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| Status |
Public on Feb 19, 2014 |
| Title |
786-O-RNA-seq |
| Sample type |
SRA |
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| Source name |
786-O-RNA-seq
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| Organism |
Homo sapiens |
| Characteristics |
cell type: renal
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| Growth protocol |
one renal cancer cell line (786-O),another renal cancer cell line OS-RC-2 was from Riken Cell Bank (Tsukuba, Japan). Cells were cultured according to the supplier’s recommendations.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 786-O and OS-RC-2 cells using the miRNeasy Kit (Qiagen 74104) according to the manufacturer's protocol. An additional DNaseI digestion step was performed to ensure that the samples were not contaminated with genomic DNA. The RNA purity was assessed using the Agilent bioanalyzer. Total RNA was converted to cDNA using the NuGEN Ovation RNA-Seq System according to the manufacturer's protocol (NuGEN, San Carlos, CA, USA). The cDNA was then used for Illumina sequencing library preparation. DNA fragments were end-repaired to generate blunt ends with 5′ phosphatase and 3′ hydroxyls, and adapters were ligated for paired-end sequencing on an 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 |
786-O-RNA-seq
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| Data processing |
Illumina BclConverter-1.9.0 software used for basecalling.
Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean reads of RNA sequencing reads were aligned to the reference genome (UCSC hg19) using the SOAP aligner with parameters -m 90 -x 500 -l 15 -s 35 -p 4
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
genome build: hg19
processed data files format and content: bed files: contained chromsome,reads strart site,reads end sites;tab-delimited text files include RPKM values for each Sample
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| Submission date |
Mar 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Desheng Gong |
| E-mail(s) |
gds19870718@163.com
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| Organization name |
Agricultural Genomes Institute at Shenzhen
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| Street address |
No.7 PengFei road
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| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE44866 |
Classification of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach |
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| Relations |
| SRA |
SRX248482 |
| BioSample |
SAMN01974780 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1093060_786-O-RNA-seq.RPKM.txt.gz |
318.0 Kb |
(ftp)(http) |
TXT |
| GSM1093060_786-O_RNA-seq.bed.gz |
61.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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