|
| Status |
Public on Dec 01, 2017 |
| Title |
shCtrl rep2 |
| Sample type |
SRA |
| |
|
| Source name |
tamoxifen-resistant breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TamR MCF-7
transfection: Cells were infected with scrambled control shRNAs
|
| Treatment protocol |
TamR MCF-7 cells were stably transfected with shCtrl and shEZH2 and maintained in phenol-red-free RPMI 1640 supplemented with 100 nM of 4-OHT.
|
| Growth protocol |
Cells were cultured in phenol-red-free RPMI 1640 supplemented with 10% charcoal stripped FBS and 1% PSG (Penicillin-Streptomycin-L-Glutamine). 100 nM of 4-hydroxytamoxifen was added to maintain the tamoxifen resistant feature. Cells were 1:3 split twice per week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 (Cat.# RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using Tophat 2.0.10 with parameters -G. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by edgeR with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample
|
| |
|
| Submission date |
Dec 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kexin Xu |
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Molecular Medicine
|
| Street address |
7703 Floyd Curl, MC 8257
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE92316 |
The transcriptome effect of knocking down EZH2 in TamR MCF7L |
| GSE103243 |
Tamoxifen Resistance in Breast Cancer is Regulated by the EZH2-ERa-GREB1 Transcriptional Axis |
|
| Relations |
| BioSample |
SAMN06134777 |
| SRA |
SRX2417208 |
