|
| Status |
Public on May 06, 2015 |
| Title |
QKI5 |
| Sample type |
SRA |
| |
|
| Source name |
K562 cells transduced with QKI5-overexpressing lentivirus
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
cell type: erythroleukemia
|
| Treatment protocol |
lentivirus transduction
|
| Growth protocol |
K562 cells are maintained in 1640 medium with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA was isolated from total RNA with the mirVana™ miRNA Isolation Kit
Small RNA libraries were prepared with the Ion Total RNA-Seq Kit v2 (Life Technologies), and then were sequenced on the Ion Torrent Proton™ System using Ion PI™ Chips.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent PGM |
| |
|
| Data processing |
Torrent Suite and Ion Reporter™ software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mirBase release 19 hsa miRNA library using bowtie v0.12.3 with parameters -v 2 -M 1 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
May 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jia Yu |
| E-mail(s) |
j-yu@ibms.pumc.edu.cn
|
| Organization name |
Peking Union Medical College & Chinese Academy of Medical Sciences
|
| Department |
Department of Biochemistry and Molecular Biology Institute of Basic Medical Sciences
|
| Street address |
Dong Dan San Tiao 5
|
| City |
Beijing |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL17301 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN02754403 |
| SRA |
SRX534327 |
