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| Status |
Public on Jun 10, 2014 |
| Title |
RNA-seq alignment to individualized genomes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The source of most errors in RNA sequencing (RNA-seq) read alignment is in the repetitive structure of the genome and not with the alignment algorithm. Genetic variation away from the reference sequence exacerbates this problem causing reads to be assigned to the wrong location. We developed a method, implemented as the software package Seqnature, to construct the imputed genomes of individuals (individualized genomes) of experimental model organisms including inbred mouse strains and genetically unique outbred animals. Alignment to individualized genomes increases read mapping accuracy and improves transcript abundance estimates. In an application to expression QTL mapping, this approach corrected erroneous linkages and unmasked thousands of hidden associations. Individualized genomes accounting for genetic variation will be useful for human short-read sequencing and other sequencing applications including ChIP-seq.
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| Overall design |
Illumina 100bp single-end liver RNA-seq from 277 male and female Diversity Outbred 26-week old mice raised on standard chow or high fat diet. In addition, Illumina 100bp single-end liver RNA-seq from 128 male 26-week old male mice (20 weeks for NZO strain) from each of the DO founder strains raised on standard chow or high fat diet (8 males per strain by diet group). Each sample was sequenced in 2-4x technical replicates across multiple flowcells. Samples were randomly assigned lanes and multiplexed at 12-24x.
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| Contributor(s) |
Munger SC, Churchill GA, Chesler EJ, Raghupathy N, Choi K, Simons AK, Gatti DM, Hinerfeld DA, Svenson KL, Keller MP, Attie AD, Hibbs MA, Graber JH |
| Citation(s) |
25236449, 26614740, 28592500 |
| Submission date |
Apr 01, 2013 |
| Last update date |
Aug 28, 2019 |
| Contact name |
Steven C Munger |
| E-mail(s) |
steven.munger@jax.org
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| Organization name |
The Jackson Laboratory
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| Lab |
Steven Munger
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| Street address |
600 Main Street
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| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (1086)
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| Relations |
| SRA |
SRP020636 |
| BioProject |
PRJNA196894 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE45684_DOsamples_aligntoDOindividualized_processedmatrix.txt.gz |
14.6 Mb |
(ftp)(http) |
TXT |
| GSE45684_DOsamples_aligntoNCBIM37_processedmatrix.txt.gz |
13.6 Mb |
(ftp)(http) |
TXT |
| GSE45684_FounderStrainsamples_alignedtoStraingenomes_processedmatrix.txt.gz |
6.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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