|
| Status |
Public on Sep 10, 2019 |
| Title |
MYOD Remodeling of the Genome Architecture during Myogenic Conversion of Somatic Cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Other
|
| Summary |
We provide here an unprecedented analysis of the three-dimensional re-organization of the genome during cellular reprograming of one cell type into another by the ectopic expression of one single transcription factor. By integrating Hi-C analysis with ChIPseq-based detection of MYOD genome-wide binding and RNAseq profiling of gene expression, we discovered that MYOD causes profound alterations in the high order chromatin structure during fibroblast reprogramming into skeletal muscle cells. We also used CTCF ChIPSeq in IMR90 GSE31477 (GSM935404); CTCF ChIPSeq in human myoblasts (hMB) GSE29611 (GSM733762); CTCF ChIPSeq human myotubes (hMT) GSE29611 (GSM733783); H3K27Ac in IMR90 GSE43070 (GSM1055818); H3K27Ac in hMB GSE29611 (GSM733755); H3K27Ac in hMT GSE29611 (GSM733666) Same number of reads was used for H3K27Ac ChIP comparison. ChIPSeq p300 IMR90 GSE43070 (GSM1055812). We also used RNASeq from GSE90895 (GSM2417196, GSM2417197, GSM2417198, GSM2417204, GSM2417203)
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| |
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| Overall design |
Integration of RNASeq, ChIPSeq and HiC experiments to characterize the 3D regulatory mechanisms for the myogenic conversion of fibrobalsts. For this project we used CTCF ChIPSeq in IMR90 GSE31477 (GSM935404); CTCF ChIPSeq in human myoblasts (hMB) GSE29611 (GSM733762); CTCF ChIPSeq human myotubes (hMT) GSE29611 (GSM733783); H3K27Ac in IMR90 GSE43070 (GSM1055818); H3K27Ac in hMB GSE29611 (GSM733755); H3K27Ac in hMT GSE29611 (GSM733666) Same number of reads was used for H3K27Ac ChIP comparison. We also used RNASeq from GSE90895 (GSM2417196, GSM2417197, GSM2417204, GSM2417203)
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| |
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| Contributor(s) |
Dall'Agnese A, Puri PL |
| Citation(s) |
31519520 |
| |
| Submission date |
May 03, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Alessandra Dall'Agnese |
| E-mail(s) |
aled@wi.mit.edu
|
| Organization name |
Whitehead Institute
|
| Street address |
455 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (16)
|
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| This SubSeries is part of SuperSeries: |
| GSE98530 |
Re-Wiring 3D Nuclear Architecture by a Single Transcription Factor during Somatic Cell Reprogramming |
|
| Relations |
| Reanalysis of |
GSM935404 |
| Reanalysis of |
GSM733762 |
| Reanalysis of |
GSM733783 |
| Reanalysis of |
GSM733755 |
| Reanalysis of |
GSM733666 |
| Reanalysis of |
GSM1055818 |
| Reanalysis of |
GSM1055812 |
| BioProject |
PRJNA385348 |
| SRA |
SRP106379 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE98509_Bin_ID_4000.bed.gz |
4.8 Mb |
(ftp)(http) |
BED |
| GSE98509_Bin_ID_40000.bed.gz |
455.8 Kb |
(ftp)(http) |
BED |
| GSE98509_CTCF_ChIP_IMR90_merge_sorted_rmdup.pileup.bw |
348.2 Mb |
(ftp)(http) |
BW |
| GSE98509_CTCF_ChIP_peaksq0.01.bed.gz |
786.5 Kb |
(ftp)(http) |
BED |
| GSE98509_EGM_K3K27Ac_Macs14_p1e9_peaks.bed.gz |
747.7 Kb |
(ftp)(http) |
BED |
| GSE98509_E_GMvsM_GM_differentials.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE98509_H3K27Ac-EGM-17_S5_L005_R1_001_sorted_rmdup.pileup.bw |
259.2 Mb |
(ftp)(http) |
BW |
| GSE98509_IMR90_MYOD_DM_T_over_EMPTY_DM_T.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE98509_IMR90_MYOD_GM_T_over_EMPTY_GM_T.csv.gz |
952.3 Kb |
(ftp)(http) |
CSV |
| GSE98509_MB_CTCF_peaks.narrowPeak.gz |
1.4 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE98509_MB_H3K27Ac_sorted_rmdup.pileup.bw |
153.5 Mb |
(ftp)(http) |
BW |
| GSE98509_MEF_vs_PreiPSC.csv.gz |
799.7 Kb |
(ftp)(http) |
CSV |
| GSE98509_MT_CTCF_peaks.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE98509_MT_H3K27Ac_sorted_rmdup.pileup.bw |
154.1 Mb |
(ftp)(http) |
BW |
| GSE98509_M_GMvsM_DM_differentials.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
| GSE98509_RAW.tar |
16.3 Gb |
(http)(custom) |
TAR (of BW, TXT) |
| GSE98509_SRR639057_p300_sorted_rmdup.pileup.bw |
224.0 Mb |
(ftp)(http) |
BW |
| GSE98509_Tutti_H3K27Ac_IMR90_BingRen_sorted_rmdup.pileup.bw |
148.7 Mb |
(ftp)(http) |
BW |
| GSE98509_diff_IMR90_vs_MB_H3K27Ac_c3.0_cond1.bed.gz |
562.2 Kb |
(ftp)(http) |
BED |
| GSE98509_diff_IMR90_vs_MB_H3K27Ac_c3.0_cond2.bed.gz |
576.9 Kb |
(ftp)(http) |
BED |
| GSE98509_filename2_readme.txt |
5.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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