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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 01, 2012 |
| Title |
polyAplus_hela_RNAseq |
| Sample type |
SRA |
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| Source name |
HeLa cells, poly(A)+
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
cell type: human epithelial cervical cancer cells
ploidy: highly polyploid
rna polyadenylation: plus
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| Growth protocol |
HeLa cells were cultured under standard conditions. hES H9 cells were maintained on plates coated with Matrigel (BD Biosciences) in either defined mTeSR medium (StemCell Technologies Inc.) or conditioned medium (CM) with irradiated mouse embryo fibroblasts supplemented with 4 ng/mL human Basic Fibroblast Growth Factor (bFGF).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared using the Trizol Reagent (Life Technologies, Inc., Grand Island, NY, USA). After treatment with DNase I (DNA-free kit; Ambion), total RNAs were incubated with oligo(dT) magnetic beads to isolate either poly(A)+ RNAs, which were bound to the beads, or poly(A)- RNAs, which were present in the flowthrough after incubation. The poly(A)- RNA population was further processed with the RiboMinus kit (Human/Mouse Module, Invitrogen) to deplete most of the abundant ribosomal RNAs. All RNA-Seq libraries were prepared using the Illumina mRNA-Seq Sample Prep Kits (P/N 1004814) according to the manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
PolyA-plus RNA.
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| Data processing |
Alignment: Sequencing reads were obtained with Illumina Genome Analyzer Pipeline (version 1.3). All reads were uniquely aligned to the human (March, 2006; NCBI Build 36; UCSC hg18) genome by using Bowtie (version 0.10.1) with up to 2 mismatches.
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| Submission date |
Jul 01, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Ling-Ling Chen |
| E-mail(s) |
linglingchen@sibcb.ac.cn
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| Organization name |
Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
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| Street address |
320 Yue-Yang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE22666 |
Genome-wide characterization of long nonpolyadenylated RNAs |
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| Relations |
| SRA |
SRX022750 |
| BioSample |
SAMN00016757 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM562118_polyAplus_hela.bedgraph.gz |
36.0 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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