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| Status |
Public on Jul 20, 2020 |
| Title |
Madena.HMO |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Hylobates moloch |
| Characteristics |
tissue: blood
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total gDNA was extracted from blood of gibbons and randomly sheared
sheared gDNA was used to generate illumina libraries using the NEBNext Ultra II library contruction kit (NEB)
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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: WGS
All gibbon genomic shot-gun data were aligned to the gibbon genome reference (Nleu3.0) using BWA
MELT v2.1.3 was used to predict de novo LAVA insertions and deletions (indels) from each of the 23 whole genome shot-gun alignments
We characterized all LAVA inserts based on information such as genomic location, length, and insertion position relative to closest gene [intergenic, exonic, intronic, promoter (<3Kb upstream of gene) or terminator (<3Kb downstream of gene)]
The initial set of LAVA predictions was next filtered to remove: 1) low quality inserts, as assessed by MELT, 2) single copy inserts in the population, 3) inserts shorter than 290bp (the minimum length required to discriminate a composite LAVA from its non-SVA subunits), and 4) inserts found on unplaced Nleu3.0 contigs.
We generated binary LAVA genotype profiles for all gibbon individuals (heterozygous or homozygous LAVA insertion=1, homozygous absence of LAVA= 0)
Genome_build: Nleu3.0
Supplementary_files_format_and_content: an excel spreadsheet containing position, genomic and genotype information for all LAVA insertions across 23 gibbons
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| Submission date |
Sep 05, 2019 |
| Last update date |
Jul 20, 2020 |
| Contact name |
Mariam Okhovat |
| Organization name |
Oregon Health and Science University
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| Department |
Medicine
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| Street address |
3030 S Moody Ave.
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| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platform ID |
GPL27437 |
| Series (2) |
| GSE136966 |
Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome [WGS] |
| GSE136968 |
Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome |
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| Relations |
| BioSample |
SAMN12702584 |
| SRA |
SRX6808839 |
| 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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