|
Status |
Public on Jan 12, 2022 |
Title |
MCF7 WT Fulv_Rep1 |
Sample type |
SRA |
|
|
Source name |
MCF-7
|
Organism |
Homo sapiens |
Characteristics |
disease state: ER+ breast cancer cell line: MCF-7 genotype: wild type treatment: 1uM Fulvestrant
|
Treatment protocol |
MCF-7 cells were grown in DMEM or in the presence of 1uM Fulvestrant during 20 days.
|
Growth protocol |
MCF-7 cells were routinely grown in DMEM supplemented with 10% FCS and 1% Streptomycin/Penicillin, at 37°C in a 5% CO2 humidified incubator
|
Extracted molecule |
total RNA |
Extraction protocol |
The cells were subsequently harvested and frozen at −80 °C until extraction of RNA using the PureLink RNA mini kit (Invitrogen) including Dnase treatment. llumina TruSeq Stranded mRNA
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 2000 |
|
|
Description |
Replicate 1
|
Data processing |
Bcl files were converted and demultiplexed to fastq using the bcl2fastq v2.20.0.422 program Fastq files were aligned to human reference genome (hg38/GRCh38, obtained from ensembl) using STAR v2.7.5b. Reads in exons were counted using featureCounts v1.5.1 in paired end mode (using flag -p) with hg38/GRCh38 ensembl annotations Genome_build: hg38/GRCh38 Supplementary_files_format_and_content: Tab separated text file containing gene expression values
|
|
|
Submission date |
Aug 11, 2021 |
Last update date |
Jan 12, 2022 |
Contact name |
Anastasios Erik Damdimopoulos |
Organization name |
Karolinska Institute
|
Department |
Department of Biosciences and Nutrition
|
Lab |
Bioinformatics and Expression Analysis Core Facility
|
Street address |
Hälsovägen 7c
|
City |
Stockholm |
State/province |
Huddinge |
ZIP/Postal code |
141 83 |
Country |
Sweden |
|
|
Platform ID |
GPL30173 |
Series (1) |
GSE181909 |
Prolonged estrogen deprivation triggers a broad immunosuppressive phenotype in breast cancer cells |
|
Relations |
BioSample |
SAMN20713239 |
SRA |
SRX11719308 |