|
| Status |
Public on May 05, 2023 |
| Title |
SOX9CNR_W2_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse back skin
|
| Organism |
Mus musculus |
| Characteristics |
antibody: SOX9 (Millipore AB5535)
antibody dilution: 1:250
strain: CD1
age: P35
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
W2_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 |
SAMN29669337 |
| SRA |
SRX16145682 |
