|
| Status |
Public on Feb 09, 2016 |
| Title |
HeLa RNC-mRNA |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNC-mRNA extraction protocol: see PMID: 23519614
RNC-mRNA: NEBNext mRNA library construction kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
random fragmentation
translating mRNA (polyA+)
|
| Data processing |
Basecalling and basic quality filtering was performed in Illumina HiSeq-2000 by default settings.
Reads were truncated at the first nucleotide whose Phred score is less than 10.
Reads shorter than 18nt are discarded
Mapping reference sequence: RefSeq-RNA (accessed from UCSC genome browser on Jan 21. 2013)
For mRNA and RNC-mRNA datasets: reads were mapped to RefSeq-RNA using FANSe2 -S10 -E4 -U0
For RFP dataset: reads were mapped to RefSeq-RNA using FANSe2 -S10 -E2 -U1
Genes were quantified using rpkM method
Genome_build: hg19
Supplementary_files_format_and_content: HeLa rpkM all.txt
Supplementary_files_format_and_content: Content: rpkM of all quantified genes in all three datasets
|
| |
|
| Submission date |
May 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gong Zhang |
| E-mail(s) |
zhanggong@jnu.edu.cn
|
| Organization name |
Jinan University
|
| Department |
Institute of Life and Health Engineering
|
| Lab |
Translatomics Lab
|
| Street address |
Huang-Pu Avenue West 601
|
| City |
Guangzhou |
| ZIP/Postal code |
510632 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46613 |
Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells |
|
| Relations |
| BioSample |
SAMN02116921 |
| SRA |
SRX273670 |
