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immunoblotting rabbit anti mpp8  (Proteintech)


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    Proteintech immunoblotting rabbit anti mpp8
    Immunoblotting Rabbit Anti Mpp8, supplied by Proteintech, used in various techniques. Bioz Stars score: 93/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/rabbit+anti+mpp8/MPP8+Antibody/pmc11754731-57-2-5
    Average 93 stars, based on 37 article reviews
    immunoblotting rabbit anti mpp8 - by Bioz Stars, 2026-09
    93/100 stars

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    Western Blot:

    Article Title: Genome surveillance by HUSH-mediated silencing of intronless mobile elements
    Article Snippet: Cell cultures were routinely tested and found to be negative for mycoplasma infection (MycoAlert, Lonza). .. Antibodies for immunoblotting: rabbit anti-TASOR (Atlas, HPA006735, 1:5,000), rabbit anti-MPP8 (Proteintech, 16796-1-AP, 1:5,000), rabbit anti-periphilin1 (Sigma-Aldrich, HPA038902, 1:5,000), rabbit anti-MORC2 (Bethyl Laboratories, A300-149A, 1:5,000), rabbit anti-SETDB1 (Proteintech, 11231-1-AP; 1:5,000), rat anti-haemagglutinin (HA) tag (3F10, Sigma-Aldrich, 11867423001, 1:10,000), mouse anti-β-actin peroxidase conjugate (Sigma-Aldrich, A3854; 1:20,000), mouse anti-p97 (Abcam, ab11433, 1:5,000), rabbit anti-α-tubulin (11H10, CST, 2125, 1:5,000). .. Horseradish peroxidase (HRP)-conjugated secondary antibodies for immunoblotting were obtained from Jackson ImmunoResearch: Peroxidase AffiniPure Goat Anti-Mouse IgG (H+L) (115-035-146, 1:10,000), Peroxidase AffiniPure Goat Anti-Rabbit IgG (H+L) (111-035-144, 1:10,000), Peroxidase AffiniPure Goat Anti-Rat IgG (H+L) (112-035-143, 1:10,000).

    Article Title: Genome surveillance by HUSH-mediated silencing of intronless mobile elements.
    Article Snippet: Cell cultures were routinely tested and found to be negative for mycoplasma infection (MycoAlert, Lonza). .. Antibodies for immunoblotting: rabbit anti-TASOR (Atlas, HPA006735, 1:5,000), rabbit anti-MPP8 (Proteintech, 16796-1-AP, 1:5,000), rabbit anti-periphilin1 (Sigma-Aldrich, HPA038902, 1:5,000), rabbit anti-MORC2 (Bethyl Laboratories, A300-149A, 1:5,000), rabbit anti-SETDB1 (Proteintech, 11231-1-AP; 1:5,000), rat anti-haemagglutinin (HA) tag (3F10, Sigma-Aldrich, 11867423001, 1:10,000), mouse anti-β-actin peroxidase conjugate (Sigma-Aldrich, A3854; 1:20,000), mouse anti-p97 (Abcam, ab11433, 1:5,000), rabbit anti-α-tubulin (11H10, CST, 2125, 1:5,000). .. Horseradish peroxidase (HRP)-conjugated secondary antibodies for immunoblotting were obtained from Jackson ImmunoResearch: Peroxidase AffiniPure Goat Anti-Mouse IgG (H+L) (115-035-146, 1:10,000), Peroxidase AffiniPure Goat Anti-Rabbit IgG (H+L) (111-035-144, 1:10,000), Peroxidase AffiniPure Goat Anti-Rat IgG (H+L) (112-035-143, 1:10,000).

    Article Title: RNA binding by Periphilin plays an essential role in initiating silencing by the HUSH complex
    Article Snippet: .. Antibodies for immunoblotting: rabbit anti-TASOR (Atlas, HPA006735, 1:5,000), rabbit anti-MPP8 (Proteintech, 16796-1-AP, 1:10,000), rabbit anti-Periphilin1 (Sigma-Aldrich, HPA038902, 1:5,000), rabbit anti-SETDB1 (Proteintech, 11231-1-AP; 1:5,000), mouse anti FLAG (M2, Sigma-Aldrich, F3165, 1:10000), mouse anti-haemagglutinin (HA.11) tag (16B12, Covance, MMS-101P, 1:20,000), mouse anti-β-actin peroxidase conjugate (Sigma-Aldrich, A3854; 1:20,000). .. Secondary antibodies for immunoblotting: Horseradish peroxidase (HRP)-conjugated AffiniPure goat anti-mouse IgG (H+L) (Jackson ImmunoResearch, 115-035-146, 1:10,000), Antibodies for FACS analysis: mouse anti-MHC (W6/32 hybridoma S/N), Secondary antibody for FACS: Donkey anti-mouse IgG (H+L) Alexa FluorTM 647 (Thermo, A32787).

    Article Title: Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2.
    Article Snippet: All cell lines were routinely tested for mycoplasma contamination with an ATCC Universal Mycoplasma Detection Kit. .. The following primary antibodies were used: rabbit anti-MORC2 (Bethyl Laboratories, A300-149A used for immunoblotting), rabbit antiMORC2 (Santa Cruz Biotechnology, sc-366271, used for immunofluorescence), rabbit anti-TASOR (Atlas Antibodies, HPA006735), rabbit anti-MPP8 (Proteintech, 16796-1-AP), rabbit anti-SETDB1 (Proteintech, 11231-1-AP), mouse anti-GFP (Life Technologies, A11120), mouse anti-V5 (Abcam, ab27671), rabbit anti-V5 (Abcam, ab15828), goat anti-Lamin B1 (Santa Cruz, sc-6217), rabbit anti-H3K9me3 (Abcam, ab8898), rabbit anti-histone H3 (Biolegend, 601902), rabbit IgG (Cell Signaling, 2729), mouse anti-calnexin (AF8, a kind gift from M. Brenner) and mouse anti-β-actin (Sigma-Aldrich, A5316). .. Alexa Fluor 488– and Alexa Fluor 546–conjugated secondary antibodies for immunofluorescence were obtained from Molecular Probes (A32723 and A-11010).

    other:

    Article Title: Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2.
    Article Snippet: Alexa Fluor 488– and Alexa Fluor 546–conjugated secondary antibodies for immunofluorescence were obtained from Molecular Probes (A32723 and A-11010).

    Immunofluorescence:

    Article Title: Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2.
    Article Snippet: All cell lines were routinely tested for mycoplasma contamination with an ATCC Universal Mycoplasma Detection Kit. .. The following primary antibodies were used: rabbit anti-MORC2 (Bethyl Laboratories, A300-149A used for immunoblotting), rabbit antiMORC2 (Santa Cruz Biotechnology, sc-366271, used for immunofluorescence), rabbit anti-TASOR (Atlas Antibodies, HPA006735), rabbit anti-MPP8 (Proteintech, 16796-1-AP), rabbit anti-SETDB1 (Proteintech, 11231-1-AP), mouse anti-GFP (Life Technologies, A11120), mouse anti-V5 (Abcam, ab27671), rabbit anti-V5 (Abcam, ab15828), goat anti-Lamin B1 (Santa Cruz, sc-6217), rabbit anti-H3K9me3 (Abcam, ab8898), rabbit anti-histone H3 (Biolegend, 601902), rabbit IgG (Cell Signaling, 2729), mouse anti-calnexin (AF8, a kind gift from M. Brenner) and mouse anti-β-actin (Sigma-Aldrich, A5316). .. Alexa Fluor 488– and Alexa Fluor 546–conjugated secondary antibodies for immunofluorescence were obtained from Molecular Probes (A32723 and A-11010).



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    Figure 3. Two classes of HUSH targets distinguished by H3K9me3, transposon content, and response to HUSH depletion (A) Heatmaps showing ChIP-seq coverage for <t>MPP8,</t> TASOR, H3K9me3, and SETDB1 at MPP8 peaks. The x axis represents distance from MPP8 ChIP peak in kb. Heatmaps were sorted first by H3K9me3 and then by MPP8 and TASOR signal. Regions with high coverage of both MPP8 and TASOR were classified as HUSH targets (H3K9me3-positive; orange and H3K9me3-negative; light blue), whereas regions with low or no TASOR were delineated as MPP8-only (gray). The number of peaks for each class (n) is indicated. ChIP peak orientation in heatmaps is stranded based on the ratio of positive- and negative-stranded PRO-seq signals. (B) Scatterplots showing all MPP8 and TASOR ChIP-seq peaks as a function of log coverage for MPP8 (x axis) and SETDB1 (y axis) ChIP-seq. Marked in red are peaks overlapping H3K9me3 (left) or TASOR (right). (C) Heatmaps showing the presence and relative position of repetitive elements as annotated by repeat masker, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (D) Heatmaps showing relative position of transcribed exons as annotated by custom transcriptome models derived from RNA-Seq of WT mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (E) Heatmaps showing RNA-seq coverage in WT mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (F) Heatmaps showing subtraction of RNA-seq coverage in MPP8-depleted mESCs (treated with auxin for 7 days) from control mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (G) Heatmaps showing subtraction of RNA-seq coverage in TASOR-depleted mESCs (treated with auxin for 1 day) from untreated control mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb.
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    Proteintech immunoblotting rabbit α tasor
    Fig. 1 | Diverse intronless transgenes are HUSH-repressed. a, Repression of L1 reporter lentivirus in wild-type (WT) (black) or <t>TASOR-knockout</t> (KO) (purple) HeLa cells, measured by flow cytometry. b, c, L1 reporter integrated by piggyBac transposase. b, Doxycycline (Dox)-induced expression in wild-type and TASOR KO HeLa cells measured by flow cytometry. CMV, cytomegalovirus promoter. c, Chromatin immunoprecipitation with quantitative PCR (ChIP–qPCR) assays of H3K9me3 (left; mean of n = 2 biological replicates ± s.d.) and RNA polymerase II (Pol II) (middle; mean of n = 3 biological replicates ± s.d.) in wild-type and TASOR KO HeLa cells at the reporter. L1 transcript levels assayed by quantitative PCR with reverse transcription (RT–qPCR) (right; mean of n = 3 technical replicates ± s.d.). d, Doxycycline-induced expression of piggyBac reporter without ORF2 sequence (left) and with ORF2 sequence (4 kb) replaced by 4×ORF1 (4×1 kb in size) (right) integrated into wild-type or TASOR KO HeLa cells. e, HUSH-mediated repression of GFP lentiviral reporters bearing different untranslated cDNA sequences measured by flow cytometry 72 h after transduction. Length of the cDNA sequence is indicated in brackets and fold change of reporter expression in TASOR KD and wild-type cells measured by geometric mean fluorescence is indicated on the graph. Frequency is normalized to mode (a, b, d, e).
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    Proteintech rabbit α mpp8
    Fig. 1 | Diverse intronless transgenes are HUSH-repressed. a, Repression of L1 reporter lentivirus in wild-type (WT) (black) or <t>TASOR-knockout</t> (KO) (purple) HeLa cells, measured by flow cytometry. b, c, L1 reporter integrated by piggyBac transposase. b, Doxycycline (Dox)-induced expression in wild-type and TASOR KO HeLa cells measured by flow cytometry. CMV, cytomegalovirus promoter. c, Chromatin immunoprecipitation with quantitative PCR (ChIP–qPCR) assays of H3K9me3 (left; mean of n = 2 biological replicates ± s.d.) and RNA polymerase II (Pol II) (middle; mean of n = 3 biological replicates ± s.d.) in wild-type and TASOR KO HeLa cells at the reporter. L1 transcript levels assayed by quantitative PCR with reverse transcription (RT–qPCR) (right; mean of n = 3 technical replicates ± s.d.). d, Doxycycline-induced expression of piggyBac reporter without ORF2 sequence (left) and with ORF2 sequence (4 kb) replaced by 4×ORF1 (4×1 kb in size) (right) integrated into wild-type or TASOR KO HeLa cells. e, HUSH-mediated repression of GFP lentiviral reporters bearing different untranslated cDNA sequences measured by flow cytometry 72 h after transduction. Length of the cDNA sequence is indicated in brackets and fold change of reporter expression in TASOR KD and wild-type cells measured by geometric mean fluorescence is indicated on the graph. Frequency is normalized to mode (a, b, d, e).
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    Figure 3. Two classes of HUSH targets distinguished by H3K9me3, transposon content, and response to HUSH depletion (A) Heatmaps showing ChIP-seq coverage for MPP8, TASOR, H3K9me3, and SETDB1 at MPP8 peaks. The x axis represents distance from MPP8 ChIP peak in kb. Heatmaps were sorted first by H3K9me3 and then by MPP8 and TASOR signal. Regions with high coverage of both MPP8 and TASOR were classified as HUSH targets (H3K9me3-positive; orange and H3K9me3-negative; light blue), whereas regions with low or no TASOR were delineated as MPP8-only (gray). The number of peaks for each class (n) is indicated. ChIP peak orientation in heatmaps is stranded based on the ratio of positive- and negative-stranded PRO-seq signals. (B) Scatterplots showing all MPP8 and TASOR ChIP-seq peaks as a function of log coverage for MPP8 (x axis) and SETDB1 (y axis) ChIP-seq. Marked in red are peaks overlapping H3K9me3 (left) or TASOR (right). (C) Heatmaps showing the presence and relative position of repetitive elements as annotated by repeat masker, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (D) Heatmaps showing relative position of transcribed exons as annotated by custom transcriptome models derived from RNA-Seq of WT mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (E) Heatmaps showing RNA-seq coverage in WT mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (F) Heatmaps showing subtraction of RNA-seq coverage in MPP8-depleted mESCs (treated with auxin for 7 days) from control mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (G) Heatmaps showing subtraction of RNA-seq coverage in TASOR-depleted mESCs (treated with auxin for 1 day) from untreated control mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb.

    Journal: Molecular cell

    Article Title: Co-transcriptional genome surveillance by HUSH is coupled to termination machinery.

    doi: 10.1016/j.molcel.2023.04.014

    Figure Lengend Snippet: Figure 3. Two classes of HUSH targets distinguished by H3K9me3, transposon content, and response to HUSH depletion (A) Heatmaps showing ChIP-seq coverage for MPP8, TASOR, H3K9me3, and SETDB1 at MPP8 peaks. The x axis represents distance from MPP8 ChIP peak in kb. Heatmaps were sorted first by H3K9me3 and then by MPP8 and TASOR signal. Regions with high coverage of both MPP8 and TASOR were classified as HUSH targets (H3K9me3-positive; orange and H3K9me3-negative; light blue), whereas regions with low or no TASOR were delineated as MPP8-only (gray). The number of peaks for each class (n) is indicated. ChIP peak orientation in heatmaps is stranded based on the ratio of positive- and negative-stranded PRO-seq signals. (B) Scatterplots showing all MPP8 and TASOR ChIP-seq peaks as a function of log coverage for MPP8 (x axis) and SETDB1 (y axis) ChIP-seq. Marked in red are peaks overlapping H3K9me3 (left) or TASOR (right). (C) Heatmaps showing the presence and relative position of repetitive elements as annotated by repeat masker, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (D) Heatmaps showing relative position of transcribed exons as annotated by custom transcriptome models derived from RNA-Seq of WT mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (E) Heatmaps showing RNA-seq coverage in WT mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (F) Heatmaps showing subtraction of RNA-seq coverage in MPP8-depleted mESCs (treated with auxin for 7 days) from control mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb. (G) Heatmaps showing subtraction of RNA-seq coverage in TASOR-depleted mESCs (treated with auxin for 1 day) from untreated control mESCs, centered and sorted as in (A). The x axis represents distance from MPP8 ChIP peak in kb.

    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies MPP8 – Rabbit polyclonal Proteintech Cat# 16796-1; RRID: AB_2266644 GFP – Rabbit polyclonal Thermo Fisher Scientific Cat# A11122; RRID: AB_221569 H3K9me3 – Rabbit polyclonal Abcam Cat# Ab8898; RRID: AB_306848 WDR82 – Rabbit monoclonal Cell Signaling Technology Cat# 99715; RRID: AB_2800319 H3K4me3 – Rabbit polyclonal Abcam Cat# ab8580; RRID: AB_306649 HRP conjugated mouse monoclonal anti-HSP90 Cell Signaling Technology Cat# 79641S; RRID: AB_2799937 HA – Rabbit polyclonal Abcam Cat# ab9110; RRID: AB_307019 LINE-1 ORF1p – Rabbit monoclonal Abcam Cat# ab216324; RRID: AB_2921327 Bacterial and virus strains 10-beta Competent E. coli (high efficiency) NEB C3019H 5-alpha Competent E. coli NEB C2987H Chemicals, peptides, and recombinant proteins MEK inhibitor PD0325901 Selleck Chemicals Cat# S1036 GSK3b inhibitor CHIR99021 Selleck Chemicals Cat# S2924 polyL-ornithine Sigma-Aldrich Cat# P4638-100MG Laminin Life Technologies Cat# 23017015 Fibronectin ThermoFisher Cat# FC01010MG Indole-3-acetic acid sodium salt (auxin analog) Sigma-Aldrich Cat# 5148-2G cOmplete, EDTA-free Protease Inhibitor Cocktail Millipore Sigma 11873580001 PhosSTOP Millipore Sigma 4906845001 SUPERaseIn ThermoFisher AM2694 Critical commercial assays Lipofectamine2000 ThermoFisher Cat#11668019 NEBNext Ultra II DNA Library Prep Kit for Illumina New England BioLabs Cat# E7645S TRIzol Reagent Invitrogen Cat# 15596018 NEBNext Multiplex Oligos for Illumina kit New England BioLabs Cat# E7335S AMPure XP Beckman Coulter Cat# A63881 Dynabeads Protein G for Immunoprecipitation Invitrogen Cat# 10004D Qubit dsDNA HS Assay Kit Invitrogen Cat# Q32854 Ovation RNA-seq FFPE Nugen discontinued Unicersal Plus Total RNA-seq library preparation kit with NuQuant, mouse any-deplete Tecan Cat# 9157-24 RNeasy Plus Mini Qiagen Cat# 74134 DNA Clean & Concentrator-5 Zymo Cat# D4014 HyperSep C18 Plates ThermoFisher 60300-425 Deposited data ChIP-seq, RNA-seq, and PRO-seq This paper GEO: GSE208753 Western blot raw images This paper Mendeley DOI: 0.17632/v5y87syfcc.1 Experimental models: Cell lines R1 mESC WT This paper N/A R1 mESC TASOR-AGH TIR1 mCherry This paper N/A R1 mESC TASOR-AGH TIR1-mCherry KO T1 This paper N/A R1 mESC TASOR-AGH TIR1 mCherry WDR82 KO T5 This paper N/A (Continued on next page) e1 Molecular Cell 83, 1623–1639.e1–e8, May 18, 2023

    Techniques: ChIP-sequencing, Derivative Assay, RNA Sequencing, Control

    Figure 4. The HUSH complex interacts with RNA polymerase II termination factors and binds nascent RNA (A) Log of label-free quantification (LFQ) intensity for HA immunoprecipitation (IP) followed by mass-spectrometry in TASOR-AGH (y axis) and untagged control mESCs (x axis). Colored dots highlight associations of proteins with the HUSH complex (blue) or with RNA polymerase II (red). (B) Same as (A), for MPP8-AGH IP-MS. (C) Western blot showing coIP of MPP8 and WDR82 with TASOR (HA IP) in the TASOR-AGH cell line. Samples were incubated with RNaseA at 2 ng/mL during the IP. Inputs (in), non-bound flowthrough (NB), and HA peptide eluted (E) fractions at shown. (D) Enrichment of MPP8 irCLIP-seq for various genomic features. y axis was calculated by normalizing the number of RT stops to both length and level of transcription, as measured by PRO-seq. Exons were annotated by custom transcriptome models derived from RNA-seq of WT mESCs. (E) Aggregate plot showing MPP8 CLIP-seq normalized read count (y axis) relative to the distance from HUSH or MPP8-only ChIP peaks (x axis). HUSH peaks were divided into H3K9me3-positive (blue), H3K9me3-negative (purple), or MPP8-only regions based on the classification in Figure 3A. (F) Heatmaps showing ChIP-seq coverage for RNA polymerase II using different antibodies that recognize various C-terminal domain (CTD) modifications, centered and sorted as in Figure 3A. The x axis represents distance from MPP8 ChIP peak in kb.

    Journal: Molecular cell

    Article Title: Co-transcriptional genome surveillance by HUSH is coupled to termination machinery.

    doi: 10.1016/j.molcel.2023.04.014

    Figure Lengend Snippet: Figure 4. The HUSH complex interacts with RNA polymerase II termination factors and binds nascent RNA (A) Log of label-free quantification (LFQ) intensity for HA immunoprecipitation (IP) followed by mass-spectrometry in TASOR-AGH (y axis) and untagged control mESCs (x axis). Colored dots highlight associations of proteins with the HUSH complex (blue) or with RNA polymerase II (red). (B) Same as (A), for MPP8-AGH IP-MS. (C) Western blot showing coIP of MPP8 and WDR82 with TASOR (HA IP) in the TASOR-AGH cell line. Samples were incubated with RNaseA at 2 ng/mL during the IP. Inputs (in), non-bound flowthrough (NB), and HA peptide eluted (E) fractions at shown. (D) Enrichment of MPP8 irCLIP-seq for various genomic features. y axis was calculated by normalizing the number of RT stops to both length and level of transcription, as measured by PRO-seq. Exons were annotated by custom transcriptome models derived from RNA-seq of WT mESCs. (E) Aggregate plot showing MPP8 CLIP-seq normalized read count (y axis) relative to the distance from HUSH or MPP8-only ChIP peaks (x axis). HUSH peaks were divided into H3K9me3-positive (blue), H3K9me3-negative (purple), or MPP8-only regions based on the classification in Figure 3A. (F) Heatmaps showing ChIP-seq coverage for RNA polymerase II using different antibodies that recognize various C-terminal domain (CTD) modifications, centered and sorted as in Figure 3A. The x axis represents distance from MPP8 ChIP peak in kb.

    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies MPP8 – Rabbit polyclonal Proteintech Cat# 16796-1; RRID: AB_2266644 GFP – Rabbit polyclonal Thermo Fisher Scientific Cat# A11122; RRID: AB_221569 H3K9me3 – Rabbit polyclonal Abcam Cat# Ab8898; RRID: AB_306848 WDR82 – Rabbit monoclonal Cell Signaling Technology Cat# 99715; RRID: AB_2800319 H3K4me3 – Rabbit polyclonal Abcam Cat# ab8580; RRID: AB_306649 HRP conjugated mouse monoclonal anti-HSP90 Cell Signaling Technology Cat# 79641S; RRID: AB_2799937 HA – Rabbit polyclonal Abcam Cat# ab9110; RRID: AB_307019 LINE-1 ORF1p – Rabbit monoclonal Abcam Cat# ab216324; RRID: AB_2921327 Bacterial and virus strains 10-beta Competent E. coli (high efficiency) NEB C3019H 5-alpha Competent E. coli NEB C2987H Chemicals, peptides, and recombinant proteins MEK inhibitor PD0325901 Selleck Chemicals Cat# S1036 GSK3b inhibitor CHIR99021 Selleck Chemicals Cat# S2924 polyL-ornithine Sigma-Aldrich Cat# P4638-100MG Laminin Life Technologies Cat# 23017015 Fibronectin ThermoFisher Cat# FC01010MG Indole-3-acetic acid sodium salt (auxin analog) Sigma-Aldrich Cat# 5148-2G cOmplete, EDTA-free Protease Inhibitor Cocktail Millipore Sigma 11873580001 PhosSTOP Millipore Sigma 4906845001 SUPERaseIn ThermoFisher AM2694 Critical commercial assays Lipofectamine2000 ThermoFisher Cat#11668019 NEBNext Ultra II DNA Library Prep Kit for Illumina New England BioLabs Cat# E7645S TRIzol Reagent Invitrogen Cat# 15596018 NEBNext Multiplex Oligos for Illumina kit New England BioLabs Cat# E7335S AMPure XP Beckman Coulter Cat# A63881 Dynabeads Protein G for Immunoprecipitation Invitrogen Cat# 10004D Qubit dsDNA HS Assay Kit Invitrogen Cat# Q32854 Ovation RNA-seq FFPE Nugen discontinued Unicersal Plus Total RNA-seq library preparation kit with NuQuant, mouse any-deplete Tecan Cat# 9157-24 RNeasy Plus Mini Qiagen Cat# 74134 DNA Clean & Concentrator-5 Zymo Cat# D4014 HyperSep C18 Plates ThermoFisher 60300-425 Deposited data ChIP-seq, RNA-seq, and PRO-seq This paper GEO: GSE208753 Western blot raw images This paper Mendeley DOI: 0.17632/v5y87syfcc.1 Experimental models: Cell lines R1 mESC WT This paper N/A R1 mESC TASOR-AGH TIR1 mCherry This paper N/A R1 mESC TASOR-AGH TIR1-mCherry KO T1 This paper N/A R1 mESC TASOR-AGH TIR1 mCherry WDR82 KO T5 This paper N/A (Continued on next page) e1 Molecular Cell 83, 1623–1639.e1–e8, May 18, 2023

    Techniques: Immunoprecipitation, Mass Spectrometry, Control, Protein-Protein interactions, Western Blot, Incubation, Derivative Assay, RNA Sequencing, ChIP-sequencing

    Journal: Molecular cell

    Article Title: Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression

    doi: 10.1016/j.molcel.2022.03.004

    Figure Lengend Snippet:

    Article Snippet: Rabbit polyclonal anti-MPP8 , Proteintech , Cat# 16796-1AP; RRID:AB_2266644.

    Techniques: Recombinant, Reverse Transcription, SYBR Green Assay, Library Quantification, Transfection, Cloning, Purification, Software

    Fig. 1 | Diverse intronless transgenes are HUSH-repressed. a, Repression of L1 reporter lentivirus in wild-type (WT) (black) or TASOR-knockout (KO) (purple) HeLa cells, measured by flow cytometry. b, c, L1 reporter integrated by piggyBac transposase. b, Doxycycline (Dox)-induced expression in wild-type and TASOR KO HeLa cells measured by flow cytometry. CMV, cytomegalovirus promoter. c, Chromatin immunoprecipitation with quantitative PCR (ChIP–qPCR) assays of H3K9me3 (left; mean of n = 2 biological replicates ± s.d.) and RNA polymerase II (Pol II) (middle; mean of n = 3 biological replicates ± s.d.) in wild-type and TASOR KO HeLa cells at the reporter. L1 transcript levels assayed by quantitative PCR with reverse transcription (RT–qPCR) (right; mean of n = 3 technical replicates ± s.d.). d, Doxycycline-induced expression of piggyBac reporter without ORF2 sequence (left) and with ORF2 sequence (4 kb) replaced by 4×ORF1 (4×1 kb in size) (right) integrated into wild-type or TASOR KO HeLa cells. e, HUSH-mediated repression of GFP lentiviral reporters bearing different untranslated cDNA sequences measured by flow cytometry 72 h after transduction. Length of the cDNA sequence is indicated in brackets and fold change of reporter expression in TASOR KD and wild-type cells measured by geometric mean fluorescence is indicated on the graph. Frequency is normalized to mode (a, b, d, e).

    Journal: Nature

    Article Title: Genome surveillance by HUSH-mediated silencing of intronless mobile elements.

    doi: 10.1038/s41586-021-04228-1

    Figure Lengend Snippet: Fig. 1 | Diverse intronless transgenes are HUSH-repressed. a, Repression of L1 reporter lentivirus in wild-type (WT) (black) or TASOR-knockout (KO) (purple) HeLa cells, measured by flow cytometry. b, c, L1 reporter integrated by piggyBac transposase. b, Doxycycline (Dox)-induced expression in wild-type and TASOR KO HeLa cells measured by flow cytometry. CMV, cytomegalovirus promoter. c, Chromatin immunoprecipitation with quantitative PCR (ChIP–qPCR) assays of H3K9me3 (left; mean of n = 2 biological replicates ± s.d.) and RNA polymerase II (Pol II) (middle; mean of n = 3 biological replicates ± s.d.) in wild-type and TASOR KO HeLa cells at the reporter. L1 transcript levels assayed by quantitative PCR with reverse transcription (RT–qPCR) (right; mean of n = 3 technical replicates ± s.d.). d, Doxycycline-induced expression of piggyBac reporter without ORF2 sequence (left) and with ORF2 sequence (4 kb) replaced by 4×ORF1 (4×1 kb in size) (right) integrated into wild-type or TASOR KO HeLa cells. e, HUSH-mediated repression of GFP lentiviral reporters bearing different untranslated cDNA sequences measured by flow cytometry 72 h after transduction. Length of the cDNA sequence is indicated in brackets and fold change of reporter expression in TASOR KD and wild-type cells measured by geometric mean fluorescence is indicated on the graph. Frequency is normalized to mode (a, b, d, e).

    Article Snippet: Materials & experimental systems n/a Involved in the study Antibodies Eukaryotic cell lines Palaeontology and archaeology Animals and other organisms Human research participants Clinical data Dual use research of concern Methods n/a Involved in the study ChIP-seq Flow cytometry MRI-based neuroimaging Antibodies Antibodies used Antibodies for immunoblotting: rabbit α-TASOR (Atlas, HPA006735, 1:5000), rabbit α-MPP8 (Proteintech, 16796-1-AP, 1:5000), rabbit α-Periphilin1 (Sigma-Aldrich, HPA038902, 1:5000), rabbit anti-MORC2 (Bethyl Laboratories, A300-149A, 1:5000), rabbit α-SETDB1 (Proteintech, 11231-1-AP; 1:5000), rat α-HA tag (3F10, Sigma-Aldrich, 11867423001, 1:10 000), 3 nature research | reporting sum m ary April 2020 mouse α-β-actin peroxidase conjugate (Sigma-Aldrich, A3854; 1:20 000), mouse α-p97 (Abcam, ab11433, 1:5000), rabbit α-α-tubulin (11H10, CST, #2125, 1:5000).

    Techniques: Knock-Out, Flow Cytometry, Expressing, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, ChIP-qPCR, Reverse Transcription, Quantitative RT-PCR, Sequencing, Transduction, Fluorescence

    Fig. 3 | Introns protect against HUSH, even in the absence of intron splicing. HUSH-mediated repression of intronless and intron-containing iRFP-ORF2 piggyBac reporters. a, b, Second intron from the human β-globin gene (HBB IVS2) cloned within the iRFP gene. a, Flow cytometry histograms showing expression in wild-type and TASOR KO HeLa cells. b, ChIP–qPCR quantification of H3K9me3 and total histone H3 at reporters in wild-type and TASOR KO HeLa cells. Data are mean of n = 3 independent experiments ± s.d.; **P < 0.008, *P = 0.02 versus intronless wild type, ratio-paired two-tailed t-test. c, HUSH-mediated repression of reporter with intron(s) or control sequence cloned at the 5′ or 3′ of ORF2, measured by flow cytometry and shown as the ratio of reporter expression in TASOR KO and wild-type cells. Data are mean from n biological replicates ± s.d.; ***P ≤ 0.0001, one-way analysis of variance (ANOVA) post hoc pairwise comparisons versus no-intron condition with Bonferroni correction.

    Journal: Nature

    Article Title: Genome surveillance by HUSH-mediated silencing of intronless mobile elements.

    doi: 10.1038/s41586-021-04228-1

    Figure Lengend Snippet: Fig. 3 | Introns protect against HUSH, even in the absence of intron splicing. HUSH-mediated repression of intronless and intron-containing iRFP-ORF2 piggyBac reporters. a, b, Second intron from the human β-globin gene (HBB IVS2) cloned within the iRFP gene. a, Flow cytometry histograms showing expression in wild-type and TASOR KO HeLa cells. b, ChIP–qPCR quantification of H3K9me3 and total histone H3 at reporters in wild-type and TASOR KO HeLa cells. Data are mean of n = 3 independent experiments ± s.d.; **P < 0.008, *P = 0.02 versus intronless wild type, ratio-paired two-tailed t-test. c, HUSH-mediated repression of reporter with intron(s) or control sequence cloned at the 5′ or 3′ of ORF2, measured by flow cytometry and shown as the ratio of reporter expression in TASOR KO and wild-type cells. Data are mean from n biological replicates ± s.d.; ***P ≤ 0.0001, one-way analysis of variance (ANOVA) post hoc pairwise comparisons versus no-intron condition with Bonferroni correction.

    Article Snippet: Materials & experimental systems n/a Involved in the study Antibodies Eukaryotic cell lines Palaeontology and archaeology Animals and other organisms Human research participants Clinical data Dual use research of concern Methods n/a Involved in the study ChIP-seq Flow cytometry MRI-based neuroimaging Antibodies Antibodies used Antibodies for immunoblotting: rabbit α-TASOR (Atlas, HPA006735, 1:5000), rabbit α-MPP8 (Proteintech, 16796-1-AP, 1:5000), rabbit α-Periphilin1 (Sigma-Aldrich, HPA038902, 1:5000), rabbit anti-MORC2 (Bethyl Laboratories, A300-149A, 1:5000), rabbit α-SETDB1 (Proteintech, 11231-1-AP; 1:5000), rat α-HA tag (3F10, Sigma-Aldrich, 11867423001, 1:10 000), 3 nature research | reporting sum m ary April 2020 mouse α-β-actin peroxidase conjugate (Sigma-Aldrich, A3854; 1:20 000), mouse α-p97 (Abcam, ab11433, 1:5000), rabbit α-α-tubulin (11H10, CST, #2125, 1:5000).

    Techniques: Clone Assay, Flow Cytometry, Expressing, ChIP-qPCR, Two Tailed Test, Control, Sequencing