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Series GSE101905 Query DataSets for GSE101905
Status Public on Dec 06, 2017
Title Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Somatic cell reprogramming into pluripotent stem cells (iPSC) through the forced expression of defined factors induces changes in genome architecture reflective of the embryonic stem cell state. However, only a small minority of cells typically transition to pluripotency, which has limited our understanding of what defines cells that successfully reprogram. Here, we characterize the changes that occur across the DNA regulatory landscape during reprogramming by time-course profiling of isolated sub-populations of reprogramming intermediates poised to become iPSC. Widespread reconfiguration of chromatin states and transcription factor occupancy occurs early during reprogramming, and cells that fail to reprogram partially retain regulatory elements active in their somatic cell state. A second wave of reconfiguration occurs just prior to cells achieving pluripotency, where a majority of early changes revert to the somatic cell state and many of the changes that define the pluripotent state become established. Our comprehensive characterization of the molecular changes that occur during reprogramming broaden our understanding of the reprogramming process by providing crucial insights into iPSC generation, and shed light on how transcription factors in general access and change the chromatin during cell fate transitions.
 
Overall design Profiling of transcription factor occupancy, chromatin accessibility, gene expression and DNA methylation during the reprogramming of MEF cells to iPS cells. Timecourse profiling of MEF cells, FACS sorted reprogramming intermediate cells, and iPS cells with biological replicates.
 
Contributor(s) Buckberry S, Polo J, Lister R, Knaupp A
Citation(s) 29220667, 29741478
Submission date Jul 26, 2017
Last update date May 15, 2019
Contact name Ryan Lister
E-mail ryanlister@gmail.com
Phone 61864884407
Organization name The University of Western Australia
Street address 35 Stirling Highway
City Perth
State/province WA
ZIP/Postal code 6009
Country Australia
 
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (85)
GSM2718340 ChIPseq_Input_MEF_rep1
GSM2718341 ChIPseq_Input_day3_SSEA1+_rep1
GSM2718342 ChIPseq_Input_day6_SSEA1+_rep1
Relations
BioProject PRJNA395898
SRA SRP113606

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
GSE101905_RAW.tar 1.7 Gb (http)(custom) TAR (of BIGWIG)
GSE101905_all_chip_peak_calls.xlsx 29.4 Mb (ftp)(http) XLSX
GSE101905_atac_MEF_combined_replicates_peaks.txt.gz 1.1 Mb (ftp)(http) TXT
GSE101905_atac_all_peaks_union.bed.gz 820.8 Kb (ftp)(http) BED
GSE101905_atac_d12_combined_replicates_peaks.txt.gz 1012.7 Kb (ftp)(http) TXT
GSE101905_atac_d3_combined_replicates_peaks.txt.gz 1.1 Mb (ftp)(http) TXT
GSE101905_atac_d6_combined_replicates_peaks.txt.gz 715.3 Kb (ftp)(http) TXT
GSE101905_atac_d9_combined_replicates_peaks.txt.gz 851.3 Kb (ftp)(http) TXT
GSE101905_atac_iPSC_combined_replicates_peaks.txt.gz 1.7 Mb (ftp)(http) TXT
GSE101905_polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt.gz 1.5 Mb (ftp)(http) TXT
Raw data are available in SRA
Processed data is available on Series record
Processed data provided as supplementary file

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