|
| Status |
Public on Jun 11, 2021 |
| Title |
Ring1b-trpaux-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
mESC TC1 (129) passage 15-20
|
| Organism |
Mus musculus |
| Characteristics |
drug: 0.5mM auxin, 10 µM triptolide
time treated: 8h
cell type: mESC
chip antibody: Cell Signalling Technologies Cat #5694; RRID:AB_10705604
|
| Treatment protocol |
Cells were treated with 0.5mM auxin, 10 µM triptolide, 0.5mM auxin plus 10 µM triptolide for 8h, or 1µM Tamoxifen for 72h unless otherwise specified.
|
| Growth protocol |
Before experiments cells were grown on gelatin coated dishes in KO DMEM supplemented with 7.5% ES-qualified serum and 7.5% KSR, with LIF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extracts were made by crosslinking cells with formaldehyde and then shearing DNA by sonication
NEBNext Ultra II
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Genome build: mm10
Reads were aligned to mm10 genome build using Bowtie 2 version 2.3.4.1 with option --very-sensitive. Multimapping, secondary alignment, supplementary alignment, low-quality (q<20), and PCR duplicates were removed using Samtools and Picard.
Bigwig files were generated with deeptools 3.3.0 bamCoverage with the following flags: --binSize 10, --normalizeUsing RPGC, --ignoreForNormalization chrM ChrUn ChrRandom, --extendReads 200, --effectiveGenomeSize 2652783500.
|
| |
|
| Submission date |
Apr 29, 2021 |
| Last update date |
Jun 11, 2021 |
| Contact name |
Christopher Michael Weber |
| E-mail(s) |
webercm@stanford.edu, weber.christopherm@gmail.com
|
| Organization name |
Stanford University
|
| Department |
Pathology
|
| Lab |
Crabtree lab
|
| Street address |
B209 Beckman Center
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE145016 |
mSWI/SNF promotes distal repression by titrating polycomb dosage |
| GSE173550 |
mSWI/SNF promotes polycomb repression both directly and through genome-wide redistribution [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN18921415 |
| SRA |
SRX10710578 |
