|
| Status |
Public on May 05, 2023 |
| Title |
The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [MINT ChIP-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
When stem cells activate a member of the SOX family of pioneer factors, they bind their cognate sequences within condensed chromatin, not only evicting the associated nucleosome, but also recruiting H3K4-monomethylases, which modify flanking nucleosomes to open chromatin and activate one lineage program; simultaneously, pioneer factors also silence alternative fates, but in this case act indirectly, through competing for H3K4-monomethylases pre-existing at the original fate genes.
|
| |
|
| Overall design |
FACS sorted cells were used for MINT-ChIP according to van Galen et al (doi::10.1016/j.molcel.2015.11.003). All MINT-ChIP libraries are sequenced on NextSeq.
|
| |
|
| Contributor(s) |
Yang Y, Gomez N, Fuchs E |
| Citation(s) |
37488435 |
| |
| Submission date |
Jul 12, 2022 |
| Last update date |
Aug 04, 2023 |
| Contact name |
Yihao Yang |
| E-mail(s) |
yyang03@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Lab |
Elaine Fuchs
|
| Street address |
1230 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (38)
|
|
| This SubSeries is part of SuperSeries: |
| GSE208072 |
The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates |
|
| Relations |
| BioProject |
PRJNA858099 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE208069_D0_H3K4me1_Epic2_Peaks_cut.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE208069_D0_POOL_H3K27ac_bg_peaks.narrowPeak.gz |
498.1 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE208069_D0_barcode_high.txt.gz |
95 b |
(ftp)(http) |
TXT |
| GSE208069_D0_barcode_low.txt.gz |
93 b |
(ftp)(http) |
TXT |
| GSE208069_SOX9_12W_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw |
166.3 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_6W_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw |
523.7 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_D0_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw |
56.4 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_D0_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw |
273.6 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_D0_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw |
529.9 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_D14_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw |
522.9 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_D7_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw |
31.3 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_D7_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw |
112.9 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_D7_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw |
216.5 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_Truncation_barcode_high.txt.gz |
130 b |
(ftp)(http) |
TXT |
| GSE208069_SOX9_Truncation_barcode_low.txt.gz |
127 b |
(ftp)(http) |
TXT |
| GSE208069_SOX9_W12_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw |
11.2 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_W12_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw |
111.2 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_W2_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw |
40.8 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_W2_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw |
119.2 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_W6_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw |
77.4 Mb |
(ftp)(http) |
BW |
| GSE208069_SOX9_W6_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw |
228.0 Mb |
(ftp)(http) |
BW |
| GSE208069_W12_H3K4me1_Epic2_Peaks_cut.bed.gz |
1.1 Mb |
(ftp)(http) |
BED |
| GSE208069_W12_Q05_bg_POOL_H3K27ac_peaks.narrowPeak.gz |
556.6 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE208069_W1_H3K4me1_Epic2_Peaks_cut.bed.gz |
1.1 Mb |
(ftp)(http) |
BED |
| GSE208069_W1_POOL_H3K27ac_bg_peaks.narrowPeak.gz |
515.1 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE208069_W1_barcode_high.txt.gz |
98 b |
(ftp)(http) |
TXT |
| GSE208069_W1_barcode_low.txt.gz |
97 b |
(ftp)(http) |
TXT |
| GSE208069_W2_H3K4me1_Epic2_Peaks_cut.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE208069_W2_POOL_H3K27ac_bg_peaks.narrowPeak.gz |
470.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE208069_W2_rep1_W12_2reps_barcode_high.txt.gz |
128 b |
(ftp)(http) |
TXT |
| GSE208069_W2_rep1_W12_2reps_barcode_low.txt.gz |
127 b |
(ftp)(http) |
TXT |
| GSE208069_W2_rep2_barcode_high.txt.gz |
91 b |
(ftp)(http) |
TXT |
| GSE208069_W2_rep2_barcode_low.txt.gz |
89 b |
(ftp)(http) |
TXT |
| GSE208069_W6_H3K4me1_Epic2_Peaks_cut.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE208069_W6_POOL_H3K27ac_bg_peaks.narrowPeak.gz |
510.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE208069_W6_rep1_barcode_high.txt.gz |
84 b |
(ftp)(http) |
TXT |
| GSE208069_W6_rep1_barcode_low.txt.gz |
82 b |
(ftp)(http) |
TXT |
| GSE208069_W6_rep2_barcode_high.txt.gz |
81 b |
(ftp)(http) |
TXT |
| GSE208069_W6_rep2_barcode_low.txt.gz |
79 b |
(ftp)(http) |
TXT |
| GSE208069_WT_dox_H3K4me1_MERGE_POOL_RPKM.bw |
114.2 Mb |
(ftp)(http) |
BW |
| GSE208069_WT_dox_H3K4me1_MERGE_POOL_peaks.broadPeak.gz |
2.8 Mb |
(ftp)(http) |
BROADPEAK |
| GSE208069_WT_nodox_H3K4me1_MERGE_POOL_RPKM.bw |
95.3 Mb |
(ftp)(http) |
BW |
| GSE208069_WT_nodox_H3K4me1_MERGE_POOL_peaks.broadPeak.gz |
2.7 Mb |
(ftp)(http) |
BROADPEAK |
| GSE208069_noHMG_dox_H3K4me1_MERGE_POOL_RPKM.bw |
91.9 Mb |
(ftp)(http) |
BW |
| GSE208069_noHMG_dox_H3K4me1_MERGE_POOL_peaks.broadPeak.gz |
2.8 Mb |
(ftp)(http) |
BROADPEAK |
| GSE208069_noTA_dox_H3K4me1_MERGE_POOL_RPKM.bw |
101.3 Mb |
(ftp)(http) |
BW |
| GSE208069_noTA_dox_H3K4me1_MERGE_POOL_peaks.broadPeak.gz |
3.0 Mb |
(ftp)(http) |
BROADPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...