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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2017 |
| Title |
Hypoxia rep2 |
| Sample type |
SRA |
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| Source name |
MCF-7 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
cell type: breast cancer cell
passages: 14
oxygen status: hypoxia
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| Treatment protocol |
Normoxia:21%O2 24h Hypoxia:0.5%O2 24h Re-oxygenation:0.5%O2 24h shift to 21%O2 24h
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| Growth protocol |
MCF-7, the breast cancer cell line was maintained in Dulbecco’s modified Eagle’s medium (DMEM) (GIBCO, Carlsbad, CA, USA). It was supplemented with 10% fetal bovine serum (FBS) (GIBCO) and 1% penicillin-streptomycin-amphotericin solution (Biological Industries, Beit-Haemek, Israel). It was incubated at 37 °C in a humidified atmosphere with 5% CO2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by TRIpure reagent (Roche Diagnostics, Branchburg, NJ, USA) according to the manufacturer’s protocol.
The total RNA extracted from MCF-7 were digested to 180 bp fragments after removing out rRNA by Ribo-Zero Gold kit (Illumina, San Diego, CA). The fragments of RNA were reverse-transcribed to cDNA by TruSeq Stranded total RNA kit (Illumina), then the specific adapters were ligated to the both ends of these cDNA fragments and become sequencing library.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
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| Data processing |
RNA-seq reads were aligned to the hg19 genome assembly using Tophat version 2.0.9 with parameters -p 12 --library-type fr-firststrand
Cufflinks verson 2.2.1 was then applied to assemble transcripts and quantify their abundance in terms of FPKM (fragments per kilobase of transcript per million fragments mapped)
All possible lncRNA from transcripts assembly were annotated based on the LNCipedia database (http://www.lncipedia.org/)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Jul 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Liang-Chuan Lai |
| E-mail(s) |
llai@ntu.edu.tw
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| Phone |
886-2-23123456
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| Organization name |
National Taiwan University
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| Department |
Physiology
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| Street address |
1 Jen-Ai Road, Sec 1
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| City |
Taipei |
| State/province |
Taiwan |
| ZIP/Postal code |
10051 |
| Country |
Taiwan |
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| Platform ID |
GPL15456 |
| Series (1) |
| GSE84167 |
Oxygen responsive lncRNAs in MCF-7 breast cancer cells |
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| Relations |
| BioSample |
SAMN05356467 |
| SRA |
SRX1896462 |
| 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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