|
| Status |
Public on Dec 19, 2021 |
| Title |
ESR1-e6>ARID1B, +E2 |
| Sample type |
SRA |
| |
|
| Source name |
T47D cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: T47D
cell subtype: Stable ESR1-e6>ARID1B fusion expressing cell
condition: Hormone-deprived media, +E2
|
| Treatment protocol |
Cells were hormone-deprived in phenol red-free, RPMI media containing charcoal stripped serum as supplemented as above for 7 days before RNA-seq processing
|
| Growth protocol |
Stable T47D cells expressing ESR1 constructs were cultured in RPMI1640 media supplemented with 10% FBS, 4.5 g/L glucose, 10 mM HEPES, 1 mM sodium pyruvate, and 50 µg/mL gentamycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were grown in hormone-deprived media for 5 days followed by treatment with or without 10 nM E2 for 2 days. RNA was isolated using Qiagen RNeasy kit and treated with Dnase.
Illumina TruSeq Stranded mRNA prep kit was used for library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were aligned to hg19 (GRCh37) reference genome using RSEM v1.2.31 and Bowtie 2
Differential gene expression was performed using edgeR (FDR < 0.05)
Unsupervised hierarchical clustering was performed using a metric of Euclidean distance and the average linkage method
Heatmap was generated using Morpheus
Genome_build: hg19
Supplementary_files_format_and_content: Processed RSEM tab-delimited files are provided for each sample containing read count quantification, FPKM, and TPM.
|
| |
|
| Submission date |
Dec 17, 2021 |
| Last update date |
Dec 20, 2021 |
| Contact name |
Jonathan Thomas Lei |
| E-mail(s) |
jlei@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Department |
Medicine - Lester and Sue Smith Breast Center
|
| Lab |
Eric C. Chang Lab
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE191158 |
Transcriptional profiling of estrogen receptor fusion genes in breast cancer cell lines |
|
| Relations |
| BioSample |
SAMN24173561 |
| SRA |
SRX13441820 |
