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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 03, 2017 |
| Title |
WaplKO_rep1 |
| Sample type |
SRA |
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| Source name |
HAP1 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: HAP1
genotype: WaplKO
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| Treatment protocol |
Infection occurred over the consecutive days using the pelleted gene trap retrovirus in the presence of 8 ug/ml protamine sulfate. The mutagenized ∆WAPL cells were passaged for 10-12 days following the last infection with the mutagen, collected following dissociation using trypsin-EDTA by pelleting, and fixed using fix buffer I (BD biosciences).
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| Growth protocol |
One day prior to infection, ∆WAPL cells were seeded with 40 million cells in a single T175 flask.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from 30 million sorted cells using a DNA mini kit (Qiagen) with the lysis step occurring overnight at 56 o C for decrosslinking.The gene trap insertion sites were amplified using a LAM-PCR procedure as described (Blomen et al., 2015).
Using a biotinylated primer in the gene trap cassette, single-stranded DNA (ssDNA) products were generated for 120 cycles, captured on magnetic beads, a pre-adenylated ssDNA linker ligated to the 3’ end, and a final round of exponential amplificationusing a primer containing Illumina sequencing compatible overhangs at the end of the LTR andin the ssDNA linker.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Library strategy: ESS
Insertion sites were mapped by aligning the deep sequencing reads to the human genome (hg19) using bowtie (Langmead et al., 2009) allowing for a single mismatch.
Reads from the HiSeq 2500 (65bp) were cropped to 50 bp similar to the output for the HiSeq 2000 runs
Unique aligned reads were subsequently assigned to Refseq gene coordinates using Bedtools (Quinlan and Hall, 2010).
Overlapping gene regions on opposite strands were disregarded (since orientation bias in that region is not readily interpretable), while genes with overlapping regions on the same strand the names were concatenated.
For each replicate a binomial test for the distribution of sense and antisense orientation insertions was performed.
Genome_build: hg19
Supplementary_files_format_and_content: Screen-results. Columns are Gene-name, Fwd Integrations, Rev Integrations, P-value, and FDR-corrected P-value.
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| Submission date |
Feb 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Robin H. van der Weide |
| Organization name |
Hubrecht Institute
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| Lab |
Kind Lab
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE95015 |
The cohesin release factor WAPL restricts chromatin loop extension. |
| GSE95521 |
The cohesin release factor WAPL restricts chromatin loop extension [ESS] |
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| Relations |
| BioSample |
SAMN06471278 |
| SRA |
SRX2599601 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2515800_WAPL-1-counts.txt.gz |
288.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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