|
| Status |
Public on Jun 10, 2017 |
| Title |
HCC1143_Nontarget_siRNA_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HCC1143 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC1143
treatment: Nontargeting siRNA
cell type: HCC1143 (Human TNM stage IIA, grade 3, primary ductal carcinoma)
|
| Treatment protocol |
HCC70, MDA-MB-231, MDA-MB-468, MDA-MB-157, HCC1143 were treated with Ethanol, STAT3 pooled siRNA (L-003544-00-0005, GE Healthcare, Logan, UT), Nontargeting siRNA (D-001810-01-05, GE Healthcare, Logan, UT)
|
| Growth protocol |
TNBC cells were grown under recommended growth conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ChIP-seq was performed as previously described (Reddy et al. Molecular Cell 2013). RNA-seq was performed as previously outlned (Gertz et al. 2012)
Illumina Single End for ChIP-seq, Illumina Paired End for RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
HCC1143_STAT3_Lib_list.txt.SharedGeneCounts.txt
|
| Data processing |
RNA-seq paired-end FASTQ files were aligned to hg19 female using Tophat and Cufflinks
Sequence counts for each transcript were compiled across all experiments for each time point
Genome_build: hg19 female
Supplementary_files_format_and_content: [.txt] Gene transcript sequence counts for all genes across all experiments in each time point
|
| |
|
| Submission date |
Aug 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joy Agee |
| E-mail(s) |
jagee@hudsonalpha.org
|
| Phone |
2059945492
|
| Organization name |
HudsonAlpha Institute for Biotechnology
|
| Street address |
601 Genome Way
|
| City |
Huntsville |
| State/province |
AL |
| ZIP/Postal code |
35806 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE85579 |
Genomic Regulation of Invasion by STAT3 in Triple Negative Breast Cancer |
|
| Relations |
| BioSample |
SAMN05572288 |
| SRA |
SRX2020874 |
