Staining:
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.
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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