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Series GSE102486 Query DataSets for GSE102486
Status Public on Apr 02, 2018
Title A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Subsets of endogenous retroviruses (ERVs) are derepressed in mouse embryonic stem cells (mESCs) deficient for Setdb1, which catalyzes histone H3 lysine 9 trimethylation (H3K9me3). Most of those ERVs, including IAPs, remain silent if Setdb1 is deleted in differentiated embryonic cells; however they are derepressed when deficient for Dnmt1, suggesting that Setdb1 is dispensable for ERV silencing in somatic cells. However, H3K9me3 enrichment on ERVs is maintained in differentiated cells and is mostly diminished in mouse embryonic fibroblasts (MEFs) lacking Setdb1. We find that distinctive sets of ERVs are reactivated in different types of Setdb1-deficient somatic cells, including the VL30-class of ERVs in MEFs, whose derepression is dependent on cell type-specific transcription factors (TFs). These data suggest a more general role for Setdb1 in ERV silencing, which provides an additional layer of epigenetic silencing through the H3K9me3 modification.
Overall design Analyses of transcriptional profiles and chromatin state in Setdb1 WT and KO cells
Contributor(s) Kato M, Takemoto K, Shinkai Y
Citation(s) 29703894
Submission date Aug 10, 2017
Last update date Jul 25, 2021
Contact name Masaki Kato
Organization name RIKEN
Lab Cellular Memory Laboratory
Street address 2-1 Hirosawa
City Wako
State/province Saitama
ZIP/Postal code 3510198
Country Japan
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (27)
GSM2739369 RNAseq_Setdb1 cKO iMEFs_WT_1
GSM2739370 RNAseq_Setdb1 cKO iMEFs_WT_2
GSM2739371 RNAseq_Setdb1 cKO iMEFs_WT_3
This SubSeries is part of SuperSeries:
GSE102490 A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing
BioProject PRJNA398190
SRA SRP115380

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE102486_RAW.tar 20.5 Mb (http)(custom) TAR (of TXT)
GSE102486_WT_KO.gene_exp.diff.yes.txt.gz 184.9 Kb (ftp)(http) TXT
GSE102486_WT_KOL.gene_exp.diff.yes.txt.gz 363.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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