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Sample GSM2140801 Query DataSets for GSM2140801
Status Public on Apr 17, 2017
Title Cis_4
Sample type SRA
 
Source name H1 POU5F1-IRES-eGFP
Organism Homo sapiens
Characteristics cell type: H1 POU5F4-eGFP reporter cells
Treatment protocol Regular hESC culture without any special treatment.
Growth protocol Cells were cultured at 37 celsius degree in 5% CO2, in Essential 8 media (Stemcell Technologies).
Extracted molecule genomic DNA
Extraction protocol For Samples 1-10, genomic DNA was extracted from H1 POU5F1-eGFP reporter cells after CREST-seq screen. For Sample 11, the plasmid DNA was extracted from E coli using Qiagen Giga prep kit.
The genomic DNA (samples 1-10) or CREST-seq plasmid DNA library (Sample 11) was PCR amplified with the following primers containing illumina TruSeq adaptor sequence. Forward primer: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTctTGTGGAAAGGACGAAAC; Reverse Primer: CAAGCAGAAGACGGCATACGAGATAAGGCCACGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTttttAACTTGCTATTTCTAGCTCTAAAAC. The PCR product was Gel purified, quantified and subjected to sequencing.
Other, CREST-seq
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description eGFP-/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 5
Data processing MAGeCK, a model-based analysis of genome-wide CRISPR knockout method, was applied to estimate for each dual-sgRNA the statistical significance of read count enrichment in the experimental samples versus the control samples.
Next, we partitioned the screened region (chr6:30,132,134-32,138,339) into a set of non-overlapping bins of the same length (100bp), and a bin is considered functional if many of the dual-sgRNAs cover it rank near the top of the sorted dual-sgRNAs list.
We then employed Robust Rank Aggression (RRA) (ref) algorithm to identify significant bins.
P-value is finally adjusted to FDR using Benjamini approach. A bin is predicted as significant if its FDR is smaller than given threshold.
Genome_build: hg19
 
Submission date May 02, 2016
Last update date May 15, 2019
Contact name Bing Ren
Organization name University of California, San Diego School of Medicine
Street address 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL20301
Series (1)
GSE81026 Cis Regulatory Element Scan by Tiling-deletion and Sequencing
Relations
BioSample SAMN04932287
SRA SRX1738665

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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