PUBLICATION

Viral Insertion Mutants Removed Data

Authors
Burgess, S. and Lin, S.
ID
ZDB-PUB-121121-2
Date
2012
Source
ZFIN Direct Data Submission : (Curation)
Registered Authors
Keywords
none
MeSH Terms
none
PubMed
none
Abstract
Viral integration sites were amplified by linker-mediated PCR with 6base sequence “barcodes” associated with each fish. Samples were pooled and sequenced on an Illumina Genome Analyzer II. Prior to mapping the reads, a custom script was run to trim off the 3’' retroviral LTR and linker cassette (LC) sequences and identify the barcodes. The six nucleotides directly adjacent to the LC primer sequence was the identifying barcode. Sequences were trimmed of the 3’' LTR and/or LC sequence as well as the barcode, the barcode was noted for sample identification, and the trimmed sequence was used for mapping integrations. Bowtie was used to map the trimmed retroviral sequence tags to the Zv9 zebrafish genome assembly, allowing for one mismatch. The integration site was defined as the site of LTR insertion. After mapping, corresponding ends were paired and uniquely mapping read pairs were used to identify insertion sites. If a single mate of a pair contained both the 3'’ LTR and the barcode, that single sequence, if mapped to only one position in the genome, was used to map the integration site. Reads were defined as redundant and subsequently collapsed if they aligned to the same chromosome at the same start position (the genomic location of the integration), occurred on the same DNA strand and had the same barcode. The number of redundant sequences was recorded. Integration sites with e60 redundant sequence reads were used for downstream analyses. The genomic position of retroviral integrations was compared to those of zebrafish gene models obtained from Ensembl Zv9 e65. A custom perl script was run to identify those retroviral insertions that occurred within a gene or 1 kb upstream or downstream of a gene.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping