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Series GSE90906 Query DataSets for GSE90906
Status Public on Jun 13, 2018
Title Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary The conserved and essential histone chaperone FACT (Facilitates Chromatin Transcription) reorganizes nucleosomes during DNA transcription, replication and repair and ensures both, efficient elongation of RNA Pol II and nucleosome integrity. In mammalian cells, FACT is a heterodimer, consisting of SSRP1 and SUPT16. Here, we show that in contrast to yeast, FACT accumulates at the transcription start site of genes reminiscent of RNA Polymerase II profile. Depletion of FACT in mouse embryonic stem cells leads to de-regulation of developmental and pro-proliferative genes concomitant with hyper-proliferation of mES cells. Using MNase-, ATAC-, and Nascent Elongating Transcript Sequencing (NET-seq) we show that up-regulation of genes coincides with loss of nucleosomes upstream of the TSS and concomitant increase in antisense transcription, indicating that FACT impacts the promoter architecture to regulate expression of these genes. Finally, we demonstrate a role for FACT in cell fate determination and show that FACT depletion primes ES cells for the neuronal lineage.
 
Overall design ChIP-seq for FACT and RNA-seq, MNase-seq, ATAC-seq, and NET-seq profiles following knock-down of FACT were generated
 
Contributor(s) Mylonas C, Tessarz P
Citation(s) 30456357
Submission date Dec 05, 2016
Last update date May 15, 2019
Contact name Peter Tessarz
E-mail(s) ptessarz@age.mpg.de
Organization name Max Planck Institute
Street address Joseph-Stelzman-Str 9b
City Cologne
State/province Nordrhein-Westfalen
ZIP/Postal code 50931
Country Germany
 
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (28)
GSM2417328 Ssrp1_ChIP_seq_rep1,rep2
GSM2417329 Supt16_ChIP_seq_rep1,rep2
GSM2417330 Input_ChIP_seq_rep1,rep2
Relations
BioProject PRJNA356303
SRA SRP094584

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

Supplementary file Size Download File type/resource
GSE90906_ATAC.Control_merged.bw 525.7 Mb (ftp)(http) BW
GSE90906_ATAC.Ssrp1KD_merged.bw 434.9 Mb (ftp)(http) BW
GSE90906_MNase.Control_merged.bw 1.6 Gb (ftp)(http) BW
GSE90906_MNase.Ssrp1KD_merged.bw 1.5 Gb (ftp)(http) BW
GSE90906_NET-seq.Control.merged.fw.bw 35.4 Mb (ftp)(http) BW
GSE90906_NET-seq.Control.merged.rv.bw 34.7 Mb (ftp)(http) BW
GSE90906_NET-seq.Ssrp1KD.merged.fw.bw 48.1 Mb (ftp)(http) BW
GSE90906_NET-seq.Ssrp1KD.merged.rv.bw 46.9 Mb (ftp)(http) BW
GSE90906_Normalized.counts.RNA-seq.Control_vs_Ssrp1KD.txt.gz 1.2 Mb (ftp)(http) TXT
GSE90906_RAW.tar 41.2 Gb (http)(custom) TAR (of BW, TAB)
GSE90906_RNAseq.diffsplice.exons.tab.gz 74.1 Kb (ftp)(http) TAB
GSE90906_RNAseq.limma.NPC-WT.tab.gz 935.5 Kb (ftp)(http) TAB
GSE90906_RNAseq.limma.allgenes.tab.gz 2.0 Mb (ftp)(http) TAB
GSE90906_raw_counts_combined_chromatin_RNA-seq_samples.txt.gz 2.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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