|
| Status |
Public on Dec 01, 2017 |
| Title |
EZH2 + Vehicle rep2 |
| Sample type |
SRA |
| |
|
| Source name |
tamoxifen-sensitive breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
transfection: pLenti-HA-EZH2
treatment: Vehicle
|
| Treatment protocol |
MCF-7 cells were stably transfected with pLenti-CMV-hygro-GFP or pLenti-HA-EZH2. Hormone stripped cells were treated with either vehicle (EtOH) or 4-OHT (100 nM) for 6 hr.
|
| Growth protocol |
Cells were cultured in regular RPMI 1640 (10% FBS + 1% PSG [Penicillin-Streptomycin-L-Glutamine]) and hormone stripped in phenol-red-free RPMI 1640 (10% charcoal stripped FBS + 1% PSG) for 3 days before hormone treatment.
|
| Extracted molecule |
polyA 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 |
Aug 29, 2017 |
| 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) |
| GSE103242 |
The transcriptome effect of overexpressing EZH2 in MCF7 |
| GSE103243 |
Tamoxifen Resistance in Breast Cancer is Regulated by the EZH2-ERa-GREB1 Transcriptional Axis |
|
| Relations |
| BioSample |
SAMN07571859 |
| SRA |
SRX3144309 |
