|
| Status |
Public on Feb 22, 2013 |
| Title |
H9_stranded |
| Sample type |
SRA |
| |
|
| Source name |
hES h9 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: human embryonic stem cells
chromosome: diploid
passages: ~30
|
| Growth protocol |
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)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared using Trizol Reagent and treatment with DNase I
RNA-Seq libraries preparation with prereleased Directional mRNA-seq Libraty Kit with minor modifications.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
stranded RNAseq
|
| Data processing |
Basecalling using Illumina Casava1.8.2 software.
Map to human genome hg19 using Bowtie( v 0.12.8) with parameters “-5 5 -3 5 -m 1 -k 1 -v 3 -y -p 40 -B 1 --best”.
Separate reads from sense or anti-sense strand, respectively.
Pileup the mapping results and call A-to-I RNA editing after filtering
Validate selected A-to-I RNA editing sites from non-stranded H9 sequencing dataset (GEO:GSE24399).
Genome_build: hg19
Supplementary_files_format_and_content: txt file. Genomic locations of predicted A-to-I RNA editing sites and stranded information.
|
| |
|
| Submission date |
Feb 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Yang |
| E-mail(s) |
liyang_fudan@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Institutes of Biological Sciences
|
| Street address |
131 Dong-An Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
|
| Relations |
| SRA |
SRX243742 |
| BioSample |
SAMN01923904 |
