|
| Status |
Public on Jun 23, 2020 |
| Title |
MCF7, dDBD_E2_rep1 (RNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
transfection: Cells were infected with dDBD ER
treatment: 100 nM E2, 6hrs
|
| Treatment protocol |
MCF7 cells were first infected with lentivirus-based ER truncations, and then transiently infected shControl(for vector group) or shER(for WT and dDBD group) targeting 3'UTR to knock down endogenous ER. Cells were kept in hormone stripped condition for at least three days before treating with 100 nM estradiol or corresponding condition of ethanol for six hours.
|
| Growth protocol |
MCF7 obtained from ATCC were cultured in DMEM media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted by Trizol Reagent from Invitrogen (Cat no 15596026).
RNA library was prepared by the KAPA Stranded mRNA-Seq kit (KK8421), according to the manufacturer’s instructions.
|
| |
|
| 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 STAR 2.5.2b. 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 DESeq2 with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes reads counts for each Sample
|
| |
|
| Submission date |
Aug 03, 2019 |
| Last update date |
Jun 23, 2020 |
| 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) |
| GSE135339 |
Enhancer RNA mediate estrogen-induced transcriptional repression by recruiting ERa and its cofactor to selective enhancers [RNA-Seq] |
| GSE135341 |
Enhancer RNAs mediate estrogen-induced decommissioning of selective enhancers by recruiting ER and its cofactor |
|
| Relations |
| BioSample |
SAMN12491187 |
