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| Status |
Public on Mar 05, 2013 |
| Title |
A549RNC |
| Sample type |
SRA |
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| Source name |
A549
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| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: lung cancer
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| Growth protocol |
Cells were maintained in DMEM (Invitrogen, Carlsbad, CA), supplemented with 10% fetal bovine serum (FBS) (PAA Australia, Weike Biochemical Reagent, Shanghai, China), 1% penicillin/streptomycin and 10 μg/mL ciprofloxacin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNC extraction: Esposito AM, Mateyak M, He D, Lewis M, Sasikumar AN, Hutton J, Copeland PR, Kinzy TG. 2010. Eukaryotic polyribosome profile analysis. J Vis Exp(40). RNA extraction: standard Trizol protocol.
Standard Illumina TruSeq mRNA library prep
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
High quality reads which passed Illumina filter were kept. RNC-mRNA was extracted and the polyA+ mRNA was sequenced.
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| Data processing |
Reads were mapped to RefSeq RNA reference sequence using FANSe v7.2 with the options –L78 –S8 –I0 –E9 –B1.
Splice variants were summed
The reads mapped to splice variants of one gene were summed. The mRNA abundance was calculated using rpkM (reads per kilobase per million reads) normalization (Mortazavi et al. 2008)
Supplementary_files_format_and_content: Text files with RPKMs
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| Submission date |
Nov 02, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gong Zhang |
| E-mail(s) |
zhanggong@jnu.edu.cn
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| Organization name |
Jinan University
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| Department |
Institute of Life and Health Engineering
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| Lab |
Translatomics Lab
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| Street address |
Huang-Pu Avenue West 601
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| City |
Guangzhou |
| ZIP/Postal code |
510632 |
| Country |
China |
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| Platform ID |
GPL10999 |
| Series (1) |
| GSE42006 |
Translatome of A549, H1299 and HBE cells |
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| Relations |
| SRA |
SRX202757 |
| BioSample |
SAMN01798242 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1030555_A549RNC-mRNA.txt.gz |
583.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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