RNA-Seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly. This track shows RNA-seq data performed by a variety of labs on a variety of tissues for the mouse strains sequenced and assembled for the Mouse Genomes Project.
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Strain-specific RNA-seq data was extracted from NCBI SRA or provided directly to UCSC and aligned to the strain specific assembly using STAR with the ENCODE standard parameters. For each tissue, expression wiggle tracks were generated and normalized by bamCoverage, then averaged by wiggletools. High confidence splice junctions were parsed from the STAR splice junction tab file and combined between replicates. Scores are on a 0-1000 range and measure the proportion of individual accessions that support this junction.
These sequencing data were generated in a variety of institutes and labs, including the Jackson Lab, UNC, EBI and the Sanger Institute. Please see the individual accessions on NCBI SRA for more information. Thanks to Thomas Keane for collating and providing these data to UCSC. Ian Fiddes performed the alignments and data processing.
Genome | Tissue | Institute | Accessions |
---|---|---|---|
129S1/SvImJ | brain | Sanger | ERR033018,ERR033019 |
liver | Jackson Labs | SRR826284,SRR826285,SRR826286,SRR826287,SRR826288,SRR826289,SRR826290,SRR826291,SRR826292,SRR826293,SRR826294,SRR826295,SRR826296,SRR826297,SRR826298,SRR826299 | |
A/J | brain | Sanger | ERR033008,ERR033009 |
liver | Jackson Labs | SRR826300,SRR826301,SRR826302,SRR826303,SRR826304,SRR826305,SRR826306,SRR826307,SRR826308,SRR826309,SRR826310,SRR826311,SRR826312,SRR826313,SRR826314,SRR826315 | |
AKR/J | brain | Sanger | ERR033010,ERR033011 |
BALB/cJ | brain | Sanger | ERR033005,ERR033014 |
C3H/HeJ | brain | Sanger | ERR032995,ERR032996 |
C57BL/6NJ | brain | Sanger | ERR033015,ERR033016 |
CAST/EiJ | brain | Sanger | ERR032997,ERR032998 |
UNC | SRR1920268,SRR1920269,SRR1920270,SRR1921023,SRR1924463,SRR1924464,SRR1924465 | ||
liver | EBI | ERR120692,ERR120694 | |
Jackson Labs | SRR826332,SRR826333,SRR826334,SRR826335,SRR826336,SRR826337,SRR826338,SRR826339,SRR826340,SRR826341,SRR826342,SRR826343,SRR826344,SRR826345,SRR826346,SRR826347 | ||
Sanger | 16493_7_3 | ||
spleen | Sanger | 16493_7_6 | |
CBA/J | brain | Sanger | ERR032993,ERR032994 |
DBA/2J | brain | Sanger | ERR033006,ERR033007 |
FVB/NJ | brain | Sanger | 16493_7_8 |
LP/J | brain | Sanger | ERR032992 |
NOD/ShiLtJ | brain | Sanger | ERR032989,ERR032990,ERR032991,ERR033017 |
liver | Jackson Labs | SRR826348,SRR826349,SRR826350,SRR826351,SRR826352,SRR826353,SRR826354,SRR826355,SRR826356,SRR826357,SRR826358,SRR826359,SRR826360,SRR826361,SRR826362,SRR826363 | |
NZO/HlLtJ | brain | Sanger | ERR033001,ERR033002 |
liver | Jackson Labs | SRR826364,SRR826365,SRR826366,SRR826367,SRR826368,SRR826369,SRR826370,SRR826371,SRR826372,SRR826373,SRR826374,SRR826375,SRR826376,SRR826377,SRR826378,SRR826379 | |
PWK/PhJ | brain | Sanger | ERR033003,ERR033004 |
UNC | SRR1924499,SRR1924500,SRR1924501,SRR1924502,SRR1924503,SRR1924504,SRR1924505,SRR1924506 | ||
liver | Jackson Labs | SRR826380,SRR826381,SRR826382,SRR826383,SRR826384,SRR826385,SRR826386,SRR826387,SRR826388,SRR826389,SRR826390,SRR826391,SRR826392,SRR826393,SRR826394,SRR826395 | |
Sanger | 16493_7_2 | ||
spleen | Sanger | 16493_7_5 | |
SPRET/EiJ | brain | Sanger | ERR033012,ERR033013 |
liver | EBI | ERR476403,ERR476405,ERR476407 | |
Sanger | 16493_7_1 | ||
WSB/EiJ | brain | Sanger | ERR032999,ERR033000 |
UNC | SRR1924541,SRR1924542,SRR1924543,SRR1924544,SRR1924545,SRR1924546,SRR1924547,SRR1924548 | ||
liver | Jackson Labs | SRR826396,SRR826397,SRR826398,SRR826399,SRR826400,SRR826401,SRR826402,SRR826403,SRR826404,SRR826405,SRR826406,SRR826407,SRR826408,SRR826409,SRR826410,SRR826411 |
Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R. Gingeras. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (2013) 29 (1): 15-21 first published online October 25, 2012 doi:10.1093/bioinformatics/bts635