|
| Status |
Public on Feb 08, 2014 |
| Title |
IgG_RIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
HCC cells SMMC-7721
|
| Organism |
Homo sapiens |
| Characteristics |
rip antibody: Normal Mouse IgG (Millipore, CS200621)
cell type: hepatocellular carcinoma
cell line: SMMC-7721
|
| Treatment protocol |
SMMC-7721 cells were co-transfected with pcDNA3.1-MS2-ATB and pMS2-GFP.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After 48 hrs, cells were used to perform RNA immunoprecipitation (RIP) experiments using a GFP antibody or nonspecific mouse IgG and the Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore, Bedford, MA) according to the manufacturer’s instructions.
The sequencing libraries were generated using 100 ng of RNA and the TruSeq Stranded Total RNA kits from Illumina according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The samples were single-end sequenced with a read length of 50 bp on an Illumina HiSeq 2500 sequencer.
Sequencing reads were mapped against the human reference genome version 19 using the TopHat algorithm version 2.0.9 supplying Ensembl gene annotations version GRCh37.65 and default settings.
Further analysis was performed using the R statistical programming language version 2.15.0.
After alignment to the genome, the expression level of genes was determined based on the value of RPKM (reads per kilobase per million reads), which was calculated by cuffdiff (version: 2.1.1).
Genome_build: human reference genome version 19
|
| |
|
| Submission date |
Feb 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
shu-han sun |
| E-mail(s) |
shsun@vip.sina.com
|
| Organization name |
Second Military Medical University
|
| Street address |
800 Xiang-Yin Road
|
| City |
shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE54799 |
Genome-wide identification of transcripts associated with lncRNA-ATB by RIP-seq |
| GSE54800 |
lncRNA-Activated by TBGF-β-induced transcriptional changes and binding targets in hepatocellular carcinoma cells |
|
| Relations |
| BioSample |
SAMN02630994 |
| SRA |
SRX467590 |
