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Sample GSM6336724 Query DataSets for GSM6336724
Status Public on May 05, 2023
Title SOX9CNR_D0_rep2
Sample type SRA
 
Source name mouse back skin
Organism Mus musculus
Characteristics antibody: SOX9 (Millipore AB5535)
antibody dilution: 1:250
strain: CD1
age: P21
genotype: K14rtTA; TRE-myc-Sox9
mouse sex: Male
sorting scheme: CD31/45/117/140a-neg CD49f-high CD34-neg Ly6A-high
Treatment protocol Mouse was injected with doxycycline at P21 and maintained on dox feed for indicated period of time. Cells in culture are treated with 1ug/ml dox for indicated period of time
Extracted molecule genomic DNA
Extraction protocol 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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description Biological replicate 2
D0_rep1_rep2_POOL_under120bp_RPKM.bw
Data processing All CUT&RUN libraries were sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were trimmed with Skewer (version 0.2.2) and aligned to reference genome (mm10) using Bowtie2 (version 2.2.9) and deduplicated with Java (version 2.3.0) Picard tools (http://broadinstitute.github.io/picard). Reads were flittered to reads smaller or equal to 120bp using Samtools (version 1.3.1). BAM files for each replicate were combined using samtools.
Bigwigs were generated using Deeptools (version 3.1.2) with RPKM normalization
Assembly: mm10 (UCSC release)
Supplementary files format and content: BIGWIG file generated from combined bamfiles
Library strategy: CUT&RUN
 
Submission date Jul 12, 2022
Last update date May 05, 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
 
Platform ID GPL19057
Series (2)
GSE208070 The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [CUT&RUN]
GSE208072 The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates
Relations
BioSample SAMN29669341
SRA SRX16145678

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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