|
| Status |
Public on Jul 01, 2014 |
| Title |
AGS-RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
gastric adenocarcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: gastric adenocarcinoma cells
cell line: AGS
|
| Growth protocol |
A lymphoblastoid cell line was generated from a male Han Chinese individual (YH), whose genome sequence was reported previously [28]. Two human gastric cancer cell lines (BGC-823 and AGS) were provided by Beijing Tumor Hospital; the HeLa cell line was purchased from the American Type Culture Collection (ATCC). Cells were cultured with RPMI1640 (Gibco C22400500BT) supplemented with 10% fetal bovine serum (Gibco 12657-029) in a humidified incubator with 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from BGC-823, AGS cells and YH 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
stomach epithelial cells
AGS-RNA-seq
|
| 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 hg18) 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: hg18
Supplementary_files_format_and_content: bed files: contained chromsome,reads strart site,reads end sites;tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Dec 21, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Desheng Gong |
| E-mail(s) |
gds19870718@163.com
|
| Organization name |
Agricultural Genomes Institute at Shenzhen
|
| Street address |
No.7 PengFei road
|
| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE43093 |
Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells (RNA-seq) |
| GSE43096 |
Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells |
|
| Relations |
| SRA |
SRX212297 |
| BioSample |
SAMN01840351 |
