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Sample GSM1334456 Query DataSets for GSM1334456
Status Public on Jun 01, 2018
Title RNA-Seq_TAMR7
Sample type SRA
 
Source name Breast cancer cell line derived from MCF-7
Organism Homo sapiens
Characteristics tissue: Breast cancer
cell line: TAMR7
Treatment protocol For the TAMR cell line model, the MCF-7 cells were gradually adapted to grow in low serum concentration (initially 0.5% fetal calf serum (FCS) and 1% FCS after phenol-red was omitted from the culture medium) and the tamoxifen-sensitive sub-line MCF-7/S0.5 was used to establish tamoxifen-resistant (TAMR) cell lines by extended treatment with 1 µM tamoxifen. The 4 TAMR cell lines: MCF-7/TAMR-1 (TAMR-1), MCF-7/TAMR-4 (TAMR-4), MCF-7/TAMR-7 (TAMR-7) and MCF-7/TAMR-8 (TAMR-8) were derived from distinct colonies that emerged in cultures of MCF-7/S0.5 cells treated with 1 µM tamoxifen. For the LCC cell line model, LCC0 is derived from MCF-7 presenting estrogen-dependent and tamoxifen-responsive phenotype. LCC1 was established from the estrogen-dependent parent cell line MCF-7 through prolonged withdrawal from potent estrogenic stimuli both in vivo and in vitro. The above in vivo selected cell line was further passaged in ovary-comprised nude mice and re-established in vitro to generate a new cell line, MCF-7/LCC1, which is estrogen-independent, but tamoxifen-responsive as its parent cell line. Furthermore, a new cell hormone-independent, tamoxifen-resistant subline, LCC2 was developed through growth of LCC1 in incrementally increased dosages of tamoxifen in vitro. And a new cell hormone-independent, cross-resistance to tamoxifen and fluvestrant subline, LCC9 was developed through growth of LCC1 in incrementally increased dosage of fluvestrant.
Growth protocol The TAMR cell lines were maintained in DME/F12 (1:1) medium supplemented with 1% FCS and 1 μM tamoxifen. The LCC cell lines were cultured in DMEM/F12 without phenol red, supplemented with 5% DCC and 1% penicillin/streptomycin. The cells were maintained at 37°C in a humidified atmosphere of 95% ambient air and 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the cell lines with TRI Reagent (Sigma) according to the manufacturer’s protocol. The extracted total RNA was verified by agarose gel electrophoresis, and the concentration was estimated by NanoDrop (Thermo Scientific). Furthermore, BioAnalyzer 2100 RNA Chip (Agilent) were used to ensure the quality, quantity and integrity for the messenger RNA (mRNA). Subsequently, the total RNA was subject to digestion of DNase I (New England BioLabs), and then purified by ethanol precipitation for subsequent analyses.
RNA libraries were prepared for sequencing using standard Illumina RNA-seq protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description tamoxifen-resistant
messenger RNA
LB_new11
processed data file: TAMRs_RNAseq_processed_data.txt
Data processing Base calling software: Illumina Casava1.7
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 using TopHat
Estimation of the expression levels of the identified mRNAs was performed by calculating the value of FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using TopHat and Cufflinks. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Significantly differented expressed genes were revealed between the tamoxifen-resistant cell lines and their parental cell lines in the two cell line models.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
 
Submission date Feb 25, 2014
Last update date May 15, 2019
Contact name Jian Li
E-mail(s) jianlij@gmail.com
Phone 45+40608651
Organization name Aarhus University
Department Institute of Biomedicine
Lab 10
Street address The Bartholin Building
City Aarhus
ZIP/Postal code DK-8000
Country Denmark
 
Platform ID GPL11154
Series (2)
GSE55343 Integrative Analysis of Tamoxifen-resistant Cell Line Models Based on Sequencing Genomes, Transcriptomes and Epigenomes [seq]
GSE55383 Integrative Analysis of Tamoxifen-resistant Cell Line Models Based on Sequencing Genomes, Transcriptomes and Epigenomes
Relations
BioSample SAMN02664981
SRA SRX475999

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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