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Sample GSM5585302 Query DataSets for GSM5585302
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: v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: v1.3.1
All details and code:
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
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
BioSample SAMN21490439
SRA SRX12234089

Supplementary file Size Download File type/resource
GSM5585302_T47D_DMSO_rep1_minus_PE1.bigWig 15.6 Mb (ftp)(http) BIGWIG
GSM5585302_T47D_DMSO_rep1_minus_PE2.bigWig 15.2 Mb (ftp)(http) BIGWIG
GSM5585302_T47D_DMSO_rep1_plus_PE1.bigWig 13.7 Mb (ftp)(http) BIGWIG
GSM5585302_T47D_DMSO_rep1_plus_PE2.bigWig 13.8 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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