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Series GSE90454 Query DataSets for GSE90454
Status Public on Jan 29, 2018
Title Genetic determinants and epigenetic effects of pioneer factor binding [ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Summary Transcription factors (TFs) are the core drivers of gene regulatory networks that control developmental transitions and a complete understanding of how they access, alter and maintain specific gene expression patterns remains an important goal. To begin a systematic dissection of the molecular components that either enable or constrain TF activity, we investigated the genomic occupancy of two distinct TFs, the pioneer factor FOXA2 and the pluripotency-associated factor OCT4 (POU5F1), in both endogenous and ectopic settings. We find that, while stable binding of FOXA2 is highly cell type specific and similar to what is observed for most TFs including OCT4, pioneer activity can be distinguished by notable sampling of additional loci that are occupied in alternative lineages. In our ectopic system, FOXA2 binding can be selectively stabilized at previously sampled sites by co-expressing the lineage specific regulator GATA4. Alternatively, we observe minimal influence of chromatin state on discrete, stabilized binding choices for FOXA2 but a strong bias towards open chromatin for ectopic OCT4 targets. Finally, we demonstrate that FOXA2 binding and nucleosome remodeling at silent loci can occur when the cell cycle is halted in G1, but surprisingly subsequent changes in DNA methylation require DNA replication. Taken together, our results provide several new molecular insights that contribute to our basic understanding of gene regulation and pave the way for a more rational use of ectopic TFs for cellular reprogramming.
Overall design In order to understand the binding dynamics of a pioneer transcription factor and its underlying chromatin environment, we performed high through-put sequencing for FOXA1 ChIP along with several histone marks. Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, and quenched with 125mM glycine at room temperature. Chips were performed as previously described(Gifford et al., 2013) by isolating nuclei and shearing DNA to 200-600 basepair fragments using Branson sonicator.Antibody incubation with chromatin was performed overnight. ~10 million cells were used per FOXA2 ChIP with 1ug of antibody/ million cells. ~1 million cells were used for each histone ChIP. Following an overnight incubation, antibody-protein complexes were isolated using Protein G/A beads (Life Technologies) and sequencing libraries were generated. Libraries were generated as previously described (Mikkelsen et al., 2010, Gifford et al., 2013) and Libraries were sequenced on a HiSeq 2500 at 11pmol.

Please note that the processed data 'RPKM_Table.txt' was generated from all ATAC-seq and ChIP-seq studies (GSE90453, GSE90454, GSE92490, GSE92491) and is linked to the GSE90454 records.

The file MatchingSampleTable.xlsx includes a key to the column headers in RPKM_Table.txt and the sample titles from all the above-listed ATAC-seq and ChIP-seq studies. The RPKM table includes re-analyzed data and these samples are listed in Re-AnalysisTable.xlsx. Links to the re-analyzed samples can be found below.
Contributor(s) Donaghey J, Thakurela S, Meissner A
Citation(s) 29358654
Submission date Nov 22, 2016
Last update date May 15, 2019
Contact name Sudhir Thakurela
Organization name HSCRB
Street address 7 Divinity Avenue
City Cambridge
ZIP/Postal code 02138
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (44)
GSM2401446 BJ FOXA2 ChIP Rep1
GSM2401447 BJ FOXA2 ChIP Rep2
GSM2401448 BJ K27ac Rep1
This SubSeries is part of SuperSeries:
GSE90456 Genetic determinants and epigenetic effects of pioneer factor binding
Reanalysis of GSM1003526
Reanalysis of GSM1112828
Reanalysis of GSM1112830
Reanalysis of GSM1112831
Reanalysis of GSM1112848
Reanalysis of GSM1521721
Reanalysis of GSM1521722
Reanalysis of GSM1521723
Reanalysis of GSM1521724
Reanalysis of GSM1521725
Reanalysis of GSM1521726
Reanalysis of GSM1521727
Reanalysis of GSM1521728
Reanalysis of GSM1521729
Reanalysis of GSM1521762
Reanalysis of GSM733650
Reanalysis of GSM733662
Reanalysis of GSM733745
Reanalysis of GSM733750
Reanalysis of GSM772856
Reanalysis of GSM772971
Reanalysis of GSM772977
Reanalysis of GSM772978
Reanalysis of GSM773002
Reanalysis of GSM817239
Reanalysis of GSM916051
Reanalysis of GSM916060
BioProject PRJNA354651
SRA SRP093788

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
GSE90454_MatchingSampleTable.xlsx 6.3 Kb (ftp)(http) XLSX
GSE90454_RPKM_Table.txt.gz 10.0 Mb (ftp)(http) TXT
GSE90454_Re-AnalysisTable.xlsx 9.4 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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