|
| Status |
Public on Jan 12, 2022 |
| Title |
MCF7 WT DMSO_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: ER+ breast cancer
cell line: MCF-7
genotype: wild type
treatment: DMSO
|
| 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 2
|
| 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 |
SAMN20713249 |
| SRA |
SRX11719300 |
