|
Status |
Public on Feb 09, 2016 |
Title |
HeLa Ribosome footprints |
Sample type |
SRA |
|
|
Source name |
HeLa cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: HeLa
|
Extracted molecule |
total RNA |
Extraction protocol |
RFP extraction protocol: see Ingolia et al. Nature Protocols RFP: NEBNext small RNA library construction kit
|
|
|
Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
directional library construction Ribosome footprints (mRNA fragments covered by ribosomes)
|
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 |
SAMN02116922 |
SRA |
SRX273671 |