|
Status |
Public on Dec 01, 2016 |
Title |
k562_EPB41L4A-AS1_2 |
Sample type |
SRA |
|
|
Source name |
k562_EPB41L4A-AS1
|
Organism |
Homo sapiens |
Characteristics |
cell type: K562 sgrna infected: common:TSS80057_+_111496631.23-P1P2
|
Growth protocol |
Cells were infected for 48 hr, followed by 2 d puromycin treatment (3 μg/mL) and 2 d recovery
|
Extracted molecule |
polyA RNA |
Extraction protocol |
DirectZol RNA TruSeq HT Stranded mRNA
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
processed data file: rnaseq_tpm.txt
|
Data processing |
RNA-seq: Reads were aligned to the human genome (GRCh37) using the spliced read aligner HISAT2 v2.0.3 against an index containing SNP and transcript information (genome_snp_tran). Quantification of Ensembl build 75 genes was carried out with featureCounts using only uniquely mapped reads. ChIP-seq: Reads were aligned to the human genome (GRCh37) using bowtie v2.2.8. Enrichment at promoter regions, which were defined as +/- 1kb of each TSS and generated from Ensembl GRCh37 build 75, were quantified using featureCounts v1.5.0-p2. Genome_build: GRCh37
|
|
|
Submission date |
Jul 29, 2016 |
Last update date |
May 15, 2019 |
Contact name |
John Liu |
E-mail(s) |
john.liu@ucsf.edu
|
Organization name |
UCSF
|
Street address |
35 Medical Center Way
|
City |
SAN FRANCISCO |
State/province |
California |
ZIP/Postal code |
94143 |
Country |
USA |
|
|
Platform ID |
GPL20301 |
Series (1) |
GSE85011 |
CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells |
|
Relations |
BioSample |
SAMN05464747 |
SRA |
SRX1989801 |