NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2902877 Query DataSets for GSM2902877
Status Public on Jan 09, 2020
Title HepG2_C_rep2
Sample type SRA
 
Source name HepG2
Organism Homo sapiens
Characteristics cell line: HepG2
cell type: hepatocellular carcinoma
treatment: control
Treatment protocol K562 cells and HepG2 cells were infected with the virus library at MOI 0.5 by spin infection. Two days after infection, cells were selected by 2mg/ml puromycin for another 5 days. K562 cells infected with virus library and selected with puromycin were divided into two portions. The genomic DNA was isolated from one half of the cells and these genomic DNA fragments were the control library representation. For the other half of the cells, 1nM AP20187 was added to induce apoptosis. 1 day later, dead cell removal kit (Miltenyi Biotec) was used to deplete the apoptotic cells, and live cells were further cultured for another 5 days. Genomic DNA was extracted from these cells. For HepG2 cells, the experiment procedures were similar except that dead cells were removed by taking away the media, because HepG2 cells are adherent cells and live cells remained attached to the tissue culture flasks.
Growth protocol K562 cells were cultured in RPMI 1640 with LĀ­glutamine, 10% FBS and Pen-Strep. HepG2 cells were cultured in DMEM, 10% FBS and Antibiotic-Antimycotic. Cell density and culture conditions were maintained according to the ENCODE Cell Culture Guidelines.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using QIAamp DNA Blood Maxi Kit.
Genome DNA was amplified using Illumina PCR primer 1.0 and 2.0 using PCR. PCR products were then size-selected and purified. Final products were sequenced by Illumina MiSeq platform. Sequence reads were aligned using bowtie.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Description Amplification of virus inserts
HepG2_FDR_0.01.bed
Data processing Sequence reads were aligned using bowtie.
A GFF file was made from aligned reads pooled from all experiments. Then read counts were calculated using HTSeq.
Final enrichment was calculated by MAGeCK.
Genome_build: hg19
Supplementary_files_format_and_content: .bed file reports significantly enriched fragments
 
Submission date Dec 26, 2017
Last update date Jan 09, 2020
Contact name Baoxu Pang
Organization name Stanford University
Department Genetics
Lab Michael Snyder
Street address 3165 Porter Drive
City Palo Alto
State/province CALIFORNIA
ZIP/Postal code 94304
Country USA
 
Platform ID GPL15520
Series (1)
GSE108536 Systematic identification of silencers in human cells
Relations
BioSample SAMN08243219
SRA SRX3513428

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap