 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 28, 2010 |
| Title |
SPR |
| Sample type |
SRA |
| |
|
| Source name |
adult testis
|
| Organism |
Mus spretus |
| Characteristics |
strain: spr
|
| Treatment protocol |
none
|
| Growth protocol |
adult mice were sacrifieced at an age of 6-8 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library construction protocol: Paired-end
We extracted RNA from flash-frozen testis tissue using TRIZOL (Invitrogen, Carlsbad, CA), and isolated mRNA from total RNA using the μMACS mRNA isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Sample integrity of total RNA and mRNA were verified using the RNA 6000 Nano chip kit on an Agilent Technologies 2100 Bioanalyzer (Waldbronn, Germany).
We synthesized cDNA from mRNA using Superscript III reverse transcriptase (Invitrogen) and a 10:1 primer mixture of random dodecamers and oligo(dT)18. The insert size was 200 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
sample 19 (SPR.1_1), paired with sample 20
sample 20 (SPR.1_2), paired with sample 19
sample 21 (SPR.2_1), paired with sample 22
sample 22 (SPR.2_2), paired with sample 21
|
| Data processing |
Library preparation and deep sequencing using a Genome Analyzer II (Illumina, San Diego, CA) was performed by the National Center for Genome Resources (Santa Fe, NM) following paired-end sequencing and mRNA sequencing protocols from Illumina.
FASTQ files were generated using the Illumina pipeline version 1.0. The program Tophat/Bowtie was used to align the reads to the mouse reference genome [Ensembl Build NCBIM37.50 (mm9, NCBI Build 37)]. The outfiles (in .sam format) were then filtered for reads that matched uniquely in the genome and in the expected "paired-end" fashion.
|
| |
|
| Submission date |
Nov 05, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Bettina Harr |
| E-mail(s) |
harr@evolbio.mpg.de
|
| Organization name |
Max-Planck-Institute for Evolutionary Biology
|
| Lab |
Evolutionary Genetics
|
| Street address |
August-Thienemannstrasse 2
|
| City |
Ploen |
| ZIP/Postal code |
24306 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9538 |
| Series (1) |
| GSE18905 |
Genome-wide analysis of alternative splicing evolution among Mus subspecies |
|
| Relations |
| SRA |
SRX017333 |
| BioSample |
SAMN00009591 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM468503_SPR_accepted_hits_Filtered.sam.gz |
141.6 Mb |
(ftp)(http) |
SAM |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
