RNA-seq analysis and raw data

Description

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:

Expression

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.

Splice_Junctions

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.

Alignments

The Alignments view shows raw reads mapped to the genome by STAR in BAM format.

Methods

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.

Credits

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

References

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