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| Status |
Public on Jun 01, 2018 |
| Title |
DGE_LCC9 |
| Sample type |
SRA |
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| Source name |
Breast cancer cell line derived from MCF-7
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer
cell line: LCC9
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| Treatment protocol |
The 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.
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| Growth protocol |
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.
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| 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.
The DGE analysis used NlaIII and MmeI to produce 20-21 bp tag. The indexed single-end 50 nt sequencing was performed by Illumina HiSeq 2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
derived from LCC1 with increased small-dosage fluvestrant treatment, estrogen-independent, and cross-resistance to fluvestrant and tamoxifen
messenger RNA
DGE
processed data file: lcc_dge_cn_ln_20130313.txt
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| Data processing |
Base calling software: Illumina Casava1.7
FASTX-Toolkit implemented in Perl was used to trim the adaptor sequence. The trimmed tags were subjected to quality filtering, so that only the tags with sequencing quality higher than 30 for more than 80% of the nucleotides of each tag were used for subsequent analysis. The refMrna (hg19, UCSC) was used as reference for mapping cDNA tags. Subsequently, the Burrows–Wheeler Aligner (BWA) procedure was applied for aligning the DGE tags to the refMrna reference library.
Estimation of the expression levels of the identified mRNAs was performed by calculating the value of normalized uniquely mapped tag numbers.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes normalized tag numbers for each sample in the LCC cell line model.
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| Submission date |
Feb 25, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Li |
| E-mail(s) |
jianlij@gmail.com
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| Phone |
45+40608651
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| Organization name |
Aarhus University
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| Department |
Institute of Biomedicine
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| Lab |
10
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| Street address |
The Bartholin Building
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| City |
Aarhus |
| ZIP/Postal code |
DK-8000 |
| Country |
Denmark |
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| 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 |
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| Relations |
| BioSample |
SAMN02664976 |
| SRA |
SRX476021 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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