|
| Status |
Public on May 05, 2023 |
| Title |
The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [CUT&RUN] |
| 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.
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| Overall design |
Epidermal stem cells were FACS isolated as mentioned above and CUT&RUN was performed as previously described with minor modifications indicated in methods. CUT&RUN sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina. PCR-amplified libraries were purified using 1x ratio of SPRI beads and eluted in 15μL 0.1x TE buffer. All CUT&RUN libraries were sequenced on Illumina NextSeq using 40-bp paired-end reads.
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| |
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| 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 |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (41)
|
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| This SubSeries is part of SuperSeries: |
| GSE208072 |
The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates |
|
| Relations |
| BioProject |
PRJNA858098 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE208070_D0_mllF7_under120bp_RPKMbw_SEACR.bed.gz |
687.0 Kb |
(ftp)(http) |
BED |
| GSE208070_D0_rep1_rep2_POOL_under120bp_RPKM.bw |
257.5 Mb |
(ftp)(http) |
BW |
| GSE208070_D0_under120bp_RPKM_SEACR001stringent_thresh1800.bed.gz |
17.8 Kb |
(ftp)(http) |
BED |
| GSE208070_RAW.tar |
96.6 Mb |
(http)(custom) |
TAR (of BW) |
| GSE208070_Sox9_0D_mllF7_1to50_rep1_rep2_POOL_fragmentsAtOrUnder120bp.bw |
135.9 Mb |
(ftp)(http) |
BW |
| GSE208070_Sox9_14D_mllF7_1to50_rep1_rep2_POOL_fragmentsAtOrUnder120bp.bw |
120.1 Mb |
(ftp)(http) |
BW |
| GSE208070_Sox9_7D_mllF7_1to50_rep1_rep2_POOL_fragmentsAtOrUnder120bp.bw |
165.2 Mb |
(ftp)(http) |
BW |
| GSE208070_W12_rep1_rep2_POOL_under120bp_RPKM.bw |
152.4 Mb |
(ftp)(http) |
BW |
| GSE208070_W12_under120bp_RPKM_SEACR001stringent_thresh1800.bed.gz |
200.3 Kb |
(ftp)(http) |
BED |
| GSE208070_W1_mllF7_under120bp_RPKMbw_SEACR.bed.gz |
585.5 Kb |
(ftp)(http) |
BED |
| GSE208070_W1_rep1_rep2_POOL_under120bp_RPKM.bw |
111.7 Mb |
(ftp)(http) |
BW |
| GSE208070_W1_under120bp_RPKM_SEACR001stringent_thresh1800.bed.gz |
322.0 Kb |
(ftp)(http) |
BED |
| GSE208070_W2_mllF7_under120bp_RPKMbw_SEACR.bed.gz |
545.4 Kb |
(ftp)(http) |
BED |
| GSE208070_W2_rep1_rep2_POOL_under120bp_RPKM.bw |
57.7 Mb |
(ftp)(http) |
BW |
| GSE208070_W2_under120bp_RPKM_SEACR001stringent_thresh1800.bed.gz |
371.7 Kb |
(ftp)(http) |
BED |
| GSE208070_W6_rep1_rep2_POOL_under120bp_RPKM.bw |
122.2 Mb |
(ftp)(http) |
BW |
| GSE208070_W6_under120bp_RPKM_SEACR001stringent_thresh1800.bed.gz |
421.8 Kb |
(ftp)(http) |
BED |
| GSE208070_WT_GSE208070_nodox_mllCNR_rep1_under120bp_RPKM_SEACR.bed.gz |
740.8 Kb |
(ftp)(http) |
BED |
| GSE208070_WT_GSE208070_nodox_mycCNR_rep1_under120bp_RPKM_SEACR.bed.gz |
119.8 Kb |
(ftp)(http) |
BED |
| GSE208070_WT_dox3d_mllCNR_POOL_sorted_fragmentunder120bp_RPKM.bw |
13.8 Mb |
(ftp)(http) |
BW |
| GSE208070_WT_dox3d_mycCNR_under120bp_POOL_sorted.bw |
41.5 Mb |
(ftp)(http) |
BW |
| GSE208070_WT_dox_mllCNR_POOL_under120bp_SEACR.bed.gz |
203.0 Kb |
(ftp)(http) |
BED |
| GSE208070_WT_nodox_mllCNR_POOL_sorted_fragmentunder120bp_RPKM.bw |
46.9 Mb |
(ftp)(http) |
BW |
| GSE208070_WT_nodox_mllCNR_POOL_under120bp_SEACR.bed.gz |
643.1 Kb |
(ftp)(http) |
BED |
| GSE208070_WT_nodox_mycCNR_under120bp_POOL_sorted.bw |
33.3 Mb |
(ftp)(http) |
BW |
| GSE208070_WTdox_mycCNR_under120bp_RPKM_SEACR001stringent_thresh1800.bed.gz |
131.8 Kb |
(ftp)(http) |
BED |
| GSE208070_WTnodox_mycCNR_under120bp_RPKM_SEACR001stringent_thresh1800.bed.gz |
43.3 Kb |
(ftp)(http) |
BED |
| GSE208070_noHMG_dox_mllCNR_POOL_under120bp_SEACR.bed.gz |
441.4 Kb |
(ftp)(http) |
BED |
| GSE208070_noHMG_mllCNR_POOL_sorted_fragmentunder120bp_RPKM.bw |
30.7 Mb |
(ftp)(http) |
BW |
| GSE208070_noHMG_mycCNR_under120bp_POOL_sorted.bw |
27.4 Mb |
(ftp)(http) |
BW |
| GSE208070_noHMG_mycCNR_under120bp_RPKM_SEACR001stringent_thresh1800.bed.gz |
73.0 Kb |
(ftp)(http) |
BED |
| GSE208070_noTA_dox_mllCNR_POOL_under120bp_SEACR.bed.gz |
490.7 Kb |
(ftp)(http) |
BED |
| GSE208070_noTA_mllCNR_POOL_sorted_fragmentunder120bp_RPKM.bw |
34.3 Mb |
(ftp)(http) |
BW |
| GSE208070_noTA_mycCNR_under120bp_POOL_sorted.bw |
32.7 Mb |
(ftp)(http) |
BW |
| GSE208070_noTA_mycCNR_under120bp_RPKM_SEACR001stringent_thresh1800.bed.gz |
222.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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