|
| Status |
Public on Dec 11, 2019 |
| Title |
RNA-seq TAMR Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
TAMR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: breast cancer cells
resistant phenotype: tamoxifen-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.TAMR.TPM
TKCC20150326_Rep3_TAMR_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 |
SAMN09848837 |
| SRA |
SRX4564994 |
