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Sample GSM742953 Query DataSets for GSM742953
Status Public on Jan 05, 2012
Title mouse_brain.B
Sample type SRA
Source name brain
Organism Mus musculus
Characteristics strain: C57BL/6J
library type: paired-end
read length: 80
insert size: 165
insert standard deviation: 29
Extracted molecule polyA RNA
Extraction protocol Human: RNA-Seq libraries are from the Body Map 2.0 dataset distributed by Illumina, available at the ENA archive with accession number ERP000546.
Mouse: Tissues from a 10-week-old male were extracted immediately after death and stored in RNAlater per the manufacturer’s instructions (Ambion). Tissue was lysed in Trizol and RNA was extracted with Qiagen miRNeasy mini columns. Using 5ug of total RNA, we performed polyA selection and prepared strand-specific libraries for Illumina sequencing following the dUTP protocol and the SPRIworks Fragment library system (Beckman Coulter). We obtained final insert sizes of approximately 160 bp. We sequenced these libraries using the Illumina HiSeq 2000 and the GAIIx machines.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Alignment: The files human.nagnag.junctions.gff and mouse.nagnag.junctions.gff (see Series supplementary files) give the intron-proximal and intron-distal splice junctions of all NAGNAG splicing events analyzed in this study. The 'start' field specifies the last base of the upstream exon and the 'end' field specifies the first base of the downstream exon (upstream and downstream defined with respect to the gene). For each NAGNAG, we extracted the transcript sequence flanking the proximal and distal 3' splice sites and used Bowtie version 0.12.7 to map reads to these two sequences. We required that short reads have at least 6 nt on either side of the splice junction (an "overhang" of 6 nt), and furthermore that there be no mismatches within the overhang region.
Human genome build: hg19
Mouse genome build: mm9
Submission date Jun 16, 2011
Last update date Jun 11, 2013
Contact name Robert K Bradley
Organization name MIT
Department Biology
Street address 77 Massachusetts Avenue, 68-223A
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platform ID GPL13112
Series (1)
GSE30017 Widespread regulated alternative splicing of single codons accelerates proteome evolution
BioSample SAMN02198240

Supplementary file Size Download File type/resource
GSM742953_mouse_brain.B.bwtout.txt.gz 156.1 Mb (ftp)(http) TXT
Raw data not provided for this record
Processed data provided as supplementary file

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