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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 17, 2017 |
| Title |
Cis_2 |
| Sample type |
SRA |
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| Source name |
H1 POU5F1-IRES-eGFP
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| Organism |
Homo sapiens |
| Characteristics |
cell type: H1 POU5F2-eGFP reporter cells
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| Treatment protocol |
Regular hESC culture without any special treatment.
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| Growth protocol |
Cells were cultured at 37 celsius degree in 5% CO2, in Essential 8 media (Stemcell Technologies).
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| 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
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
eGFP-/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 2
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| 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
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| 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
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| Street address |
9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE81026 |
Cis Regulatory Element Scan by Tiling-deletion and Sequencing |
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| Relations |
| BioSample |
SAMN04932285 |
| SRA |
SRX1738663 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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