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Sample GSM2256104 Query DataSets for GSM2256104
Status Public on Dec 01, 2016
Title hela_XLOC_017263_1
Sample type SRA
 
Source name hela_XLOC_017263
Organism Homo sapiens
Characteristics cell type: HeLa
sgrna infected: k562_hela_mcf7:TSS34793_-_85640780.23-CUFF.16540.1
Growth protocol Cells were infected with sgRNA lentiviruses for 48 hr, followed by 4 d puromycin treatment (1 μg/mL) and 1 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 SAMN05464750
SRA SRX1989798

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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