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Sample GSM4081763 Query DataSets for GSM4081763
Status Public on Oct 05, 2019
Title RNA-seq_control
Sample type SRA
 
Source name untreated control cells
Organism Homo sapiens
Characteristics cell line: MCF7
tumor: adenocarcinoma
Sex: female
age: 69 years
tissue/cells: breast
Treatment protocol Cells were seeded on culture plates. Next day the medium was replaced into phenol-free DMEM/F12 medium supplemented with 5% dextran-activated charcoal-stripped FBS and 48 hours later 17β-estradiol was added to final concentration of 100nM for 4hour or cells were subjected to hyperthermia (43°C) for 1hour with 2hours of recovery.
Growth protocol The wild-type MCF7 cells were purchased from ATCC (HTB-22) and used as a primary model. Cells were grown in DMEM/F12 medium supplemented with 10% fetal bovine serum and antibiotic-antimycotic cocktail (penicillin, streptomycin, amphotericin) at 37 °C in a humidified 5% CO2 atmosphere.
Extracted molecule total RNA
Extraction protocol Total RNA from 10^6 cells was isolated using the Direct-ZolTM RNA MiniPrep Kit (Zymo Research) and digested with DNase I (Worthington Biochemical Corporation, NY, USA)
RNA libraries were prepared for sequencing according to the standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description untreated control cells
NG.7926_wt_k_lib80492_4027_8_1
Data processing alignment of reads to reference genome using hisat 2.0.5
feature counting using featureCounts
normalization using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab separated text counts file with samples in columns and genes in rows
Supplementary_files_format_and_content: tab separated text normalized expression file with samples in columns and genes in rows
 
Submission date Sep 17, 2019
Last update date Oct 05, 2019
Contact name Tomasz Stokowy
E-mail(s) tomasz.stokowy@uib.no
Organization name University of Bergen
Department IT Division
Lab Scientific Computing
Street address Nygardsgaten 5
City Bergen
ZIP/Postal code 5020
Country Norway
 
Platform ID GPL16791
Series (2)
GSE137559 Heat Shock Factor 1 (HSF1) acquires transcriptional competence under 17b-estradiol in ERa-positive breast cancer cells [RNA-seq]
GSE137560 Heat Shock Factor 1 (HSF1) acquires transcriptional competence under 17b-estradiol in ERa-positive breast cancer cells
Relations
BioSample SAMN12771814
SRA SRX6858243

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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