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Series GSE99009 Query DataSets for GSE99009
Status Public on Oct 24, 2018
Title SUMO safeguards somatic and pluripotent cell identities by enforcing distinct chromatin states
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Purposes: (1) compare the SUMO chromatin landscape between mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESc) (2) Decipher how hyposumoylation enhances MEF to induced pluripotent stem cells (iPSc) reprogramming (3) Decipher how hyposumoylation enhances ESc to 2C-like cells conversion. Methods : (1) ChIP-seq in MEFs and ESc for SUMO isoforms and histone marks. (2) ChIP-seq for transcription factors and histone marks at day 4 of MEF to iPSc reprogramming comparing wild type (shCtrl) and hyposumoylated cells (shUbc9). ATAC-Seq at day 4 of MEF to iPSc reprogramming comparing wild type (shCtrl) and hyposumoylated cells (shUbc9). RNA-Seq in MEFs, iPSc, at day 4 and day 7 of MEF to iPSc reprogramming comparing wild type (shCtrl) and hyposumoylated cells (shUbc9). (3) RNA-Seq in ESc comparing wild-type (siCtrl) and hyposumoylated cells (siUbc9). Results: (1) SUMO chromatin landscape is highly different between MEFs and ESc and associates to distinct chromatin marks. (2) Hyposumoylation enhances MEFs to iPSc reprogramming by favoring the extinction of the MEF transcriptional program and redistributing pluripotency factors from MEF enhancers toward ES enhancers. (3) Hyposumoylation enhances ES to 2C-like conversion by destabilizing heterochromatin thus resulting in an activation of the 2-cell transcriptional program. Conclusion: SUMO at chromatin is gate-keeper of cell-identity.
 
Overall design Duplicates for ChIP-Seq experiments. Triplicates for ATAC-Seq and RNA-Seq experiments. All replicates are provided for raw data. Pocessed data take into account replicate merge.
 
Contributor(s) Chica C, Cossec J, Theurillat I, Dejean A
Citation(s) 30401455
Submission date May 17, 2017
Last update date Jul 25, 2021
Contact name Claudia Chica
Organization name Institut Pasteur
Department C3BI
Lab Biostatistics and Bioinformatics Hub
Street address 25-28 Rue du Dr Roux
City Paris
ZIP/Postal code 75015
Country France
 
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (117)
GSM2629919 ChIP-seq_H3K4me3_MEF_rep1
GSM2629920 ChIP-seq_H3K4me3_MEF_rep2
GSM2629921 ChIP-seq_H3K4me1_MEF_rep1
Relations
BioProject PRJNA386997
SRA SRP107194

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
GSE99009_RAW.tar 6.0 Gb (http)(custom) TAR (of BED, TDF)
GSE99009_RNA-seq_MEF-D4-D7-iPS-ES_shCtr-shUbc9_counts.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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