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Sample GSM5514199 Query DataSets for GSM5514199
Status Public on Jan 12, 2022
Title MCF7 CSKko-1 Fulv_Rep3
Sample type SRA
Source name MCF-7
Organism Homo sapiens
Characteristics disease state: ER+ breast cancer
cell line: MCF-7
genotype: CSK k.o. clone 1
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 3
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
BioSample SAMN20713244
SRA SRX11719313

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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