|
| Status |
Public on Sep 05, 2017 |
| Title |
Retrovirus-EGT |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
mutagen: Retrovirus-EGT
sequencing strategy: 5'
|
| Treatment protocol |
see https://www.haplobank.at/ecommerce/control/haplobank_resource
|
| Growth protocol |
see https://www.haplobank.at/ecommerce/control/haplobank_resource
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
see https://www.haplobank.at/ecommerce/control/haplobank_resource
see https://www.haplobank.at/ecommerce/control/haplobank_resource
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mutagen mapping by iPCR
|
| Data processing |
Library strategy: iPCR
The sequence is aligned with bowtie against the mm10 genome. A maximum of 3 mismatches (-v 3) is allowed. Only the unique alignments (-m 1) in the best strata are reported.
The insert site is the 5'-end of the read. For samples of the 5' sequencing strategies, the strand gets changed to its opposite.
Insertions which are only 3bp apart, get merged into blocks. Inserts require a coverage of at least 10.
The insertions are intersected with the UCSC RefSeq annotation of all gene features including the intergenic region using BEDtools.
Genome_build: mm10
Supplementary_files_format_and_content: space separated text (chromosome, 0-based insertion site, strand, count, annotation)
|
| |
|
| Submission date |
Jul 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Rainer Burkard |
| E-mail(s) |
thomas.burkard@imba.oeaw.ac.at
|
| Organization name |
IMBA
|
| Street address |
Dr. Bohrgasse 7
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE84088 |
An inducible and reversible embryonic stem cell biobank reveals functional genomic pathways and disease targets [iPCR] |
| GSE84090 |
An inducible and reversible embryonic stem cell biobank reveals functional genomic pathways and disease targets |
|
| Relations |
| BioSample |
SAMN05362853 |
| SRA |
SRX1899231 |
