|
Status |
Public on Feb 09, 2016 |
Title |
HeLa Ribosome footprints_replicate2 |
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 2500 |
|
|
Description |
Ribosome footprints (mRNA fragments covered by ribosomes) Protocol: directional library construction
|
Data processing |
Basecalling and basic quality filtering was performed in Illumina HiSeq-2500 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 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: text file with rpkM of all quantified genes in Ribosome footprints_replicate2
|
|
|
Submission date |
Jul 14, 2014 |
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 |
GPL16791 |
Series (1) |
GSE46613 |
Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells |
|
Relations |
BioSample |
SAMN02911629 |
SRA |
SRX652261 |