|
| Status |
Public on Jun 11, 2021 |
| Title |
RNA-PRC-5e-11M-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
mESC TC1 (129) passage 25-30
|
| Organism |
Mus musculus |
| Characteristics |
drug: 5x10^-11M dTAG13
time treated: 8h
cell line: TC1
cell type: mESC
|
| Treatment protocol |
Cells were washed 1x with PBS and resuspended in Trisure. RNA was extracted and DNase I digested. The reaction was cleaned up with acid phenol and the RNA was precipitated.
|
| Growth protocol |
Cells were treated with DMSO, 0.5mM auxin, or dTAG13 (5x10^-11 to 5x10^-7M) for indicated time.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SMARTer Stranded Total RNA Sample Prep Kit - HI
Ribosomal RNA depleted total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNA-PRC-5e-11M-merged-mm10-RPKM.bw
|
| Data processing |
Transcriptome: Ensembl v96 transcriptome (https://github.com/pachterlab/kallisto-transcriptome-indices/releases)
The first three bases from read 1 were trimmed with cutadapt 1.16 using -u 3 option. Transcripts were quantified using Kallisto version 0.44.0 using -l 280-s 20 (or paired-end) and --fr-stranded.
Trimmed reads were aligned to mm10 genome build with hisat2 using --rna-strandness FR (version 2.1.0), .bam files were merged with samtools merge (version 1.7), .bw files were generated using deeptools --binSize 10 --normalizeUsing RPKM (version 3.3.0)
Genome_build: mm10
Supplementary_files_format_and_content: Kallisto abundance estimates and merged .bw files
|
| |
|
| Submission date |
Apr 28, 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 |
GPL21103 |
| Series (2) |
| GSE145016 |
mSWI/SNF promotes distal repression by titrating polycomb dosage |
| GSE173499 |
mSWI/SNF promotes polycomb repression both directly and through genome-wide redistribution [RNA-seq] |
|
| Relations |
| BioSample |
SAMN18906629 |
| SRA |
SRX10698015 |
