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Sample GSM3336907 Query DataSets for GSM3336907
Status Public on Dec 11, 2019
Title RNA-seq FASR Replicate 3
Sample type SRA
 
Source name FASR
Organism Homo sapiens
Characteristics cell line: MCF7
cell type: breast cancer cells
resistant phenotype: fulvestrant-resistant
Growth protocol MCF7 breast cancer cells, and the corresponding endocrine resistant sub cell lines were kindly given to our laboratory by Dr Julia Gee (Cardiff University, UK). MCF7 cells were maintained in RPMI-1640 based medium containing 5% (v/v) fetal calf serum (FCS). Tamoxifen-resistant MCF7 (TAMR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and 4-OH-tamoxifen (1×10-7 M) (TAM). Fulvestrant-resistant MCF7 (FASR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and fulvestrant (1×10-7 M) (FAS). Endocrine resistant sub lines were established and characterised following 6 months endocrine challenge. All cell lines were authenticated by short-tandem repeat (STR) profiling (Cell Bank, Australia) and cultured for less than 6 months after authentication.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with TRIzol reagent. 500ng of total RNA was spiked with external controls (ERCC RNA spike-in Mix, Thermo Fischer #4456740) and libraries constructed with the Illumina TruSeq Stranded mRNA sample preparation kit (ref. RS-930-1001, Illumina).
Illumina TrueSeq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Rep3.FASR.TPM
TKCC20150326_Rep3_FASR_C60DTACXX_8
Data processing 100bp paired-end reads for MCF7, TAMR and FASR cell lines in biological triplicate were processed using Trim Galore (version 0.11.2) for adapter trimming (parameter settings: --fastqc --paired --retain_unpaired --length 16) and STAR (version 2.4.0j) for mapping reads to the hg38/GRCh38 human genome build with GENCODE v21 used as a reference transcriptome (parameter settings: --quantMode TranscriptomeSAM --outFilterMatchNmin 101).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: normalized transcript abundance measurment
 
Submission date Aug 17, 2018
Last update date Dec 11, 2019
Contact name Joanna Achinger-Kawecka
E-mail(s) [email protected]
Organization name South Australian Immunogenomics Cancer Institute
Street address AHMS Building, North Terrace
City Adelaide
State/province SA
ZIP/Postal code 5005
Country Australia
 
Platform ID GPL16791
Series (2)
GSE118713 Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [RNA-seq]
GSE118716 Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine resistant breast cancer
Relations
BioSample SAMN09848360
SRA SRX4564997

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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