|
| Status |
Public on Oct 16, 2017 |
| Title |
RNA-seq_T47D_Vector_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
T47D
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D wt/R330fsl cells
passages: <10
antibody: N/A
|
| Growth protocol |
Cells were grown on 15 cm plates in high glucose DMEM medium with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared according to BIOO SCIENTIFIC instruction. ATAC-seq libraries were prepared by following the original protocol (Buenrostro et al., 2013) with several modifications (as described above)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data files:
gene_counts_per_sample.RNA-seq.txt
RNA-seq_DEGs.T47Dflp.vs.CR3flp.txt
RNA-seq_DEGs.Vector.vs.ExoR330fs.txt
|
| Data processing |
Reads were filtered based on a mean base quality score >20.
For RNA-seq analysis, filtered read pairs were mapped against the hg19 reference genome by STAR (version 2.5) with the following parameters: -- outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 -- outMultimapperOrder Random (other parameters at default settings). Mapped read counts per gene were collected by Subread featureCounts (version 1.5.0-p1). Differentially expressed genes were identified with DESeq2 (v1.10.1) using filtering thresholds of FDR <0.01 and fold change >2.
genome build: hg19
processed data files format and content: bigWig, bed, txt
|
| |
|
| Submission date |
May 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul A Wade |
| E-mail(s) |
wadep2@niehs.nih.gov
|
| Phone |
919-541-3392
|
| Organization name |
NIEHS
|
| Department |
Laboratory of Molecular Carcinogenesis
|
| Street address |
111 TW Alexander Drive
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE99479 |
A class of GATA3 mutation reprograms the breast cancer transcriptional network through gain and loss of function |
|
| Relations |
| BioSample |
SAMN07179373 |
| SRA |
SRX2871393 |
