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Series GSE208070 Query DataSets for GSE208070
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.
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.
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
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 (41)
GSM6336723 SOX9CNR_D0_rep1
GSM6336724 SOX9CNR_D0_rep2
GSM6336725 SOX9CNR_W1_rep1
This SubSeries is part of SuperSeries:
GSE208072 The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates
BioProject PRJNA858098

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
GSE208070_D0_mllF7_under120bp_RPKMbw_SEACR.bed.gz 687.0 Kb (ftp)(http) BED 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) 135.9 Mb (ftp)(http) BW 120.1 Mb (ftp)(http) BW 165.2 Mb (ftp)(http) 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 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 57.7 Mb (ftp)(http) BW
GSE208070_W2_under120bp_RPKM_SEACR001stringent_thresh1800.bed.gz 371.7 Kb (ftp)(http) BED 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 13.8 Mb (ftp)(http) BW 41.5 Mb (ftp)(http) BW
GSE208070_WT_dox_mllCNR_POOL_under120bp_SEACR.bed.gz 203.0 Kb (ftp)(http) BED 46.9 Mb (ftp)(http) BW
GSE208070_WT_nodox_mllCNR_POOL_under120bp_SEACR.bed.gz 643.1 Kb (ftp)(http) BED 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 30.7 Mb (ftp)(http) 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 34.3 Mb (ftp)(http) BW 32.7 Mb (ftp)(http) BW
GSE208070_noTA_mycCNR_under120bp_RPKM_SEACR001stringent_thresh1800.bed.gz 222.5 Kb (ftp)(http) BED
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Processed data provided as supplementary file

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