GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE45684 Query DataSets for GSE45684
Status Public on Jun 10, 2014
Title RNA-seq alignment to individualized genomes
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
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.
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.
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
Organization name The Jackson Laboratory
Lab Steven Munger
Street address 600 Main Street
City Bar Harbor
State/province ME
ZIP/Postal code 04609
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (1086)
GSM1118049 F100_1
GSM1118050 F101_1
GSM1118051 F102_1
SRA SRP020636
BioProject PRJNA196894

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap