/A CH12F3 Ung-/- Msh2-/- Elof1-/- (2 clones) This paper N/A CH12F3 Ung-/- Msh2-/- Aicda-/- (1 clone) Xie et al.45 N/A CH12F3 Aicda-/- (1 clone) Han et al.66 N/A CH12F3 Elof1-/- Aicda-/- (2 clones) This paper N/A CH12F3 Csb (Ercc6)-/- (5 clones, #1 were used in most experiments) This paper N/A CH12F3 Csb-/-Elof1-/- (1 clone) This paper N/A CH12F3 RPB1K1268R (8 clones, #1 were used in most experiments) This paper N/A CH12F3 Sa-invert (2 clones) This paper N/A (Continued on next page) Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER K-562 ATCC Cat#CCL-243 Drosophila S2 ATCC Cat#CRL-1963 Experimental models: Organisms/strains CD21-Cre Kraus et al.42 JAX stock #006368 Elof1flox/ko This paper, Shanghai Model Organisms Center N/A Aicda-/- Muramatsu et al.67 N/A See Table S3 for the information of each mouse used in this paper This paper N/A Oligonucleotides See Table S3 This paper N/A Recombinant DNA lentiCRISPRv2 Sanjana et al.68 Addgene #52961 pX330-Sm-Cas9 Liu et al.41 N/A pX330-Sg1-Cas9 Liu et al.41 N/A lenti_dcas9_3xflag_blast Liu et al.69 Addgene #112133 pX330-Sm-MS2-MCP-hA3a This paper N/A pX330-Sg1-MS2-MCP-hA3a This paper N/A pGEX6P1-GST-Dsk2 This paper N/A pMX-ELOF1-3xHA-puro This paper N/A pMX-ELOF1-DN-3xHA-puro This paper N/A pMX-ELOF1-SDK-3xHA-puro This paper N/A pMX-ELOF1-ZF-3xHA-puro This paper N/A pMX-ELOF1-Dock-3xHA-puro This paper N/A pMX-3xHA-puro This paper N/A pMX-ELOF1-GFP-3xHA-puro This paper N/A pMX-GFP-3xHA-puro This paper N/A pMX-AID-3xFlag-ER-puro This paper N/A pMX-3xFlag-ER-puro This paper N/A Software and algorithms MAGeCK (v0.5.6) Li et al.70 https://sourceforge.net/projects/mageck/ STAR (v2.7.3a) Dobin et al.71 https://github.com/alexdobin/STAR Bowtie2 (v2.3.1) Langmead and Salzberg72 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml featureCounts (v1.6.4) Liao et al.73 https://github.com/ShiLab-Bioinformatics/subread DESeq2 (v1.38.3) Love et al.74 https://bioconductor.org/packages/release/bioc/html/ DESeq2.html cutadapt (v2.3) Martin75 https://cutadapt.readthedocs.io/en/stable/ deepTools (v3.2.1) Ramı́rez et al.76 https://github.com/deeptools/deepTools SAMtools (v1.9) Li et al.77 https://www.htslib.org/ picard (v2.21.1) Broad Institute https://broadinstitute.github.io/picard/ transloc_pipeline Hu et al.78 https://github.com/robinmeyers/transloc_pipeline BEDTools (v2.29.2) Quinlan and Hall79 https://bedtools.readthedocs.io/en/latest/index.html IGV (v2.3.98) Robinson et al.80 https://software.broadinstitute.org/software/igv/ landmarc Chen et al.47 https://bitbucket.org/Fred_Alt_Lab/landmarc/src/master/ Alphafold2 (ColabFold, v1.5.2) Mirdita et al.49 https://colab.research.google.com/github/sokrypton/ ColabFold/blob/main/AlphaFold2.ipynb Tidyverse (v2.0.0) Wickham et al.81 https://www.tidyverse.org/ R (4.2.3) R Core Team https://www.r-project.org/ Python (v3.8.8) Python Software Foundation https://www.python.org/ ImageJ (v2.14.0/1.54f) Schneider et al.82 https://imagej.nih.gov/ij/download.html e3 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025

    CCK-8 Assay:

    Article Title: Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-ELOF1 Abclonal custom-ordered Rabbit Anti-AID Abclonal Cat#A16217; RRID: AB_2763671 Rabbit Anti-RPB1 S2-p Abcam Cat#ab5095; RRID: AB_304749 Rat Anti-RPB1 S5-p Abcam Cat#ab252852 Rabbit Anti-pan-RPB1 Bethyl Cat#A304-405A; RRID: AB_2620600 Rabbit Anti-RPB1 NTD Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit Anti-SPT5 Santa Cruz Cat#sc-28678; RRID: AB_668824 Mouse Anti-Flag-Tag Abmart Cat#M20008; RRID: AB_2713960 Rabbit Anti-HA-Tag Cell Signaling Technology Cat#3724; RRID: AB_1549585 Rabbit Anti-Histone H3 (acetyl K27) Abcam Cat#ab4729; RRID: AB_2118291 Mouse Anti-cyclobutane pyrimidine dimers (CPDs) Cosmo Bio Cat#NMDND001 Rat Anti-CD40 ThermoFisher Cat#16-0401-82; RRID: AB_468941 Goat Anti-IgM, APC SouthernBiotech Cat#1020-11S; RRID: AB_2794210 Rat Anti-IgA, PE eBioscience Cat#12-4204-83; RRID: AB_465918 Rat Anti-IgG1, FITC BD Bioscience Cat#553443; RRID: AB_394862 Rat Anti-IgG1, PE BD Bioscience Cat#550083; RRID: AB_393553 Rat Anti-IgE, FITC SouthernBiotech Cat#1130-02; RRID: AB_2794616 Rat Anti-IgG3, FITC BD Bioscience Cat#553403; RRID: AB_394840 Rat Anti-CD45R (B220), APC eBioscience Cat#47-0452-82; RRID: AB_1518810 Bacterial and virus strains BL21(DE3) Competent Cells NEW ENGLAND BioLabs Cat#C2527H DH5a Competent Cells TIANGEN Cat#CB101 Stbl3 Competent Cells Exinbio Cat#CC104-01 Chemicals, peptides, and recombinant proteins Recombinant Human TGF-beta 1 Novoprotein Cat#CA59 Recombinant Mouse IL-4 Novoprotein Cat#CK15 Blasticidin S Selleck Cat#S7419 Puromycin GIBCO Cat#1767008 Lipopolysaccharide (LPS) Sigma Aldrich Cat#L2630 Zeocin InvivoGen Cat#11006-33-0 Cisplatin MedChemExpress Cat#HY-17393 Biotin-11-ATP Perkinelmer Cat#NEL544001EA Biotin-11-CTP Perkinelmer Cat#NEL542001EA Biotin-11-UTP Perkinelmer Cat#NEL543001EA Biotin-11-GTP Perkinelmer Cat#NEL545001EA 5,6-Dichlorobenzimidazole riboside (DRB) MedChemExpress Cat#HY-14392 NVP-2 MedChemExpress Cat#HY-12214A dTAG-13 ligand Tocris Cat#6605 4-Hydroxytamoxifen Sigma Aldrich Cat#H7904 N-Ethylmaleimide Sangon Cat#A600450 BeyoZonase Super Nuclease Beyotime Cat#D7126 Q5 High-Fidelity DNA polymerase NEW ENGLAND BioLabs Cat#M0491L Q5U Hot Start High-Fidelity DNA Polymerase NEW ENGLAND BioLabs Cat#M0515S (Continued on next page) e1 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 RNA Ligase 1 (ssRNA Ligase) NEW ENGLAND BioLabs Cat#M0204L SuperScript II reverse transcriptase Invitrogen Cat#18064071 TransStart FastPfu DNA Polymerase TransGen Cat#AP221-03 Peanut Agglutinin (PNA), Fluorescein Vector Laboratories Cat#FL-1071 Critical commercial assays Protein A Magnetic Beads ThermoFisher Cat#88846 Anti-Mouse IgM MicroBeads Miltenyi Biotec Cat#130-047-301 Dynabeads MyOne Streptavidin C1 ThermoFisher Cat#65001 Pierce Glutathione Magnetic Agarose Beads ThermoFisher Cat#78601 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7760S NEBNext rRNA Depletion Kit (Human/Mouse/Rat) NEW ENGLAND BioLabs Cat#E6310L NEBNext Ultra II DNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7645S CellTrace CFSE Cell Proliferation Kit Invitrogen Cat#C34554 cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693159001 Cell Counting Kit-8 APExBIO Cat#K1018 EasySep mouse B cell isolation kit STEMCELL Cat#19854 4-15% BeyoGel Plus Precast PAGE Gel Beyotime Cat#P0466 Micro Bio-Spin P-30 Columns BioRad Cat#732-6250 Deposited data CRISPR screening This paper SRA: PRJNA1124255 Amplicon-seq This paper SRA: PRJNA1124255 RNA-seq This paper GEO: GSE284306 ChIP-seq This paper GEO: GSE284303 PRO-seq This paper GEO: GSE284305 HTGTS This paper SRA: PRJNA1124255 Damage-seq This paper GEO: GSE284303 PADD-seq This paper GEO: GSE284303 PRO-seq of SPT5-dTAG DLD1 cells Hu et al.14 GEO: GSE180845 GRO-seq of SPT5 depleted MEF Fitz et al.17 GEO: GSE106313 ChIP-seq of RPB1 S2-p in RPE1-iCas9 cells van der Weegen et al.30 GEO: GSE149760 All the unprocessed and uncompressed imaging data This paper Mendeley Data doi: https://doi.org/10.17632/ 3hxdrzfvsw.1 Experimental models: Cell lines CH12F3 Nakamura et al.65 N/A CH12F3-mcherry (1 clone) Yang et al.44 N/A CH12F3 Elof1-/- (5 clones, #1 and #2 were used in most experiments) This paper N/A CH12F3 Ung-/- Msh2-/- (2 clones) Yang et al.44 N/A CH12F3 Ung-/- Msh2-/- Elof1-/- (2 clones) This paper N/A CH12F3 Ung-/- Msh2-/- Aicda-/- (1 clone) Xie et al.45 N/A CH12F3 Aicda-/- (1 clone) Han et al.66 N/A CH12F3 Elof1-/- Aicda-/- (2 clones) This paper N/A CH12F3 Csb (Ercc6)-/- (5 clones, #1 were used in most experiments) This paper N/A CH12F3 Csb-/-Elof1-/- (1 clone) This paper N/A CH12F3 RPB1K1268R (8 clones, #1 were used in most experiments) This paper N/A CH12F3 Sa-invert (2 clones) This paper N/A (Continued on next page) Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER K-562 ATCC Cat#CCL-243 Drosophila S2 ATCC Cat#CRL-1963 Experimental models: Organisms/strains CD21-Cre Kraus et al.42 JAX stock #006368 Elof1flox/ko This paper, Shanghai Model Organisms Center N/A Aicda-/- Muramatsu et al.67 N/A See Table S3 for the information of each mouse used in this paper This paper N/A Oligonucleotides See Table S3 This paper N/A Recombinant DNA lentiCRISPRv2 Sanjana et al.68 Addgene #52961 pX330-Sm-Cas9 Liu et al.41 N/A pX330-Sg1-Cas9 Liu et al.41 N/A lenti_dcas9_3xflag_blast Liu et al.69 Addgene #112133 pX330-Sm-MS2-MCP-hA3a This paper N/A pX330-Sg1-MS2-MCP-hA3a This paper N/A pGEX6P1-GST-Dsk2 This paper N/A pMX-ELOF1-3xHA-puro This paper N/A pMX-ELOF1-DN-3xHA-puro This paper N/A pMX-ELOF1-SDK-3xHA-puro This paper N/A pMX-ELOF1-ZF-3xHA-puro This paper N/A pMX-ELOF1-Dock-3xHA-puro This paper N/A pMX-3xHA-puro This paper N/A pMX-ELOF1-GFP-3xHA-puro This paper N/A pMX-GFP-3xHA-puro This paper N/A pMX-AID-3xFlag-ER-puro This paper N/A pMX-3xFlag-ER-puro This paper N/A Software and algorithms MAGeCK (v0.5.6) Li et al.70 https://sourceforge.net/projects/mageck/ STAR (v2.7.3a) Dobin et al.71 https://github.com/alexdobin/STAR Bowtie2 (v2.3.1) Langmead and Salzberg72 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml featureCounts (v1.6.4) Liao et al.73 https://github.com/ShiLab-Bioinformatics/subread DESeq2 (v1.38.3) Love et al.74 https://bioconductor.org/packages/release/bioc/html/ DESeq2.html cutadapt (v2.3) Martin75 https://cutadapt.readthedocs.io/en/stable/ deepTools (v3.2.1) Ramı́rez et al.76 https://github.com/deeptools/deepTools SAMtools (v1.9) Li et al.77 https://www.htslib.org/ picard (v2.21.1) Broad Institute https://broadinstitute.github.io/picard/ transloc_pipeline Hu et al.78 https://github.com/robinmeyers/transloc_pipeline BEDTools (v2.29.2) Quinlan and Hall79 https://bedtools.readthedocs.io/en/latest/index.html IGV (v2.3.98) Robinson et al.80 https://software.broadinstitute.org/software/igv/ landmarc Chen et al.47 https://bitbucket.org/Fred_Alt_Lab/landmarc/src/master/ Alphafold2 (ColabFold, v1.5.2) Mirdita et al.49 https://colab.research.google.com/github/sokrypton/ ColabFold/blob/main/AlphaFold2.ipynb Tidyverse (v2.0.0) Wickham et al.81 https://www.tidyverse.org/ R (4.2.3) R Core Team https://www.r-project.org/ Python (v3.8.8) Python Software Foundation https://www.python.org/ ImageJ (v2.14.0/1.54f) Schneider et al.82 https://imagej.nih.gov/ij/download.html e3 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025

    Cell Isolation:

    Article Title: Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-ELOF1 Abclonal custom-ordered Rabbit Anti-AID Abclonal Cat#A16217; RRID: AB_2763671 Rabbit Anti-RPB1 S2-p Abcam Cat#ab5095; RRID: AB_304749 Rat Anti-RPB1 S5-p Abcam Cat#ab252852 Rabbit Anti-pan-RPB1 Bethyl Cat#A304-405A; RRID: AB_2620600 Rabbit Anti-RPB1 NTD Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit Anti-SPT5 Santa Cruz Cat#sc-28678; RRID: AB_668824 Mouse Anti-Flag-Tag Abmart Cat#M20008; RRID: AB_2713960 Rabbit Anti-HA-Tag Cell Signaling Technology Cat#3724; RRID: AB_1549585 Rabbit Anti-Histone H3 (acetyl K27) Abcam Cat#ab4729; RRID: AB_2118291 Mouse Anti-cyclobutane pyrimidine dimers (CPDs) Cosmo Bio Cat#NMDND001 Rat Anti-CD40 ThermoFisher Cat#16-0401-82; RRID: AB_468941 Goat Anti-IgM, APC SouthernBiotech Cat#1020-11S; RRID: AB_2794210 Rat Anti-IgA, PE eBioscience Cat#12-4204-83; RRID: AB_465918 Rat Anti-IgG1, FITC BD Bioscience Cat#553443; RRID: AB_394862 Rat Anti-IgG1, PE BD Bioscience Cat#550083; RRID: AB_393553 Rat Anti-IgE, FITC SouthernBiotech Cat#1130-02; RRID: AB_2794616 Rat Anti-IgG3, FITC BD Bioscience Cat#553403; RRID: AB_394840 Rat Anti-CD45R (B220), APC eBioscience Cat#47-0452-82; RRID: AB_1518810 Bacterial and virus strains BL21(DE3) Competent Cells NEW ENGLAND BioLabs Cat#C2527H DH5a Competent Cells TIANGEN Cat#CB101 Stbl3 Competent Cells Exinbio Cat#CC104-01 Chemicals, peptides, and recombinant proteins Recombinant Human TGF-beta 1 Novoprotein Cat#CA59 Recombinant Mouse IL-4 Novoprotein Cat#CK15 Blasticidin S Selleck Cat#S7419 Puromycin GIBCO Cat#1767008 Lipopolysaccharide (LPS) Sigma Aldrich Cat#L2630 Zeocin InvivoGen Cat#11006-33-0 Cisplatin MedChemExpress Cat#HY-17393 Biotin-11-ATP Perkinelmer Cat#NEL544001EA Biotin-11-CTP Perkinelmer Cat#NEL542001EA Biotin-11-UTP Perkinelmer Cat#NEL543001EA Biotin-11-GTP Perkinelmer Cat#NEL545001EA 5,6-Dichlorobenzimidazole riboside (DRB) MedChemExpress Cat#HY-14392 NVP-2 MedChemExpress Cat#HY-12214A dTAG-13 ligand Tocris Cat#6605 4-Hydroxytamoxifen Sigma Aldrich Cat#H7904 N-Ethylmaleimide Sangon Cat#A600450 BeyoZonase Super Nuclease Beyotime Cat#D7126 Q5 High-Fidelity DNA polymerase NEW ENGLAND BioLabs Cat#M0491L Q5U Hot Start High-Fidelity DNA Polymerase NEW ENGLAND BioLabs Cat#M0515S (Continued on next page) e1 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 RNA Ligase 1 (ssRNA Ligase) NEW ENGLAND BioLabs Cat#M0204L SuperScript II reverse transcriptase Invitrogen Cat#18064071 TransStart FastPfu DNA Polymerase TransGen Cat#AP221-03 Peanut Agglutinin (PNA), Fluorescein Vector Laboratories Cat#FL-1071 Critical commercial assays Protein A Magnetic Beads ThermoFisher Cat#88846 Anti-Mouse IgM MicroBeads Miltenyi Biotec Cat#130-047-301 Dynabeads MyOne Streptavidin C1 ThermoFisher Cat#65001 Pierce Glutathione Magnetic Agarose Beads ThermoFisher Cat#78601 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7760S NEBNext rRNA Depletion Kit (Human/Mouse/Rat) NEW ENGLAND BioLabs Cat#E6310L NEBNext Ultra II DNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7645S CellTrace CFSE Cell Proliferation Kit Invitrogen Cat#C34554 cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693159001 Cell Counting Kit-8 APExBIO Cat#K1018 EasySep mouse B cell isolation kit STEMCELL Cat#19854 4-15% BeyoGel Plus Precast PAGE Gel Beyotime Cat#P0466 Micro Bio-Spin P-30 Columns BioRad Cat#732-6250 Deposited data CRISPR screening This paper SRA: PRJNA1124255 Amplicon-seq This paper SRA: PRJNA1124255 RNA-seq This paper GEO: GSE284306 ChIP-seq This paper GEO: GSE284303 PRO-seq This paper GEO: GSE284305 HTGTS This paper SRA: PRJNA1124255 Damage-seq This paper GEO: GSE284303 PADD-seq This paper GEO: GSE284303 PRO-seq of SPT5-dTAG DLD1 cells Hu et al.14 GEO: GSE180845 GRO-seq of SPT5 depleted MEF Fitz et al.17 GEO: GSE106313 ChIP-seq of RPB1 S2-p in RPE1-iCas9 cells van der Weegen et al.30 GEO: GSE149760 All the unprocessed and uncompressed imaging data This paper Mendeley Data doi: https://doi.org/10.17632/ 3hxdrzfvsw.1 Experimental models: Cell lines CH12F3 Nakamura et al.65 N/A CH12F3-mcherry (1 clone) Yang et al.44 N/A CH12F3 Elof1-/- (5 clones, #1 and #2 were used in most experiments) This paper N/A CH12F3 Ung-/- Msh2-/- (2 clones) Yang et al.44 N/A CH12F3 Ung-/- Msh2-/- Elof1-/- (2 clones) This paper N/A CH12F3 Ung-/- Msh2-/- Aicda-/- (1 clone) Xie et al.45 N/A CH12F3 Aicda-/- (1 clone) Han et al.66 N/A CH12F3 Elof1-/- Aicda-/- (2 clones) This paper N/A CH12F3 Csb (Ercc6)-/- (5 clones, #1 were used in most experiments) This paper N/A CH12F3 Csb-/-Elof1-/- (1 clone) This paper N/A CH12F3 RPB1K1268R (8 clones, #1 were used in most experiments) This paper N/A CH12F3 Sa-invert (2 clones) This paper N/A (Continued on next page) Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER K-562 ATCC Cat#CCL-243 Drosophila S2 ATCC Cat#CRL-1963 Experimental models: Organisms/strains CD21-Cre Kraus et al.42 JAX stock #006368 Elof1flox/ko This paper, Shanghai Model Organisms Center N/A Aicda-/- Muramatsu et al.67 N/A See Table S3 for the information of each mouse used in this paper This paper N/A Oligonucleotides See Table S3 This paper N/A Recombinant DNA lentiCRISPRv2 Sanjana et al.68 Addgene #52961 pX330-Sm-Cas9 Liu et al.41 N/A pX330-Sg1-Cas9 Liu et al.41 N/A lenti_dcas9_3xflag_blast Liu et al.69 Addgene #112133 pX330-Sm-MS2-MCP-hA3a This paper N/A pX330-Sg1-MS2-MCP-hA3a This paper N/A pGEX6P1-GST-Dsk2 This paper N/A pMX-ELOF1-3xHA-puro This paper N/A pMX-ELOF1-DN-3xHA-puro This paper N/A pMX-ELOF1-SDK-3xHA-puro This paper N/A pMX-ELOF1-ZF-3xHA-puro This paper N/A pMX-ELOF1-Dock-3xHA-puro This paper N/A pMX-3xHA-puro This paper N/A pMX-ELOF1-GFP-3xHA-puro This paper N/A pMX-GFP-3xHA-puro This paper N/A pMX-AID-3xFlag-ER-puro This paper N/A pMX-3xFlag-ER-puro This paper N/A Software and algorithms MAGeCK (v0.5.6) Li et al.70 https://sourceforge.net/projects/mageck/ STAR (v2.7.3a) Dobin et al.71 https://github.com/alexdobin/STAR Bowtie2 (v2.3.1) Langmead and Salzberg72 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml featureCounts (v1.6.4) Liao et al.73 https://github.com/ShiLab-Bioinformatics/subread DESeq2 (v1.38.3) Love et al.74 https://bioconductor.org/packages/release/bioc/html/ DESeq2.html cutadapt (v2.3) Martin75 https://cutadapt.readthedocs.io/en/stable/ deepTools (v3.2.1) Ramı́rez et al.76 https://github.com/deeptools/deepTools SAMtools (v1.9) Li et al.77 https://www.htslib.org/ picard (v2.21.1) Broad Institute https://broadinstitute.github.io/picard/ transloc_pipeline Hu et al.78 https://github.com/robinmeyers/transloc_pipeline BEDTools (v2.29.2) Quinlan and Hall79 https://bedtools.readthedocs.io/en/latest/index.html IGV (v2.3.98) Robinson et al.80 https://software.broadinstitute.org/software/igv/ landmarc Chen et al.47 https://bitbucket.org/Fred_Alt_Lab/landmarc/src/master/ Alphafold2 (ColabFold, v1.5.2) Mirdita et al.49 https://colab.research.google.com/github/sokrypton/ ColabFold/blob/main/AlphaFold2.ipynb Tidyverse (v2.0.0) Wickham et al.81 https://www.tidyverse.org/ R (4.2.3) R Core Team https://www.r-project.org/ Python (v3.8.8) Python Software Foundation https://www.python.org/ ImageJ (v2.14.0/1.54f) Schneider et al.82 https://imagej.nih.gov/ij/download.html e3 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025

    Polyacrylamide Gel Electrophoresis:

    Article Title: Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-ELOF1 Abclonal custom-ordered Rabbit Anti-AID Abclonal Cat#A16217; RRID: AB_2763671 Rabbit Anti-RPB1 S2-p Abcam Cat#ab5095; RRID: AB_304749 Rat Anti-RPB1 S5-p Abcam Cat#ab252852 Rabbit Anti-pan-RPB1 Bethyl Cat#A304-405A; RRID: AB_2620600 Rabbit Anti-RPB1 NTD Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit Anti-SPT5 Santa Cruz Cat#sc-28678; RRID: AB_668824 Mouse Anti-Flag-Tag Abmart Cat#M20008; RRID: AB_2713960 Rabbit Anti-HA-Tag Cell Signaling Technology Cat#3724; RRID: AB_1549585 Rabbit Anti-Histone H3 (acetyl K27) Abcam Cat#ab4729; RRID: AB_2118291 Mouse Anti-cyclobutane pyrimidine dimers (CPDs) Cosmo Bio Cat#NMDND001 Rat Anti-CD40 ThermoFisher Cat#16-0401-82; RRID: AB_468941 Goat Anti-IgM, APC SouthernBiotech Cat#1020-11S; RRID: AB_2794210 Rat Anti-IgA, PE eBioscience Cat#12-4204-83; RRID: AB_465918 Rat Anti-IgG1, FITC BD Bioscience Cat#553443; RRID: AB_394862 Rat Anti-IgG1, PE BD Bioscience Cat#550083; RRID: AB_393553 Rat Anti-IgE, FITC SouthernBiotech Cat#1130-02; RRID: AB_2794616 Rat Anti-IgG3, FITC BD Bioscience Cat#553403; RRID: AB_394840 Rat Anti-CD45R (B220), APC eBioscience Cat#47-0452-82; RRID: AB_1518810 Bacterial and virus strains BL21(DE3) Competent Cells NEW ENGLAND BioLabs Cat#C2527H DH5a Competent Cells TIANGEN Cat#CB101 Stbl3 Competent Cells Exinbio Cat#CC104-01 Chemicals, peptides, and recombinant proteins Recombinant Human TGF-beta 1 Novoprotein Cat#CA59 Recombinant Mouse IL-4 Novoprotein Cat#CK15 Blasticidin S Selleck Cat#S7419 Puromycin GIBCO Cat#1767008 Lipopolysaccharide (LPS) Sigma Aldrich Cat#L2630 Zeocin InvivoGen Cat#11006-33-0 Cisplatin MedChemExpress Cat#HY-17393 Biotin-11-ATP Perkinelmer Cat#NEL544001EA Biotin-11-CTP Perkinelmer Cat#NEL542001EA Biotin-11-UTP Perkinelmer Cat#NEL543001EA Biotin-11-GTP Perkinelmer Cat#NEL545001EA 5,6-Dichlorobenzimidazole riboside (DRB) MedChemExpress Cat#HY-14392 NVP-2 MedChemExpress Cat#HY-12214A dTAG-13 ligand Tocris Cat#6605 4-Hydroxytamoxifen Sigma Aldrich Cat#H7904 N-Ethylmaleimide Sangon Cat#A600450 BeyoZonase Super Nuclease Beyotime Cat#D7126 Q5 High-Fidelity DNA polymerase NEW ENGLAND BioLabs Cat#M0491L Q5U Hot Start High-Fidelity DNA Polymerase NEW ENGLAND BioLabs Cat#M0515S (Continued on next page) e1 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 RNA Ligase 1 (ssRNA Ligase) NEW ENGLAND BioLabs Cat#M0204L SuperScript II reverse transcriptase Invitrogen Cat#18064071 TransStart FastPfu DNA Polymerase TransGen Cat#AP221-03 Peanut Agglutinin (PNA), Fluorescein Vector Laboratories Cat#FL-1071 Critical commercial assays Protein A Magnetic Beads ThermoFisher Cat#88846 Anti-Mouse IgM MicroBeads Miltenyi Biotec Cat#130-047-301 Dynabeads MyOne Streptavidin C1 ThermoFisher Cat#65001 Pierce Glutathione Magnetic Agarose Beads ThermoFisher Cat#78601 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7760S NEBNext rRNA Depletion Kit (Human/Mouse/Rat) NEW ENGLAND BioLabs Cat#E6310L NEBNext Ultra II DNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7645S CellTrace CFSE Cell Proliferation Kit Invitrogen Cat#C34554 cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693159001 Cell Counting Kit-8 APExBIO Cat#K1018 EasySep mouse B cell isolation kit STEMCELL Cat#19854 4-15% BeyoGel Plus Precast PAGE Gel Beyotime Cat#P0466 Micro Bio-Spin P-30 Columns BioRad Cat#732-6250 Deposited data CRISPR screening This paper SRA: PRJNA1124255 Amplicon-seq This paper SRA: PRJNA1124255 RNA-seq This paper GEO: GSE284306 ChIP-seq This paper GEO: GSE284303 PRO-seq This paper GEO: GSE284305 HTGTS This paper SRA: PRJNA1124255 Damage-seq This paper GEO: GSE284303 PADD-seq This paper GEO: GSE284303 PRO-seq of SPT5-dTAG DLD1 cells Hu et al.14 GEO: GSE180845 GRO-seq of SPT5 depleted MEF Fitz et al.17 GEO: GSE106313 ChIP-seq of RPB1 S2-p in RPE1-iCas9 cells van der Weegen et al.30 GEO: GSE149760 All the unprocessed and uncompressed imaging data This paper Mendeley Data doi: https://doi.org/10.17632/ 3hxdrzfvsw.1 Experimental models: Cell lines CH12F3 Nakamura et al.65 N/A CH12F3-mcherry (1 clone) Yang et al.44 N/A CH12F3 Elof1-/- (5 clones, #1 and #2 were used in most experiments) This paper N/A CH12F3 Ung-/- Msh2-/- (2 clones) Yang et al.44 N/A CH12F3 Ung-/- Msh2-/- Elof1-/- (2 clones) This paper N/A CH12F3 Ung-/- Msh2-/- Aicda-/- (1 clone) Xie et al.45 N/A CH12F3 Aicda-/- (1 clone) Han et al.66 N/A CH12F3 Elof1-/- Aicda-/- (2 clones) This paper N/A CH12F3 Csb (Ercc6)-/- (5 clones, #1 were used in most experiments) This paper N/A CH12F3 Csb-/-Elof1-/- (1 clone) This paper N/A CH12F3 RPB1K1268R (8 clones, #1 were used in most experiments) This paper N/A CH12F3 Sa-invert (2 clones) This paper N/A (Continued on next page) Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER K-562 ATCC Cat#CCL-243 Drosophila S2 ATCC Cat#CRL-1963 Experimental models: Organisms/strains CD21-Cre Kraus et al.42 JAX stock #006368 Elof1flox/ko This paper, Shanghai Model Organisms Center N/A Aicda-/- Muramatsu et al.67 N/A See Table S3 for the information of each mouse used in this paper This paper N/A Oligonucleotides See Table S3 This paper N/A Recombinant DNA lentiCRISPRv2 Sanjana et al.68 Addgene #52961 pX330-Sm-Cas9 Liu et al.41 N/A pX330-Sg1-Cas9 Liu et al.41 N/A lenti_dcas9_3xflag_blast Liu et al.69 Addgene #112133 pX330-Sm-MS2-MCP-hA3a This paper N/A pX330-Sg1-MS2-MCP-hA3a This paper N/A pGEX6P1-GST-Dsk2 This paper N/A pMX-ELOF1-3xHA-puro This paper N/A pMX-ELOF1-DN-3xHA-puro This paper N/A pMX-ELOF1-SDK-3xHA-puro This paper N/A pMX-ELOF1-ZF-3xHA-puro This paper N/A pMX-ELOF1-Dock-3xHA-puro This paper N/A pMX-3xHA-puro This paper N/A pMX-ELOF1-GFP-3xHA-puro This paper N/A pMX-GFP-3xHA-puro This paper N/A pMX-AID-3xFlag-ER-puro This paper N/A pMX-3xFlag-ER-puro This paper N/A Software and algorithms MAGeCK (v0.5.6) Li et al.70 https://sourceforge.net/projects/mageck/ STAR (v2.7.3a) Dobin et al.71 https://github.com/alexdobin/STAR Bowtie2 (v2.3.1) Langmead and Salzberg72 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml featureCounts (v1.6.4) Liao et al.73 https://github.com/ShiLab-Bioinformatics/subread DESeq2 (v1.38.3) Love et al.74 https://bioconductor.org/packages/release/bioc/html/ DESeq2.html cutadapt (v2.3) Martin75 https://cutadapt.readthedocs.io/en/stable/ deepTools (v3.2.1) Ramı́rez et al.76 https://github.com/deeptools/deepTools SAMtools (v1.9) Li et al.77 https://www.htslib.org/ picard (v2.21.1) Broad Institute https://broadinstitute.github.io/picard/ transloc_pipeline Hu et al.78 https://github.com/robinmeyers/transloc_pipeline BEDTools (v2.29.2) Quinlan and Hall79 https://bedtools.readthedocs.io/en/latest/index.html IGV (v2.3.98) Robinson et al.80 https://software.broadinstitute.org/software/igv/ landmarc Chen et al.47 https://bitbucket.org/Fred_Alt_Lab/landmarc/src/master/ Alphafold2 (ColabFold, v1.5.2) Mirdita et al.49 https://colab.research.google.com/github/sokrypton/ ColabFold/blob/main/AlphaFold2.ipynb Tidyverse (v2.0.0) Wickham et al.81 https://www.tidyverse.org/ R (4.2.3) R Core Team https://www.r-project.org/ Python (v3.8.8) Python Software Foundation https://www.python.org/ ImageJ (v2.14.0/1.54f) Schneider et al.82 https://imagej.nih.gov/ij/download.html e3 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025

    CRISPR:

    Article Title: Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-ELOF1 Abclonal custom-ordered Rabbit Anti-AID Abclonal Cat#A16217; RRID: AB_2763671 Rabbit Anti-RPB1 S2-p Abcam Cat#ab5095; RRID: AB_304749 Rat Anti-RPB1 S5-p Abcam Cat#ab252852 Rabbit Anti-pan-RPB1 Bethyl Cat#A304-405A; RRID: AB_2620600 Rabbit Anti-RPB1 NTD Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit Anti-SPT5 Santa Cruz Cat#sc-28678; RRID: AB_668824 Mouse Anti-Flag-Tag Abmart Cat#M20008; RRID: AB_2713960 Rabbit Anti-HA-Tag Cell Signaling Technology Cat#3724; RRID: AB_1549585 Rabbit Anti-Histone H3 (acetyl K27) Abcam Cat#ab4729; RRID: AB_2118291 Mouse Anti-cyclobutane pyrimidine dimers (CPDs) Cosmo Bio Cat#NMDND001 Rat Anti-CD40 ThermoFisher Cat#16-0401-82; RRID: AB_468941 Goat Anti-IgM, APC SouthernBiotech Cat#1020-11S; RRID: AB_2794210 Rat Anti-IgA, PE eBioscience Cat#12-4204-83; RRID: AB_465918 Rat Anti-IgG1, FITC BD Bioscience Cat#553443; RRID: AB_394862 Rat Anti-IgG1, PE BD Bioscience Cat#550083; RRID: AB_393553 Rat Anti-IgE, FITC SouthernBiotech Cat#1130-02; RRID: AB_2794616 Rat Anti-IgG3, FITC BD Bioscience Cat#553403; RRID: AB_394840 Rat Anti-CD45R (B220), APC eBioscience Cat#47-0452-82; RRID: AB_1518810 Bacterial and virus strains BL21(DE3) Competent Cells NEW ENGLAND BioLabs Cat#C2527H DH5a Competent Cells TIANGEN Cat#CB101 Stbl3 Competent Cells Exinbio Cat#CC104-01 Chemicals, peptides, and recombinant proteins Recombinant Human TGF-beta 1 Novoprotein Cat#CA59 Recombinant Mouse IL-4 Novoprotein Cat#CK15 Blasticidin S Selleck Cat#S7419 Puromycin GIBCO Cat#1767008 Lipopolysaccharide (LPS) Sigma Aldrich Cat#L2630 Zeocin InvivoGen Cat#11006-33-0 Cisplatin MedChemExpress Cat#HY-17393 Biotin-11-ATP Perkinelmer Cat#NEL544001EA Biotin-11-CTP Perkinelmer Cat#NEL542001EA Biotin-11-UTP Perkinelmer Cat#NEL543001EA Biotin-11-GTP Perkinelmer Cat#NEL545001EA 5,6-Dichlorobenzimidazole riboside (DRB) MedChemExpress Cat#HY-14392 NVP-2 MedChemExpress Cat#HY-12214A dTAG-13 ligand Tocris Cat#6605 4-Hydroxytamoxifen Sigma Aldrich Cat#H7904 N-Ethylmaleimide Sangon Cat#A600450 BeyoZonase Super Nuclease Beyotime Cat#D7126 Q5 High-Fidelity DNA polymerase NEW ENGLAND BioLabs Cat#M0491L Q5U Hot Start High-Fidelity DNA Polymerase NEW ENGLAND BioLabs Cat#M0515S (Continued on next page) e1 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 RNA Ligase 1 (ssRNA Ligase) NEW ENGLAND BioLabs Cat#M0204L SuperScript II reverse transcriptase Invitrogen Cat#18064071 TransStart FastPfu DNA Polymerase TransGen Cat#AP221-03 Peanut Agglutinin (PNA), Fluorescein Vector Laboratories Cat#FL-1071 Critical commercial assays Protein A Magnetic Beads ThermoFisher Cat#88846 Anti-Mouse IgM MicroBeads Miltenyi Biotec Cat#130-047-301 Dynabeads MyOne Streptavidin C1 ThermoFisher Cat#65001 Pierce Glutathione Magnetic Agarose Beads ThermoFisher Cat#78601 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7760S NEBNext rRNA Depletion Kit (Human/Mouse/Rat) NEW ENGLAND BioLabs Cat#E6310L NEBNext Ultra II DNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7645S CellTrace CFSE Cell Proliferation Kit Invitrogen Cat#C34554 cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693159001 Cell Counting Kit-8 APExBIO Cat#K1018 EasySep mouse B cell isolation kit STEMCELL Cat#19854 4-15% BeyoGel Plus Precast PAGE Gel Beyotime Cat#P0466 Micro Bio-Spin P-30 Columns BioRad Cat#732-6250 Deposited data CRISPR screening This paper SRA: PRJNA1124255 Amplicon-seq This paper SRA: PRJNA1124255 RNA-seq This paper GEO: GSE284306 ChIP-seq This paper GEO: GSE284303 PRO-seq This paper GEO: GSE284305 HTGTS This paper SRA: PRJNA1124255 Damage-seq This paper GEO: GSE284303 PADD-seq This paper GEO: GSE284303 PRO-seq of SPT5-dTAG DLD1 cells Hu et al.14 GEO: GSE180845 GRO-seq of SPT5 depleted MEF Fitz et al.17 GEO: GSE106313 ChIP-seq of RPB1 S2-p in RPE1-iCas9 cells van der Weegen et al.30 GEO: GSE149760 All the unprocessed and uncompressed imaging data This paper Mendeley Data doi: https://doi.org/10.17632/ 3hxdrzfvsw.1 Experimental models: Cell lines CH12F3 Nakamura et al.65 N/A CH12F3-mcherry (1 clone) Yang et al.44 N/A CH12F3 Elof1-/- (5 clones, #1 and #2 were used in most experiments) This paper N/A CH12F3 Ung-/- Msh2-/- (2 clones) Yang et al.44 N/A CH12F3 Ung-/- Msh2-/- Elof1-/- (2 clones) This paper N/A CH12F3 Ung-/- Msh2-/- Aicda-/- (1 clone) Xie et al.45 N/A CH12F3 Aicda-/- (1 clone) Han et al.66 N/A CH12F3 Elof1-/- Aicda-/- (2 clones) This paper N/A CH12F3 Csb (Ercc6)-/- (5 clones, #1 were used in most experiments) This paper N/A CH12F3 Csb-/-Elof1-/- (1 clone) This paper N/A CH12F3 RPB1K1268R (8 clones, #1 were used in most experiments) This paper N/A CH12F3 Sa-invert (2 clones) This paper N/A (Continued on next page) Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER K-562 ATCC Cat#CCL-243 Drosophila S2 ATCC Cat#CRL-1963 Experimental models: Organisms/strains CD21-Cre Kraus et al.42 JAX stock #006368 Elof1flox/ko This paper, Shanghai Model Organisms Center N/A Aicda-/- Muramatsu et al.67 N/A See Table S3 for the information of each mouse used in this paper This paper N/A Oligonucleotides See Table S3 This paper N/A Recombinant DNA lentiCRISPRv2 Sanjana et al.68 Addgene #52961 pX330-Sm-Cas9 Liu et al.41 N/A pX330-Sg1-Cas9 Liu et al.41 N/A lenti_dcas9_3xflag_blast Liu et al.69 Addgene #112133 pX330-Sm-MS2-MCP-hA3a This paper N/A pX330-Sg1-MS2-MCP-hA3a This paper N/A pGEX6P1-GST-Dsk2 This paper N/A pMX-ELOF1-3xHA-puro This paper N/A pMX-ELOF1-DN-3xHA-puro This paper N/A pMX-ELOF1-SDK-3xHA-puro This paper N/A pMX-ELOF1-ZF-3xHA-puro This paper N/A pMX-ELOF1-Dock-3xHA-puro This paper N/A pMX-3xHA-puro This paper N/A pMX-ELOF1-GFP-3xHA-puro This paper N/A pMX-GFP-3xHA-puro This paper N/A pMX-AID-3xFlag-ER-puro This paper N/A pMX-3xFlag-ER-puro This paper N/A Software and algorithms MAGeCK (v0.5.6) Li et al.70 https://sourceforge.net/projects/mageck/ STAR (v2.7.3a) Dobin et al.71 https://github.com/alexdobin/STAR Bowtie2 (v2.3.1) Langmead and Salzberg72 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml featureCounts (v1.6.4) Liao et al.73 https://github.com/ShiLab-Bioinformatics/subread DESeq2 (v1.38.3) Love et al.74 https://bioconductor.org/packages/release/bioc/html/ DESeq2.html cutadapt (v2.3) Martin75 https://cutadapt.readthedocs.io/en/stable/ deepTools (v3.2.1) Ramı́rez et al.76 https://github.com/deeptools/deepTools SAMtools (v1.9) Li et al.77 https://www.htslib.org/ picard (v2.21.1) Broad Institute https://broadinstitute.github.io/picard/ transloc_pipeline Hu et al.78 https://github.com/robinmeyers/transloc_pipeline BEDTools (v2.29.2) Quinlan and Hall79 https://bedtools.readthedocs.io/en/latest/index.html IGV (v2.3.98) Robinson et al.80 https://software.broadinstitute.org/software/igv/ landmarc Chen et al.47 https://bitbucket.org/Fred_Alt_Lab/landmarc/src/master/ Alphafold2 (ColabFold, v1.5.2) Mirdita et al.49 https://colab.research.google.com/github/sokrypton/ ColabFold/blob/main/AlphaFold2.ipynb Tidyverse (v2.0.0) Wickham et al.81 https://www.tidyverse.org/ R (4.2.3) R Core Team https://www.r-project.org/ Python (v3.8.8) Python Software Foundation https://www.python.org/ ImageJ (v2.14.0/1.54f) Schneider et al.82 https://imagej.nih.gov/ij/download.html e3 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025

    Amplification:

    Article Title: Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-ELOF1 Abclonal custom-ordered Rabbit Anti-AID Abclonal Cat#A16217; RRID: AB_2763671 Rabbit Anti-RPB1 S2-p Abcam Cat#ab5095; RRID: AB_304749 Rat Anti-RPB1 S5-p Abcam Cat#ab252852 Rabbit Anti-pan-RPB1 Bethyl Cat#A304-405A; RRID: AB_2620600 Rabbit Anti-RPB1 NTD Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit Anti-SPT5 Santa Cruz Cat#sc-28678; RRID: AB_668824 Mouse Anti-Flag-Tag Abmart Cat#M20008; RRID: AB_2713960 Rabbit Anti-HA-Tag Cell Signaling Technology Cat#3724; RRID: AB_1549585 Rabbit Anti-Histone H3 (acetyl K27) Abcam Cat#ab4729; RRID: AB_2118291 Mouse Anti-cyclobutane pyrimidine dimers (CPDs) Cosmo Bio Cat#NMDND001 Rat Anti-CD40 ThermoFisher Cat#16-0401-82; RRID: AB_468941 Goat Anti-IgM, APC SouthernBiotech Cat#1020-11S; RRID: AB_2794210 Rat Anti-IgA, PE eBioscience Cat#12-4204-83; RRID: AB_465918 Rat Anti-IgG1, FITC BD Bioscience Cat#553443; RRID: AB_394862 Rat Anti-IgG1, PE BD Bioscience Cat#550083; RRID: AB_393553 Rat Anti-IgE, FITC SouthernBiotech Cat#1130-02; RRID: AB_2794616 Rat Anti-IgG3, FITC BD Bioscience Cat#553403; RRID: AB_394840 Rat Anti-CD45R (B220), APC eBioscience Cat#47-0452-82; RRID: AB_1518810 Bacterial and virus strains BL21(DE3) Competent Cells NEW ENGLAND BioLabs Cat#C2527H DH5a Competent Cells TIANGEN Cat#CB101 Stbl3 Competent Cells Exinbio Cat#CC104-01 Chemicals, peptides, and recombinant proteins Recombinant Human TGF-beta 1 Novoprotein Cat#CA59 Recombinant Mouse IL-4 Novoprotein Cat#CK15 Blasticidin S Selleck Cat#S7419 Puromycin GIBCO Cat#1767008 Lipopolysaccharide (LPS) Sigma Aldrich Cat#L2630 Zeocin InvivoGen Cat#11006-33-0 Cisplatin MedChemExpress Cat#HY-17393 Biotin-11-ATP Perkinelmer Cat#NEL544001EA Biotin-11-CTP Perkinelmer Cat#NEL542001EA Biotin-11-UTP Perkinelmer Cat#NEL543001EA Biotin-11-GTP Perkinelmer Cat#NEL545001EA 5,6-Dichlorobenzimidazole riboside (DRB) MedChemExpress Cat#HY-14392 NVP-2 MedChemExpress Cat#HY-12214A dTAG-13 ligand Tocris Cat#6605 4-Hydroxytamoxifen Sigma Aldrich Cat#H7904 N-Ethylmaleimide Sangon Cat#A600450 BeyoZonase Super Nuclease Beyotime Cat#D7126 Q5 High-Fidelity DNA polymerase NEW ENGLAND BioLabs Cat#M0491L Q5U Hot Start High-Fidelity DNA Polymerase NEW ENGLAND BioLabs Cat#M0515S (Continued on next page) e1 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 RNA Ligase 1 (ssRNA Ligase) NEW ENGLAND BioLabs Cat#M0204L SuperScript II reverse transcriptase Invitrogen Cat#18064071 TransStart FastPfu DNA Polymerase TransGen Cat#AP221-03 Peanut Agglutinin (PNA), Fluorescein Vector Laboratories Cat#FL-1071 Critical commercial assays Protein A Magnetic Beads ThermoFisher Cat#88846 Anti-Mouse IgM MicroBeads Miltenyi Biotec Cat#130-047-301 Dynabeads MyOne Streptavidin C1 ThermoFisher Cat#65001 Pierce Glutathione Magnetic Agarose Beads ThermoFisher Cat#78601 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7760S NEBNext rRNA Depletion Kit (Human/Mouse/Rat) NEW ENGLAND BioLabs Cat#E6310L NEBNext Ultra II DNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7645S CellTrace CFSE Cell Proliferation Kit Invitrogen Cat#C34554 cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693159001 Cell Counting Kit-8 APExBIO Cat#K1018 EasySep mouse B cell isolation kit STEMCELL Cat#19854 4-15% BeyoGel Plus Precast PAGE Gel Beyotime Cat#P0466 Micro Bio-Spin P-30 Columns BioRad Cat#732-6250 Deposited data CRISPR screening This paper SRA: PRJNA1124255 Amplicon-seq This paper SRA: PRJNA1124255 RNA-seq This paper GEO: GSE284306 ChIP-seq This paper GEO: GSE284303 PRO-seq This paper GEO: GSE284305 HTGTS This paper SRA: PRJNA1124255 Damage-seq This paper GEO: GSE284303 PADD-seq This paper GEO: GSE284303 PRO-seq of SPT5-dTAG DLD1 cells Hu et al.14 GEO: GSE180845 GRO-seq of SPT5 depleted MEF Fitz et al.17 GEO: GSE106313 ChIP-seq of RPB1 S2-p in RPE1-iCas9 cells van der Weegen et al.30 GEO: GSE149760 All the unprocessed and uncompressed imaging data This paper Mendeley Data doi: https://doi.org/10.17632/ 3hxdrzfvsw.1 Experimental models: Cell lines CH12F3 Nakamura et al.65 N/A CH12F3-mcherry (1 clone) Yang et al.44 N/A CH12F3 Elof1-/- (5 clones, #1 and #2 were used in most experiments) This paper N/A CH12F3 Ung-/- Msh2-/- (2 clones) Yang et al.44 N/A CH12F3 Ung-/- Msh2-/- Elof1-/- (2 clones) This paper N/A CH12F3 Ung-/- Msh2-/- Aicda-/- (1 clone) Xie et al.45 N/A CH12F3 Aicda-/- (1 clone) Han et al.66 N/A CH12F3 Elof1-/- Aicda-/- (2 clones) This paper N/A CH12F3 Csb (Ercc6)-/- (5 clones, #1 were used in most experiments) This paper N/A CH12F3 Csb-/-Elof1-/- (1 clone) This paper N/A CH12F3 RPB1K1268R (8 clones, #1 were used in most experiments) This paper N/A CH12F3 Sa-invert (2 clones) This paper N/A (Continued on next page) Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER K-562 ATCC Cat#CCL-243 Drosophila S2 ATCC Cat#CRL-1963 Experimental models: Organisms/strains CD21-Cre Kraus et al.42 JAX stock #006368 Elof1flox/ko This paper, Shanghai Model Organisms Center N/A Aicda-/- Muramatsu et al.67 N/A See Table S3 for the information of each mouse used in this paper This paper N/A Oligonucleotides See Table S3 This paper N/A Recombinant DNA lentiCRISPRv2 Sanjana et al.68 Addgene #52961 pX330-Sm-Cas9 Liu et al.41 N/A pX330-Sg1-Cas9 Liu et al.41 N/A lenti_dcas9_3xflag_blast Liu et al.69 Addgene #112133 pX330-Sm-MS2-MCP-hA3a This paper N/A pX330-Sg1-MS2-MCP-hA3a This paper N/A pGEX6P1-GST-Dsk2 This paper N/A pMX-ELOF1-3xHA-puro This paper N/A pMX-ELOF1-DN-3xHA-puro This paper N/A pMX-ELOF1-SDK-3xHA-puro This paper N/A pMX-ELOF1-ZF-3xHA-puro This paper N/A pMX-ELOF1-Dock-3xHA-puro This paper N/A pMX-3xHA-puro This paper N/A pMX-ELOF1-GFP-3xHA-puro This paper N/A pMX-GFP-3xHA-puro This paper N/A pMX-AID-3xFlag-ER-puro This paper N/A pMX-3xFlag-ER-puro This paper N/A Software and algorithms MAGeCK (v0.5.6) Li et al.70 https://sourceforge.net/projects/mageck/ STAR (v2.7.3a) Dobin et al.71 https://github.com/alexdobin/STAR Bowtie2 (v2.3.1) Langmead and Salzberg72 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml featureCounts (v1.6.4) Liao et al.73 https://github.com/ShiLab-Bioinformatics/subread DESeq2 (v1.38.3) Love et al.74 https://bioconductor.org/packages/release/bioc/html/ DESeq2.html cutadapt (v2.3) Martin75 https://cutadapt.readthedocs.io/en/stable/ deepTools (v3.2.1) Ramı́rez et al.76 https://github.com/deeptools/deepTools SAMtools (v1.9) Li et al.77 https://www.htslib.org/ picard (v2.21.1) Broad Institute https://broadinstitute.github.io/picard/ transloc_pipeline Hu et al.78 https://github.com/robinmeyers/transloc_pipeline BEDTools (v2.29.2) Quinlan and Hall79 https://bedtools.readthedocs.io/en/latest/index.html IGV (v2.3.98) Robinson et al.80 https://software.broadinstitute.org/software/igv/ landmarc Chen et al.47 https://bitbucket.org/Fred_Alt_Lab/landmarc/src/master/ Alphafold2 (ColabFold, v1.5.2) Mirdita et al.49 https://colab.research.google.com/github/sokrypton/ ColabFold/blob/main/AlphaFold2.ipynb Tidyverse (v2.0.0) Wickham et al.81 https://www.tidyverse.org/ R (4.2.3) R Core Team https://www.r-project.org/ Python (v3.8.8) Python Software Foundation https://www.python.org/ ImageJ (v2.14.0/1.54f) Schneider et al.82 https://imagej.nih.gov/ij/download.html e3 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025

    RNA Sequencing:

    Article Title: Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-ELOF1 Abclonal custom-ordered Rabbit Anti-AID Abclonal Cat#A16217; RRID: AB_2763671 Rabbit Anti-RPB1 S2-p Abcam Cat#ab5095; RRID: AB_304749 Rat Anti-RPB1 S5-p Abcam Cat#ab252852 Rabbit Anti-pan-RPB1 Bethyl Cat#A304-405A; RRID: AB_2620600 Rabbit Anti-RPB1 NTD Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit Anti-SPT5 Santa Cruz Cat#sc-28678; RRID: AB_668824 Mouse Anti-Flag-Tag Abmart Cat#M20008; RRID: AB_2713960 Rabbit Anti-HA-Tag Cell Signaling Technology Cat#3724; RRID: AB_1549585 Rabbit Anti-Histone H3 (acetyl K27) Abcam Cat#ab4729; RRID: AB_2118291 Mouse Anti-cyclobutane pyrimidine dimers (CPDs) Cosmo Bio Cat#NMDND001 Rat Anti-CD40 ThermoFisher Cat#16-0401-82; RRID: AB_468941 Goat Anti-IgM, APC SouthernBiotech Cat#1020-11S; RRID: AB_2794210 Rat Anti-IgA, PE eBioscience Cat#12-4204-83; RRID: AB_465918 Rat Anti-IgG1, FITC BD Bioscience Cat#553443; RRID: AB_394862 Rat Anti-IgG1, PE BD Bioscience Cat#550083; RRID: AB_393553 Rat Anti-IgE, FITC SouthernBiotech Cat#1130-02; RRID: AB_2794616 Rat Anti-IgG3, FITC BD Bioscience Cat#553403; RRID: AB_394840 Rat Anti-CD45R (B220), APC eBioscience Cat#47-0452-82; RRID: AB_1518810 Bacterial and virus strains BL21(DE3) Competent Cells NEW ENGLAND BioLabs Cat#C2527H DH5a Competent Cells TIANGEN Cat#CB101 Stbl3 Competent Cells Exinbio Cat#CC104-01 Chemicals, peptides, and recombinant proteins Recombinant Human TGF-beta 1 Novoprotein Cat#CA59 Recombinant Mouse IL-4 Novoprotein Cat#CK15 Blasticidin S Selleck Cat#S7419 Puromycin GIBCO Cat#1767008 Lipopolysaccharide (LPS) Sigma Aldrich Cat#L2630 Zeocin InvivoGen Cat#11006-33-0 Cisplatin MedChemExpress Cat#HY-17393 Biotin-11-ATP Perkinelmer Cat#NEL544001EA Biotin-11-CTP Perkinelmer Cat#NEL542001EA Biotin-11-UTP Perkinelmer Cat#NEL543001EA Biotin-11-GTP Perkinelmer Cat#NEL545001EA 5,6-Dichlorobenzimidazole riboside (DRB) MedChemExpress Cat#HY-14392 NVP-2 MedChemExpress Cat#HY-12214A dTAG-13 ligand Tocris Cat#6605 4-Hydroxytamoxifen Sigma Aldrich Cat#H7904 N-Ethylmaleimide Sangon Cat#A600450 BeyoZonase Super Nuclease Beyotime Cat#D7126 Q5 High-Fidelity DNA polymerase NEW ENGLAND BioLabs Cat#M0491L Q5U Hot Start High-Fidelity DNA Polymerase NEW ENGLAND BioLabs Cat#M0515S (Continued on next page) e1 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 RNA Ligase 1 (ssRNA Ligase) NEW ENGLAND BioLabs Cat#M0204L SuperScript II reverse transcriptase Invitrogen Cat#18064071 TransStart FastPfu DNA Polymerase TransGen Cat#AP221-03 Peanut Agglutinin (PNA), Fluorescein Vector Laboratories Cat#FL-1071 Critical commercial assays Protein A Magnetic Beads ThermoFisher Cat#88846 Anti-Mouse IgM MicroBeads Miltenyi Biotec Cat#130-047-301 Dynabeads MyOne Streptavidin C1 ThermoFisher Cat#65001 Pierce Glutathione Magnetic Agarose Beads ThermoFisher Cat#78601 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7760S NEBNext rRNA Depletion Kit (Human/Mouse/Rat) NEW ENGLAND BioLabs Cat#E6310L NEBNext Ultra II DNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7645S CellTrace CFSE Cell Proliferation Kit Invitrogen Cat#C34554 cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693159001 Cell Counting Kit-8 APExBIO Cat#K1018 EasySep mouse B cell isolation kit STEMCELL Cat#19854 4-15% BeyoGel Plus Precast PAGE Gel Beyotime Cat#P0466 Micro Bio-Spin P-30 Columns BioRad Cat#732-6250 Deposited data CRISPR screening This paper SRA: PRJNA1124255 Amplicon-seq This paper SRA: PRJNA1124255 RNA-seq This paper GEO: GSE284306 ChIP-seq This paper GEO: GSE284303 PRO-seq This paper GEO: GSE284305 HTGTS This paper SRA: PRJNA1124255 Damage-seq This paper GEO: GSE284303 PADD-seq This paper GEO: GSE284303 PRO-seq of SPT5-dTAG DLD1 cells Hu et al.14 GEO: GSE180845 GRO-seq of SPT5 depleted MEF Fitz et al.17 GEO: GSE106313 ChIP-seq of RPB1 S2-p in RPE1-iCas9 cells van der Weegen et al.30 GEO: GSE149760 All the unprocessed and uncompressed imaging data This paper Mendeley Data doi: https://doi.org/10.17632/ 3hxdrzfvsw.1 Experimental models: Cell lines CH12F3 Nakamura et al.65 N/A CH12F3-mcherry (1 clone) Yang et al.44 N/A CH12F3 Elof1-/- (5 clones, #1 and #2 were used in most experiments) This paper N/A CH12F3 Ung-/- Msh2-/- (2 clones) Yang et al.44 N/A CH12F3 Ung-/- Msh2-/- Elof1-/- (2 clones) This paper N/A CH12F3 Ung-/- Msh2-/- Aicda-/- (1 clone) Xie et al.45 N/A CH12F3 Aicda-/- (1 clone) Han et al.66 N/A CH12F3 Elof1-/- Aicda-/- (2 clones) This paper N/A CH12F3 Csb (Ercc6)-/- (5 clones, #1 were used in most experiments) This paper N/A CH12F3 Csb-/-Elof1-/- (1 clone) This paper N/A CH12F3 RPB1K1268R (8 clones, #1 were used in most experiments) This paper N/A CH12F3 Sa-invert (2 clones) This paper N/A (Continued on next page) Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER K-562 ATCC Cat#CCL-243 Drosophila S2 ATCC Cat#CRL-1963 Experimental models: Organisms/strains CD21-Cre Kraus et al.42 JAX stock #006368 Elof1flox/ko This paper, Shanghai Model Organisms Center N/A Aicda-/- Muramatsu et al.67 N/A See Table S3 for the information of each mouse used in this paper This paper N/A Oligonucleotides See Table S3 This paper N/A Recombinant DNA lentiCRISPRv2 Sanjana et al.68 Addgene #52961 pX330-Sm-Cas9 Liu et al.41 N/A pX330-Sg1-Cas9 Liu et al.41 N/A lenti_dcas9_3xflag_blast Liu et al.69 Addgene #112133 pX330-Sm-MS2-MCP-hA3a This paper N/A pX330-Sg1-MS2-MCP-hA3a This paper N/A pGEX6P1-GST-Dsk2 This paper N/A pMX-ELOF1-3xHA-puro This paper N/A pMX-ELOF1-DN-3xHA-puro This paper N/A pMX-ELOF1-SDK-3xHA-puro This paper N/A pMX-ELOF1-ZF-3xHA-puro This paper N/A pMX-ELOF1-Dock-3xHA-puro This paper N/A pMX-3xHA-puro This paper N/A pMX-ELOF1-GFP-3xHA-puro This paper N/A pMX-GFP-3xHA-puro This paper N/A pMX-AID-3xFlag-ER-puro This paper N/A pMX-3xFlag-ER-puro This paper N/A Software and algorithms MAGeCK (v0.5.6) Li et al.70 https://sourceforge.net/projects/mageck/ STAR (v2.7.3a) Dobin et al.71 https://github.com/alexdobin/STAR Bowtie2 (v2.3.1) Langmead and Salzberg72 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml featureCounts (v1.6.4) Liao et al.73 https://github.com/ShiLab-Bioinformatics/subread DESeq2 (v1.38.3) Love et al.74 https://bioconductor.org/packages/release/bioc/html/ DESeq2.html cutadapt (v2.3) Martin75 https://cutadapt.readthedocs.io/en/stable/ deepTools (v3.2.1) Ramı́rez et al.76 https://github.com/deeptools/deepTools SAMtools (v1.9) Li et al.77 https://www.htslib.org/ picard (v2.21.1) Broad Institute https://broadinstitute.github.io/picard/ transloc_pipeline Hu et al.78 https://github.com/robinmeyers/transloc_pipeline BEDTools (v2.29.2) Quinlan and Hall79 https://bedtools.readthedocs.io/en/latest/index.html IGV (v2.3.98) Robinson et al.80 https://software.broadinstitute.org/software/igv/ landmarc Chen et al.47 https://bitbucket.org/Fred_Alt_Lab/landmarc/src/master/ Alphafold2 (ColabFold, v1.5.2) Mirdita et al.49 https://colab.research.google.com/github/sokrypton/ ColabFold/blob/main/AlphaFold2.ipynb Tidyverse (v2.0.0) Wickham et al.81 https://www.tidyverse.org/ R (4.2.3) R Core Team https://www.r-project.org/ Python (v3.8.8) Python Software Foundation https://www.python.org/ ImageJ (v2.14.0/1.54f) Schneider et al.82 https://imagej.nih.gov/ij/download.html e3 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025

    Chromatin Immunoprecipitation:

    Article Title: Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-ELOF1 Abclonal custom-ordered Rabbit Anti-AID Abclonal Cat#A16217; RRID: AB_2763671 Rabbit Anti-RPB1 S2-p Abcam Cat#ab5095; RRID: AB_304749 Rat Anti-RPB1 S5-p Abcam Cat#ab252852 Rabbit Anti-pan-RPB1 Bethyl Cat#A304-405A; RRID: AB_2620600 Rabbit Anti-RPB1 NTD Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit Anti-SPT5 Santa Cruz Cat#sc-28678; RRID: AB_668824 Mouse Anti-Flag-Tag Abmart Cat#M20008; RRID: AB_2713960 Rabbit Anti-HA-Tag Cell Signaling Technology Cat#3724; RRID: AB_1549585 Rabbit Anti-Histone H3 (acetyl K27) Abcam Cat#ab4729; RRID: AB_2118291 Mouse Anti-cyclobutane pyrimidine dimers (CPDs) Cosmo Bio Cat#NMDND001 Rat Anti-CD40 ThermoFisher Cat#16-0401-82; RRID: AB_468941 Goat Anti-IgM, APC SouthernBiotech Cat#1020-11S; RRID: AB_2794210 Rat Anti-IgA, PE eBioscience Cat#12-4204-83; RRID: AB_465918 Rat Anti-IgG1, FITC BD Bioscience Cat#553443; RRID: AB_394862 Rat Anti-IgG1, PE BD Bioscience Cat#550083; RRID: AB_393553 Rat Anti-IgE, FITC SouthernBiotech Cat#1130-02; RRID: AB_2794616 Rat Anti-IgG3, FITC BD Bioscience Cat#553403; RRID: AB_394840 Rat Anti-CD45R (B220), APC eBioscience Cat#47-0452-82; RRID: AB_1518810 Bacterial and virus strains BL21(DE3) Competent Cells NEW ENGLAND BioLabs Cat#C2527H DH5a Competent Cells TIANGEN Cat#CB101 Stbl3 Competent Cells Exinbio Cat#CC104-01 Chemicals, peptides, and recombinant proteins Recombinant Human TGF-beta 1 Novoprotein Cat#CA59 Recombinant Mouse IL-4 Novoprotein Cat#CK15 Blasticidin S Selleck Cat#S7419 Puromycin GIBCO Cat#1767008 Lipopolysaccharide (LPS) Sigma Aldrich Cat#L2630 Zeocin InvivoGen Cat#11006-33-0 Cisplatin MedChemExpress Cat#HY-17393 Biotin-11-ATP Perkinelmer Cat#NEL544001EA Biotin-11-CTP Perkinelmer Cat#NEL542001EA Biotin-11-UTP Perkinelmer Cat#NEL543001EA Biotin-11-GTP Perkinelmer Cat#NEL545001EA 5,6-Dichlorobenzimidazole riboside (DRB) MedChemExpress Cat#HY-14392 NVP-2 MedChemExpress Cat#HY-12214A dTAG-13 ligand Tocris Cat#6605 4-Hydroxytamoxifen Sigma Aldrich Cat#H7904 N-Ethylmaleimide Sangon Cat#A600450 BeyoZonase Super Nuclease Beyotime Cat#D7126 Q5 High-Fidelity DNA polymerase NEW ENGLAND BioLabs Cat#M0491L Q5U Hot Start High-Fidelity DNA Polymerase NEW ENGLAND BioLabs Cat#M0515S (Continued on next page) e1 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 RNA Ligase 1 (ssRNA Ligase) NEW ENGLAND BioLabs Cat#M0204L SuperScript II reverse transcriptase Invitrogen Cat#18064071 TransStart FastPfu DNA Polymerase TransGen Cat#AP221-03 Peanut Agglutinin (PNA), Fluorescein Vector Laboratories Cat#FL-1071 Critical commercial assays Protein A Magnetic Beads ThermoFisher Cat#88846 Anti-Mouse IgM MicroBeads Miltenyi Biotec Cat#130-047-301 Dynabeads MyOne Streptavidin C1 ThermoFisher Cat#65001 Pierce Glutathione Magnetic Agarose Beads ThermoFisher Cat#78601 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7760S NEBNext rRNA Depletion Kit (Human/Mouse/Rat) NEW ENGLAND BioLabs Cat#E6310L NEBNext Ultra II DNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7645S CellTrace CFSE Cell Proliferation Kit Invitrogen Cat#C34554 cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693159001 Cell Counting Kit-8 APExBIO Cat#K1018 EasySep mouse B cell isolation kit STEMCELL Cat#19854 4-15% BeyoGel Plus Precast PAGE Gel Beyotime Cat#P0466 Micro Bio-Spin P-30 Columns BioRad Cat#732-6250 Deposited data CRISPR screening This paper SRA: PRJNA1124255 Amplicon-seq This paper SRA: PRJNA1124255 RNA-seq This paper GEO: GSE284306 ChIP-seq This paper GEO: GSE284303 PRO-seq This paper GEO: GSE284305 HTGTS This paper SRA: PRJNA1124255 Damage-seq This paper GEO: GSE284303 PADD-seq This paper GEO: GSE284303 PRO-seq of SPT5-dTAG DLD1 cells Hu et al.14 GEO: GSE180845 GRO-seq of SPT5 depleted MEF Fitz et al.17 GEO: GSE106313 ChIP-seq of RPB1 S2-p in RPE1-iCas9 cells van der Weegen et al.30 GEO: GSE149760 All the unprocessed and uncompressed imaging data This paper Mendeley Data doi: https://doi.org/10.17632/ 3hxdrzfvsw.1 Experimental models: Cell lines CH12F3 Nakamura et al.65 N/A CH12F3-mcherry (1 clone) Yang et al.44 N/A CH12F3 Elof1-/- (5 clones, #1 and #2 were used in most experiments) This paper N/A CH12F3 Ung-/- Msh2-/- (2 clones) Yang et al.44 N/A CH12F3 Ung-/- Msh2-/- Elof1-/- (2 clones) This paper N/A CH12F3 Ung-/- Msh2-/- Aicda-/- (1 clone) Xie et al.45 N/A CH12F3 Aicda-/- (1 clone) Han et al.66 N/A CH12F3 Elof1-/- Aicda-/- (2 clones) This paper N/A CH12F3 Csb (Ercc6)-/- (5 clones, #1 were used in most experiments) This paper N/A CH12F3 Csb-/-Elof1-/- (1 clone) This paper N/A CH12F3 RPB1K1268R (8 clones, #1 were used in most experiments) This paper N/A CH12F3 Sa-invert (2 clones) This paper N/A (Continued on next page) Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER K-562 ATCC Cat#CCL-243 Drosophila S2 ATCC Cat#CRL-1963 Experimental models: Organisms/strains CD21-Cre Kraus et al.42 JAX stock #006368 Elof1flox/ko This paper, Shanghai Model Organisms Center N/A Aicda-/- Muramatsu et al.67 N/A See Table S3 for the information of each mouse used in this paper This paper N/A Oligonucleotides See Table S3 This paper N/A Recombinant DNA lentiCRISPRv2 Sanjana et al.68 Addgene #52961 pX330-Sm-Cas9 Liu et al.41 N/A pX330-Sg1-Cas9 Liu et al.41 N/A lenti_dcas9_3xflag_blast Liu et al.69 Addgene #112133 pX330-Sm-MS2-MCP-hA3a This paper N/A pX330-Sg1-MS2-MCP-hA3a This paper N/A pGEX6P1-GST-Dsk2 This paper N/A pMX-ELOF1-3xHA-puro This paper N/A pMX-ELOF1-DN-3xHA-puro This paper N/A pMX-ELOF1-SDK-3xHA-puro This paper N/A pMX-ELOF1-ZF-3xHA-puro This paper N/A pMX-ELOF1-Dock-3xHA-puro This paper N/A pMX-3xHA-puro This paper N/A pMX-ELOF1-GFP-3xHA-puro This paper N/A pMX-GFP-3xHA-puro This paper N/A pMX-AID-3xFlag-ER-puro This paper N/A pMX-3xFlag-ER-puro This paper N/A Software and algorithms MAGeCK (v0.5.6) Li et al.70 https://sourceforge.net/projects/mageck/ STAR (v2.7.3a) Dobin et al.71 https://github.com/alexdobin/STAR Bowtie2 (v2.3.1) Langmead and Salzberg72 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml featureCounts (v1.6.4) Liao et al.73 https://github.com/ShiLab-Bioinformatics/subread DESeq2 (v1.38.3) Love et al.74 https://bioconductor.org/packages/release/bioc/html/ DESeq2.html cutadapt (v2.3) Martin75 https://cutadapt.readthedocs.io/en/stable/ deepTools (v3.2.1) Ramı́rez et al.76 https://github.com/deeptools/deepTools SAMtools (v1.9) Li et al.77 https://www.htslib.org/ picard (v2.21.1) Broad Institute https://broadinstitute.github.io/picard/ transloc_pipeline Hu et al.78 https://github.com/robinmeyers/transloc_pipeline BEDTools (v2.29.2) Quinlan and Hall79 https://bedtools.readthedocs.io/en/latest/index.html IGV (v2.3.98) Robinson et al.80 https://software.broadinstitute.org/software/igv/ landmarc Chen et al.47 https://bitbucket.org/Fred_Alt_Lab/landmarc/src/master/ Alphafold2 (ColabFold, v1.5.2) Mirdita et al.49 https://colab.research.google.com/github/sokrypton/ ColabFold/blob/main/AlphaFold2.ipynb Tidyverse (v2.0.0) Wickham et al.81 https://www.tidyverse.org/ R (4.2.3) R Core Team https://www.r-project.org/ Python (v3.8.8) Python Software Foundation https://www.python.org/ ImageJ (v2.14.0/1.54f) Schneider et al.82 https://imagej.nih.gov/ij/download.html e3 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025

    Imaging:

    Article Title: Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-ELOF1 Abclonal custom-ordered Rabbit Anti-AID Abclonal Cat#A16217; RRID: AB_2763671 Rabbit Anti-RPB1 S2-p Abcam Cat#ab5095; RRID: AB_304749 Rat Anti-RPB1 S5-p Abcam Cat#ab252852 Rabbit Anti-pan-RPB1 Bethyl Cat#A304-405A; RRID: AB_2620600 Rabbit Anti-RPB1 NTD Cell Signaling Technology Cat#14958; RRID: AB_2687876 Rabbit Anti-SPT5 Santa Cruz Cat#sc-28678; RRID: AB_668824 Mouse Anti-Flag-Tag Abmart Cat#M20008; RRID: AB_2713960 Rabbit Anti-HA-Tag Cell Signaling Technology Cat#3724; RRID: AB_1549585 Rabbit Anti-Histone H3 (acetyl K27) Abcam Cat#ab4729; RRID: AB_2118291 Mouse Anti-cyclobutane pyrimidine dimers (CPDs) Cosmo Bio Cat#NMDND001 Rat Anti-CD40 ThermoFisher Cat#16-0401-82; RRID: AB_468941 Goat Anti-IgM, APC SouthernBiotech Cat#1020-11S; RRID: AB_2794210 Rat Anti-IgA, PE eBioscience Cat#12-4204-83; RRID: AB_465918 Rat Anti-IgG1, FITC BD Bioscience Cat#553443; RRID: AB_394862 Rat Anti-IgG1, PE BD Bioscience Cat#550083; RRID: AB_393553 Rat Anti-IgE, FITC SouthernBiotech Cat#1130-02; RRID: AB_2794616 Rat Anti-IgG3, FITC BD Bioscience Cat#553403; RRID: AB_394840 Rat Anti-CD45R (B220), APC eBioscience Cat#47-0452-82; RRID: AB_1518810 Bacterial and virus strains BL21(DE3) Competent Cells NEW ENGLAND BioLabs Cat#C2527H DH5a Competent Cells TIANGEN Cat#CB101 Stbl3 Competent Cells Exinbio Cat#CC104-01 Chemicals, peptides, and recombinant proteins Recombinant Human TGF-beta 1 Novoprotein Cat#CA59 Recombinant Mouse IL-4 Novoprotein Cat#CK15 Blasticidin S Selleck Cat#S7419 Puromycin GIBCO Cat#1767008 Lipopolysaccharide (LPS) Sigma Aldrich Cat#L2630 Zeocin InvivoGen Cat#11006-33-0 Cisplatin MedChemExpress Cat#HY-17393 Biotin-11-ATP Perkinelmer Cat#NEL544001EA Biotin-11-CTP Perkinelmer Cat#NEL542001EA Biotin-11-UTP Perkinelmer Cat#NEL543001EA Biotin-11-GTP Perkinelmer Cat#NEL545001EA 5,6-Dichlorobenzimidazole riboside (DRB) MedChemExpress Cat#HY-14392 NVP-2 MedChemExpress Cat#HY-12214A dTAG-13 ligand Tocris Cat#6605 4-Hydroxytamoxifen Sigma Aldrich Cat#H7904 N-Ethylmaleimide Sangon Cat#A600450 BeyoZonase Super Nuclease Beyotime Cat#D7126 Q5 High-Fidelity DNA polymerase NEW ENGLAND BioLabs Cat#M0491L Q5U Hot Start High-Fidelity DNA Polymerase NEW ENGLAND BioLabs Cat#M0515S (Continued on next page) e1 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER T4 RNA Ligase 1 (ssRNA Ligase) NEW ENGLAND BioLabs Cat#M0204L SuperScript II reverse transcriptase Invitrogen Cat#18064071 TransStart FastPfu DNA Polymerase TransGen Cat#AP221-03 Peanut Agglutinin (PNA), Fluorescein Vector Laboratories Cat#FL-1071 Critical commercial assays Protein A Magnetic Beads ThermoFisher Cat#88846 Anti-Mouse IgM MicroBeads Miltenyi Biotec Cat#130-047-301 Dynabeads MyOne Streptavidin C1 ThermoFisher Cat#65001 Pierce Glutathione Magnetic Agarose Beads ThermoFisher Cat#78601 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7760S NEBNext rRNA Depletion Kit (Human/Mouse/Rat) NEW ENGLAND BioLabs Cat#E6310L NEBNext Ultra II DNA Library Prep Kit for Illumina NEW ENGLAND BioLabs Cat#E7645S CellTrace CFSE Cell Proliferation Kit Invitrogen Cat#C34554 cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693159001 Cell Counting Kit-8 APExBIO Cat#K1018 EasySep mouse B cell isolation kit STEMCELL Cat#19854 4-15% BeyoGel Plus Precast PAGE Gel Beyotime Cat#P0466 Micro Bio-Spin P-30 Columns BioRad Cat#732-6250 Deposited data CRISPR screening This paper SRA: PRJNA1124255 Amplicon-seq This paper SRA: PRJNA1124255 RNA-seq This paper GEO: GSE284306 ChIP-seq This paper GEO: GSE284303 PRO-seq This paper GEO: GSE284305 HTGTS This paper SRA: PRJNA1124255 Damage-seq This paper GEO: GSE284303 PADD-seq This paper GEO: GSE284303 PRO-seq of SPT5-dTAG DLD1 cells Hu et al.14 GEO: GSE180845 GRO-seq of SPT5 depleted MEF Fitz et al.17 GEO: GSE106313 ChIP-seq of RPB1 S2-p in RPE1-iCas9 cells van der Weegen et al.30 GEO: GSE149760 All the unprocessed and uncompressed imaging data This paper Mendeley Data doi: https://doi.org/10.17632/ 3hxdrzfvsw.1 Experimental models: Cell lines CH12F3 Nakamura et al.65 N/A CH12F3-mcherry (1 clone) Yang et al.44 N/A CH12F3 Elof1-/- (5 clones, #1 and #2 were used in most experiments) This paper N/A CH12F3 Ung-/- Msh2-/- (2 clones) Yang et al.44 N/A CH12F3 Ung-/- Msh2-/- Elof1-/- (2 clones) This paper N/A CH12F3 Ung-/- Msh2-/- Aicda-/- (1 clone) Xie et al.45 N/A CH12F3 Aicda-/- (1 clone) Han et al.66 N/A CH12F3 Elof1-/- Aicda-/- (2 clones) This paper N/A CH12F3 Csb (Ercc6)-/- (5 clones, #1 were used in most experiments) This paper N/A CH12F3 Csb-/-Elof1-/- (1 clone) This paper N/A CH12F3 RPB1K1268R (8 clones, #1 were used in most experiments) This paper N/A CH12F3 Sa-invert (2 clones) This paper N/A (Continued on next page) Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER K-562 ATCC Cat#CCL-243 Drosophila S2 ATCC Cat#CRL-1963 Experimental models: Organisms/strains CD21-Cre Kraus et al.42 JAX stock #006368 Elof1flox/ko This paper, Shanghai Model Organisms Center N/A Aicda-/- Muramatsu et al.67 N/A See Table S3 for the information of each mouse used in this paper This paper N/A Oligonucleotides See Table S3 This paper N/A Recombinant DNA lentiCRISPRv2 Sanjana et al.68 Addgene #52961 pX330-Sm-Cas9 Liu et al.41 N/A pX330-Sg1-Cas9 Liu et al.41 N/A lenti_dcas9_3xflag_blast Liu et al.69 Addgene #112133 pX330-Sm-MS2-MCP-hA3a This paper N/A pX330-Sg1-MS2-MCP-hA3a This paper N/A pGEX6P1-GST-Dsk2 This paper N/A pMX-ELOF1-3xHA-puro This paper N/A pMX-ELOF1-DN-3xHA-puro This paper N/A pMX-ELOF1-SDK-3xHA-puro This paper N/A pMX-ELOF1-ZF-3xHA-puro This paper N/A pMX-ELOF1-Dock-3xHA-puro This paper N/A pMX-3xHA-puro This paper N/A pMX-ELOF1-GFP-3xHA-puro This paper N/A pMX-GFP-3xHA-puro This paper N/A pMX-AID-3xFlag-ER-puro This paper N/A pMX-3xFlag-ER-puro This paper N/A Software and algorithms MAGeCK (v0.5.6) Li et al.70 https://sourceforge.net/projects/mageck/ STAR (v2.7.3a) Dobin et al.71 https://github.com/alexdobin/STAR Bowtie2 (v2.3.1) Langmead and Salzberg72 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml featureCounts (v1.6.4) Liao et al.73 https://github.com/ShiLab-Bioinformatics/subread DESeq2 (v1.38.3) Love et al.74 https://bioconductor.org/packages/release/bioc/html/ DESeq2.html cutadapt (v2.3) Martin75 https://cutadapt.readthedocs.io/en/stable/ deepTools (v3.2.1) Ramı́rez et al.76 https://github.com/deeptools/deepTools SAMtools (v1.9) Li et al.77 https://www.htslib.org/ picard (v2.21.1) Broad Institute https://broadinstitute.github.io/picard/ transloc_pipeline Hu et al.78 https://github.com/robinmeyers/transloc_pipeline BEDTools (v2.29.2) Quinlan and Hall79 https://bedtools.readthedocs.io/en/latest/index.html IGV (v2.3.98) Robinson et al.80 https://software.broadinstitute.org/software/igv/ landmarc Chen et al.47 https://bitbucket.org/Fred_Alt_Lab/landmarc/src/master/ Alphafold2 (ColabFold, v1.5.2) Mirdita et al.49 https://colab.research.google.com/github/sokrypton/ ColabFold/blob/main/AlphaFold2.ipynb Tidyverse (v2.0.0) Wickham et al.81 https://www.tidyverse.org/ R (4.2.3) R Core Team https://www.r-project.org/ Python (v3.8.8) Python Software Foundation https://www.python.org/ ImageJ (v2.14.0/1.54f) Schneider et al.82 https://imagej.nih.gov/ij/download.html e3 Molecular Cell 85, 1280–1295.e1–e9, April 3, 2025

    Incubation:

    Article Title: Ex Vivo Spatiotemporal Characterization of Spermatogenesis in Mouse Testicular Organoids.
    Article Snippet: The slides were washed with PBS, blocked with blocking solution containing 10% normal donkey serum and 3% BSA in PBS for 40 min at room temperature and incubated with primary antibodies against GATA4 (1:200, Santa Cruz Biotechnology, sc-1237), 3β-HSD (1:200, Proteintech, 15516- 1-AP), α-SMA (1:200, Proteintech, 14395-1-AP), ZO-1 (1:200, Proteintech, 21773-1-AP), Claudin-11 (1:400; Affinity, AF5364), SOX9 (1:1000, Millipore, AB5535), TRA98 (1:2000, Abcam, ab82527), DDX4 (1:500, Abcam, ab13840), PLZF (1:400, R&D Systems, AF2944), STRA8 (1:200, Abcam, ab308124), c-KIT (1:200, R&D Systems, AF1356), SYCP3 (1:400, Abcam, ab97672), γH2AX (1:500, Abcam, ab11174), H1t (1:500, ABclonal, A18597), CREM (1:200, Proteintech, 12131-1-AP), Caspase-3 (1:200, Proteintech, 25128-1-AP), KI67 (1:1000, Abcam, ab15580), AR (1:200, Abcam, ab133273). .. After overnight incubation at 4 °C, the slides werewashed three times in PBS, followed by incubation with secondary antibodies (Jackson ImmunoResearch) or/and peanut agglutinin (PNA) (1:1000, Vectorlabs, RL-1072) and DAPI (1:500, Sigma, D9542) for 2 h at room temperature, followed by three washes with PBS. ..

    Article Title: Ex Vivo Spatiotemporal Characterization of Spermatogenesis in Mouse Testicular Organoids
    Article Snippet: The slides were washed with PBS, blocked with blocking solution containing 10% normal donkey serum and 3% BSA in PBS for 40 min at room temperature and incubated with primary antibodies against GATA4 (1:200, Santa Cruz Biotechnology, sc‐1237), 3β‐HSD (1:200, Proteintech, 15516‐1‐AP), α‐SMA (1:200, Proteintech, 14395‐1‐AP), ZO‐1 (1:200, Proteintech, 21773‐1‐AP), Claudin‐11 (1:400; Affinity, AF5364), SOX9 (1:1000, Millipore, AB5535), TRA98 (1:2000, Abcam, ab82527), DDX4 (1:500, Abcam, ab13840), PLZF (1:400, R&D Systems, AF2944), STRA8 (1:200, Abcam, ab308124), c‐KIT (1:200, R&D Systems, AF1356), SYCP3 (1:400, Abcam, ab97672), γH2AX (1:500, Abcam, ab11174), H1t (1:500, ABclonal, A18597), CREM (1:200, Proteintech, 12131‐1‐AP), Caspase‐3 (1:200, Proteintech, 25128‐1‐AP), KI67 (1:1000, Abcam, ab15580), AR (1:200, Abcam, ab133273). .. After overnight incubation at 4 °C, the slides were washed three times in PBS, followed by incubation with secondary antibodies (Jackson ImmunoResearch) or/and peanut agglutinin (PNA) (1:1000, Vectorlabs, RL‐1072) and DAPI (1:500, Sigma, D9542) for 2 h at room temperature, followed by three washes with PBS. ..



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    Vector Laboratories fitc pna fl 1071
    S6K1 activity is required for disease onset and progression in rod Tsc1 −/− mice (A) Top row: representative fundus, <t>fluorescein</t> angiography, and OCT images of an 18-month-old rod Tsc1 −/− S6k1 +/+ mouse with focal RPE atrophy and neovascular pathology (yellow arrows). Bottom row: immunofluorescence and bright field images with red signal from immunofluorescence staining superimposed on bright field of a retinal cross-section of the eye above (section shown in the same orientation as the OCT image) showing loss of RPE65 (red signal) expression in the area of RPE atrophy (dashed line on choroid demarks region of RPE cells loss), indicating a disrupted RPE layer. RPE65 expression with RPE cells is visible on the left third of each panel (area between white arrowheads). Only RPE atrophy is shown on section, not the neovascular pathology. Scale bars: 100 μm; blue, nuclear DAPI; green, peanut <t>agglutinin</t> <t>lectin</t> (PNA) marking cone PR segments; red, RPE65 expression marking RPE cells. (B) Frequency in percentage of phenotypes scored in each genotype at 18 months of age, including microglia activation (white bar), retinal folds (gray bars), focal RPE atrophy (black bars), and neovascular pathologies (green bars). The number of mice examined in each group is indicated in parentheses. Error bar = margin of error (M.O.E.). (C) Representative image of APOE (green signal) accumulation at the RPE/BrM (white arrowheads) in mice with indicated genotype at 12 months of age (4–5 mice were examined in each group). Scale bars: 50 μm; blue, nuclear DAPI; red, peanut agglutinin lectin (PNA) marking cone PR segments; layers in (A and C): RPE, retinal-pigmented epithelium; PS, PR segment region covering inner and outer segments; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer; vertical bars in sections mark height of different layers. (D) PR outer segment (POS) clearance in RPE cells of 2-month-old mice is shown as percentage of POS remaining at 11 am when compared to 8 am in genotypes indicated ( N = 4–8 RPE flat mounts/genotype). (E) Percentage of di-DHA PE (left) and PC (right) phospholipids as a total of PE (left) and PC (right) phospholipids in genotypes indicated ( N = 5–6 retinas/genotype). Results in (D and E) are shown as mean ± S.E.M. (∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗∗ p < 0.0001; n.s., not significant).
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    S6K1 activity is required for disease onset and progression in rod Tsc1 −/− mice (A) Top row: representative fundus, fluorescein angiography, and OCT images of an 18-month-old rod Tsc1 −/− S6k1 +/+ mouse with focal RPE atrophy and neovascular pathology (yellow arrows). Bottom row: immunofluorescence and bright field images with red signal from immunofluorescence staining superimposed on bright field of a retinal cross-section of the eye above (section shown in the same orientation as the OCT image) showing loss of RPE65 (red signal) expression in the area of RPE atrophy (dashed line on choroid demarks region of RPE cells loss), indicating a disrupted RPE layer. RPE65 expression with RPE cells is visible on the left third of each panel (area between white arrowheads). Only RPE atrophy is shown on section, not the neovascular pathology. Scale bars: 100 μm; blue, nuclear DAPI; green, peanut agglutinin lectin (PNA) marking cone PR segments; red, RPE65 expression marking RPE cells. (B) Frequency in percentage of phenotypes scored in each genotype at 18 months of age, including microglia activation (white bar), retinal folds (gray bars), focal RPE atrophy (black bars), and neovascular pathologies (green bars). The number of mice examined in each group is indicated in parentheses. Error bar = margin of error (M.O.E.). (C) Representative image of APOE (green signal) accumulation at the RPE/BrM (white arrowheads) in mice with indicated genotype at 12 months of age (4–5 mice were examined in each group). Scale bars: 50 μm; blue, nuclear DAPI; red, peanut agglutinin lectin (PNA) marking cone PR segments; layers in (A and C): RPE, retinal-pigmented epithelium; PS, PR segment region covering inner and outer segments; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer; vertical bars in sections mark height of different layers. (D) PR outer segment (POS) clearance in RPE cells of 2-month-old mice is shown as percentage of POS remaining at 11 am when compared to 8 am in genotypes indicated ( N = 4–8 RPE flat mounts/genotype). (E) Percentage of di-DHA PE (left) and PC (right) phospholipids as a total of PE (left) and PC (right) phospholipids in genotypes indicated ( N = 5–6 retinas/genotype). Results in (D and E) are shown as mean ± S.E.M. (∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗∗ p < 0.0001; n.s., not significant).

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: An siRNA targeting S6k1 identifies photoreceptor phospholipid metabolism as a contributor to lipid buildup in age-related macular degeneration

    doi: 10.1016/j.omtn.2026.102878

    Figure Lengend Snippet: S6K1 activity is required for disease onset and progression in rod Tsc1 −/− mice (A) Top row: representative fundus, fluorescein angiography, and OCT images of an 18-month-old rod Tsc1 −/− S6k1 +/+ mouse with focal RPE atrophy and neovascular pathology (yellow arrows). Bottom row: immunofluorescence and bright field images with red signal from immunofluorescence staining superimposed on bright field of a retinal cross-section of the eye above (section shown in the same orientation as the OCT image) showing loss of RPE65 (red signal) expression in the area of RPE atrophy (dashed line on choroid demarks region of RPE cells loss), indicating a disrupted RPE layer. RPE65 expression with RPE cells is visible on the left third of each panel (area between white arrowheads). Only RPE atrophy is shown on section, not the neovascular pathology. Scale bars: 100 μm; blue, nuclear DAPI; green, peanut agglutinin lectin (PNA) marking cone PR segments; red, RPE65 expression marking RPE cells. (B) Frequency in percentage of phenotypes scored in each genotype at 18 months of age, including microglia activation (white bar), retinal folds (gray bars), focal RPE atrophy (black bars), and neovascular pathologies (green bars). The number of mice examined in each group is indicated in parentheses. Error bar = margin of error (M.O.E.). (C) Representative image of APOE (green signal) accumulation at the RPE/BrM (white arrowheads) in mice with indicated genotype at 12 months of age (4–5 mice were examined in each group). Scale bars: 50 μm; blue, nuclear DAPI; red, peanut agglutinin lectin (PNA) marking cone PR segments; layers in (A and C): RPE, retinal-pigmented epithelium; PS, PR segment region covering inner and outer segments; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer; vertical bars in sections mark height of different layers. (D) PR outer segment (POS) clearance in RPE cells of 2-month-old mice is shown as percentage of POS remaining at 11 am when compared to 8 am in genotypes indicated ( N = 4–8 RPE flat mounts/genotype). (E) Percentage of di-DHA PE (left) and PC (right) phospholipids as a total of PE (left) and PC (right) phospholipids in genotypes indicated ( N = 5–6 retinas/genotype). Results in (D and E) are shown as mean ± S.E.M. (∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗∗ p < 0.0001; n.s., not significant).

    Article Snippet: The following reagents already had a chromophore conjugated: rhodamine phalloidin (Life Technology, Cat. #: R415; 1:100) and fluorescein peanut agglutinin lectin (PNA; Vector Laboratories, Cat. #: FL-1071; 1:500).

    Techniques: Activity Assay, Immunofluorescence, Staining, Expressing, Activation Assay

    S6k1 silencing in mouse reverses early disease pathologies in rod Tsc1 −/− mice (A and B) Long-term siRNA retention and silencing efficacy in rod Tsc1 −/− mice examined at 3, 6, and 9 months post-injection. Mice received one intravitreal injection of 15 μg of siRNA reagents at 3 months of age. (A) Distribution of tetra-siRNA S6k1 and S6K1 protein expression in rod Tsc1 −/− mouse retinas. Left: tiled retinal sections showing either tetra-siRNA NTC (top) or tetra-siRNA S6k1 (bottom, visualized with RNAScope, red signal) at 3 months post-injection (scale bars: 500 μm). Right: higher magnification of tetra-siRNA S6k1 distribution on retinal sections and S6K1 protein expression at time points indicated. Tetra-siRNA S6k1 is visualized with RNAScope (red signal), and S6K1 protein expression is visualized by immunohistochemistry (purple signal). Staining for tetra-siRNA S6k1 and S6K1 was performed on separate slides. Scale bars: 50 μm; PS, PR segment region covering inner and outer segments; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer; vertical bars in sections mark height of different layers. (B) Silencing efficiency of tetra-siRNA S6k1 (blue bars) at time points indicated post-intravitreal injection when compared to the NTC (green bars). Silencing was measured by western blotting with retinal protein extracts. Mice were all injected at 3 months of age ( N = 5–8 retinas/group). (C) Percentage silencing in PR vs. non-PR cells that were enriched by FACS at 2 months post-intravitreal delivery of siRNA. The percentage of protein expression level is normalized to the tetra-siRNA NTC treated group. (D) PR outer segment (POS) clearance in RPE cells of 4-month-old mice shown as percentage of POS remaining at 11 am when compared to the peak of shedding at 8 am in the genotypes indicated. rod Tsc1 −/− mice were injected at 2 months of age with siRNA reagents indicated ( N = 4–7 eyes/group). (E and F) Reversal of APOE accumulation at the BrM in tetra-siRNA S6k1 -treated mice. (E) APOE protein expression level measured by western blotting with RPE/choroid protein extracts of 15-month-old rod Tsc1 −/− mice that are untreated or treated with either tetra-siRNA NTC or tetra-siRNA S6k1 for 3 months (treatment started at 12 months of age). Expression levels are compared to 15-month-old littermate control rod Tsc1 +/+ mice ( N = 5–10 eyes/group). (B–E) Results are shown as mean ± S.E.M. Each dot represents one retina or RPE/choroid from one mouse. Only one eye per mouse was used for each analysis (∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001; ∗∗∗∗ p < 0.0001; green bars represent tetra-siRNA NTC and blue bars tetra-siRNA S6k1 -injected eyes). (F) Retinal cross-section of rod Tsc1 −/− eyes showing reduction in the accumulation APOE (green signal) at the BrM (white arrowheads) of tetra-siRNA S6k1 -injected eyes (right panel). Mice were injected at 12 months of age and analyzed 3 months post-injection. Scale bars: 50 μm; blue, nuclear DAPI; red, peanut agglutinin lectin (PNA) marking cone PR segments; RPE, retinal-pigmented epithelium; PS, PR segment region covering inner and outer segments; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer; vertical bars in sections mark height of different layers.

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: An siRNA targeting S6k1 identifies photoreceptor phospholipid metabolism as a contributor to lipid buildup in age-related macular degeneration

    doi: 10.1016/j.omtn.2026.102878

    Figure Lengend Snippet: S6k1 silencing in mouse reverses early disease pathologies in rod Tsc1 −/− mice (A and B) Long-term siRNA retention and silencing efficacy in rod Tsc1 −/− mice examined at 3, 6, and 9 months post-injection. Mice received one intravitreal injection of 15 μg of siRNA reagents at 3 months of age. (A) Distribution of tetra-siRNA S6k1 and S6K1 protein expression in rod Tsc1 −/− mouse retinas. Left: tiled retinal sections showing either tetra-siRNA NTC (top) or tetra-siRNA S6k1 (bottom, visualized with RNAScope, red signal) at 3 months post-injection (scale bars: 500 μm). Right: higher magnification of tetra-siRNA S6k1 distribution on retinal sections and S6K1 protein expression at time points indicated. Tetra-siRNA S6k1 is visualized with RNAScope (red signal), and S6K1 protein expression is visualized by immunohistochemistry (purple signal). Staining for tetra-siRNA S6k1 and S6K1 was performed on separate slides. Scale bars: 50 μm; PS, PR segment region covering inner and outer segments; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer; vertical bars in sections mark height of different layers. (B) Silencing efficiency of tetra-siRNA S6k1 (blue bars) at time points indicated post-intravitreal injection when compared to the NTC (green bars). Silencing was measured by western blotting with retinal protein extracts. Mice were all injected at 3 months of age ( N = 5–8 retinas/group). (C) Percentage silencing in PR vs. non-PR cells that were enriched by FACS at 2 months post-intravitreal delivery of siRNA. The percentage of protein expression level is normalized to the tetra-siRNA NTC treated group. (D) PR outer segment (POS) clearance in RPE cells of 4-month-old mice shown as percentage of POS remaining at 11 am when compared to the peak of shedding at 8 am in the genotypes indicated. rod Tsc1 −/− mice were injected at 2 months of age with siRNA reagents indicated ( N = 4–7 eyes/group). (E and F) Reversal of APOE accumulation at the BrM in tetra-siRNA S6k1 -treated mice. (E) APOE protein expression level measured by western blotting with RPE/choroid protein extracts of 15-month-old rod Tsc1 −/− mice that are untreated or treated with either tetra-siRNA NTC or tetra-siRNA S6k1 for 3 months (treatment started at 12 months of age). Expression levels are compared to 15-month-old littermate control rod Tsc1 +/+ mice ( N = 5–10 eyes/group). (B–E) Results are shown as mean ± S.E.M. Each dot represents one retina or RPE/choroid from one mouse. Only one eye per mouse was used for each analysis (∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001; ∗∗∗∗ p < 0.0001; green bars represent tetra-siRNA NTC and blue bars tetra-siRNA S6k1 -injected eyes). (F) Retinal cross-section of rod Tsc1 −/− eyes showing reduction in the accumulation APOE (green signal) at the BrM (white arrowheads) of tetra-siRNA S6k1 -injected eyes (right panel). Mice were injected at 12 months of age and analyzed 3 months post-injection. Scale bars: 50 μm; blue, nuclear DAPI; red, peanut agglutinin lectin (PNA) marking cone PR segments; RPE, retinal-pigmented epithelium; PS, PR segment region covering inner and outer segments; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer; vertical bars in sections mark height of different layers.

    Article Snippet: The following reagents already had a chromophore conjugated: rhodamine phalloidin (Life Technology, Cat. #: R415; 1:100) and fluorescein peanut agglutinin lectin (PNA; Vector Laboratories, Cat. #: FL-1071; 1:500).

    Techniques: Injection, Expressing, RNAscope, Immunohistochemistry, Staining, Western Blot, Control