|
| Status |
Public on Sep 17, 2021 |
| Title |
T47D_DMSO_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
T47D cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D
treatment: 0.1% volume/volume DMSO
molecule subtype: nascent RNA
|
| Treatment protocol |
For each sample, 2x10^6 cells were grown for 3 days in phenol red free RPMI 1640 medium containing 10% charcoal stripped FBS, 100 U/mL penicillin g-sodium, and 100 μg/mL streptomycin sulfate. After 3 days, a final concentration of 1nM beta estradiol or 0.1% volume/volume DMSO was added, and the cells were incubated for 1 hour.
|
| Growth protocol |
T47D cells from ATCC were were grown in Roswell Park Memorial Institute (RPMI) 1640 medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin g-sodium, and 100 μg/mL streptomycin sulfate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PMID: 27442863
PMID: 27442863
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Library strategy: PRO-seq
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication: https://github.com/guertinlab/fqdedup v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.3.1
All details and code: https://github.com/guertinlab/Nascent_RNA_Methods
Genome_build: hg38
Supplementary_files_format_and_content: Stranded bigWig counts files
|
| |
|
| Submission date |
Sep 17, 2021 |
| Last update date |
Oct 07, 2021 |
| Contact name |
Michael Joseph Guertin |
| E-mail(s) |
guertin@uchc.edu
|
| Organization name |
University of Connecticut
|
| Department |
Center for Cell Analysis and Modeling
|
| Lab |
Molecular Genomics
|
| Street address |
400 Farmington Ave
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE184378 |
Nascent RNA sequencing (PRO-seq) after estrogen treatment in T47D cells |
|
| Relations |
| BioSample |
SAMN21490439 |
| SRA |
SRX12234089 |
