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| Status |
Public on Jun 01, 2018 |
| Title |
smallRNA-Seq_LCC1 |
| 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: LCC1
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| 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.
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| 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.
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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.
RNA libraries were prepared for sequencing using standard Small RNA Illumina protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
estrogen-independent and tamoxifen sensitive
Small RNA
LB-new3
processed data file: LCCs_TAMRs_miRNA_processed_data.txt
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| Data processing |
Base calling software: Illumina Casava1.7
Sequenced reads were trimmed for adaptor sequence, then the miRNA sequences were subject to alignment to known human mature miRNA sequence from miRBase using miRNAkey software.
Estimation of the expression levels of the identified miRNAs was performed by calculating the value of RPKM (Reads Per Kilobase of exon per Million fragments mapped) using miRNAkey software.
Genome_build: hg19, miRBase release 20
Supplementary_files_format_and_content: Tab-delimited text files include the significantly differented expression miRNAs and the correpsonding RPKM values between the tamoxifen-resistant cell lines and their parental cell line in the LCC cell line model or the TAMR 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 |
GPL9115 |
| 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 |
SAMN02664977 |
| SRA |
SRX476011 |
| 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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