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Sample GSM3318895 Query DataSets for GSM3318895
Status Public on Jan 09, 2020
Title K562_PMA_1nM_AP_rep1
Sample type SRA
 
Source name K562
Organism Homo sapiens
Characteristics cell line: K562
cell type: chronic myelogenous leukemia
treatment: AP20187
Treatment protocol K562 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. Cells were then differentiated with 10nM PMA (phorbol 12-myristate 13-acetate) for 2 days. Cells were divided into differentiated non-treated control cells and the other half of cells were treated with 1nM AP20187 for 18hr to induce apoptosis.
Growth protocol K562 cells were cultured in RPMI 1640 with LĀ­glutamine, 10% FBS and Pen-Strep.
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 HiSeq 4000 platform. Sequence reads were aligned using bowtie.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description Amplification of virus inserts
K562_PMA_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.
 
Submission date Aug 03, 2018
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 GPL20301
Series (1)
GSE108536 Systematic identification of silencers in human cells
Relations
BioSample SAMN09765568
SRA SRX4507391

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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