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| Status |
Public on Jan 05, 2012 |
| Title |
mouse_liver.A |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
strain: DBA/2J
library type: paired-end
read length: 50
insert size: 162
insert standard deviation: 27
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| 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 manufacturerâs 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Jun 16, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Robert K Bradley |
| Organization name |
MIT
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| Department |
Biology
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| Street address |
77 Massachusetts Avenue, 68-223A
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE30017 |
Widespread regulated alternative splicing of single codons accelerates proteome evolution |
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| Relations |
| BioSample |
SAMN02198268 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM742964_mouse_liver.A.bwtout.txt.gz |
42.2 Mb |
(ftp)(http) |
TXT |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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