|
| Status |
Public on Dec 09, 2023 |
| Title |
ESR1-WT_shESR1_ICI3 |
| Sample type |
SRA |
| |
|
| Source name |
T47D shESR1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D shESR1
cell type: No special type breast cancer cell line
genotype: ESR1-WT
treatment: ICI
duration: 24hr
|
| Treatment protocol |
Biological triplicates of each cell line were treated with 100µM fulvestrant (#1047, Tocris) dissolved in 100% ethanol or equal volume 100% ethanol for 24 hours.
|
| Growth protocol |
Cells were grown in RPMI-1640 (#11875-119, Life Technologies) media at 37 °C and 5% CO2 before three days of hormone deprivation (media change to improved MEM (#MT10026CV, Fisher Scientific) supplemented with 10% CSS). Cells were seeded into 6 well plates and allowed to adhere overnight before the 24-hour treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted with Qiagen RNeasy Kit following manufacturer's instructions.
RNA sequencing library construction, quality control, and paired-end sequencing were performed by the UPMC Genome Center (Pittsburgh, Pennsylvania) according to their protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT_ICI3
|
| Data processing |
RStudio Version 4.0.0
Transcript counts were quantified using Salmon v1.3.0 with parameters --seqBias --gcBias -p 8 -o and index hg38.
Gene-level counts were generated using tximport (Soneson et al., 2015) version 1.18.0.
Differential gene expression analysis was performed using the DESeq2 package version 1.30.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files including tximport abundance, count and lengths for each gene in each sample.
|
| |
|
| Submission date |
Dec 08, 2023 |
| Last update date |
Dec 09, 2023 |
| Contact name |
Megan E. Yates |
| Organization name |
University of Pittsburgh
|
| Lab |
Lee-Oesterreich Lab
|
| Street address |
5051 Centre Ave
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE249723 |
ESR1 fusions invoke breast cancer subtype-dependent enrichment of ligand independent oncogenic signatures and phenotypes [RNA-seq] |
| GSE266408 |
ESR1 fusions invoke breast cancer subtype-dependent enrichment of ligand independent oncogenic signatures and phenotypes |
|
| Relations |
| BioSample |
SAMN38739338 |
| SRA |
SRX22839697 |
