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Series GSE115288 Query DataSets for GSE115288
Status Public on Jun 27, 2019
Title Genome-wide analysis of differential transcription in KRAB-ZFP cluster knock-out ES cells and mouse tissues
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Mammalian genomes encode several hundred Kr├╝ppel-associated box zinc finger proteins (KRAB-ZFPs) that bind DNA in a sequence-specific manner through tandem arrays of C2H2-type zinc fingers and repress transcription via KRAB-dependent recruitment of the silencing cofactor KAP1. The KRAB-ZFP family rapidly amplified and diversified in mammals by segmental gene duplications, mutations, and zinc finger rearrangements likely in response to continued transposable element invasions, but the biological functions and in vivo requirement of these proteins has gone largely unexplored. We determined the genomic binding sites of 61 murine KRAB-ZFPs and genetically deleted five large KRAB-ZFP gene clusters encoding more than 100 of the approximately 360 mouse KRAB-ZFPs. We demonstrate that most KRAB-ZFPs bind to specific retrotransposon families and that many of these retrotransposons are transcriptionally activated in KRAB-ZFP cluster KO ESCs, licensing retrotransposon-derived enhancers to activate nearby genes.
 
Overall design RNA-seq analysis of KRAB-ZFP cluster KO ES cells and tissues.
 
Contributor(s) Wolf G, De Iaco A, Tinkham M, Macfarlan TS, Trono D
Citation(s) 32479262
Submission date Jun 04, 2018
Last update date Jun 15, 2020
Contact name Gernot Wolf
Organization name NIH
Department NICHD
Lab Macfarlan lab
Street address 6 Center Drive
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (61)
GSM3173769 Chr4-cl WT B6/129 ES cells #26
GSM3173770 Chr4-cl WT B6/129 ES cells #49
GSM3173771 Chr4-cl KO B6/129 ES cells #6
This SubSeries is part of SuperSeries:
GSE115291 Retrotransposon reactivation and mobilization upon deletions of megabase-scale KRAB zinc finger gene clusters in mice
Relations
BioProject PRJNA474490
SRA SRP149700

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Supplementary file Size Download File type/resource
GSE115288_RAW.tar 1.2 Gb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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