RNA-seq analysis and raw data


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.

Display Conventions and Configuration

This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. The following views are in this track:

Density graph of signal enrichment based on a normalized aligned read density (reads per kilobase of mapped reads for each subtrack). This normalized measure assists in visualizing the relative abundance of exons and of transcripts between tissue types.
High confidence splice junctions output by STAR. Color determines strand where STAR made this determination. Splice junction calls are assigned a score on the range 0-1000 where the number represents the proportion of individual accessions that support this junction in the tissue type in question.
The Alignments view shows raw reads mapped to the genome by STAR in BAM format.


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.

Input Data Breakdown

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