|
| Status |
Public on May 02, 2010 |
| Title |
2 weeks CONTROL1_lane1 |
| Sample type |
SRA |
| |
|
| Source name |
L4 DRG
|
| Organism |
Rattus norvegicus |
| Characteristics |
time: 2 weeks
protocol: CONTROL
strain: Sprague Dawley
|
| Treatment protocol |
In vivo pain model - L5 spinal nerve ligation (SNL) model of neuropathic pain according to Chung et al., Methods Mol Med, 2004
|
| Growth protocol |
N/A
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Libraries were prepared according to Mortazavi et al., Nat Meth, 2008 [PMID: 18516045].
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
mRNA from rat dorsal root ganglion
Illumina instrument model used was GA IIx.
Chemical fragmentation of pA-RNA; non-stranded
|
| Data processing |
WIOS (Wildau In-Silico Sequence) Analysis Pipeline [www.th-wildau.de/bioinformatics/wios] : Read Preprocessing (Quality Check and Read Splitting), Eland Alignment and Read Recombination, Known Gene/Exon/SpliceJunction Expression Estimation, Gene-Level Fold Change Analysis, De-Novo Gene Discovery.
processed data file build: RGSC3.4.50
processed data file types:
*18-cut_right.eland [exon alignment, right fragment]
*32-cut_left.eland [exon alignment, left fragment]
*25-cut_left.eland [splice junction alignment, left fragment]
*25-cut_right.eland [splice junction alignment, right fragment]
|
| |
|
| Submission date |
Apr 30, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Beyerlein |
| E-mail(s) |
peter.beyerlein@googlemail.com
|
| Phone |
+493375508944
|
| Fax |
+493375500324
|
| URL |
http://www.th-wildau.de/bioinformatics
|
| Organization name |
Technische Hochschule Wildau
|
| Department |
Bioinformatics
|
| Lab |
Computational Biology & Biomedical Informatics
|
| Street address |
Bahnhofstraße 1
|
| City |
Wildau |
| State/province |
Brandenburg |
| ZIP/Postal code |
15745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10287 |
| Series (1) |
| GSE20895 |
mRNA-seq with Agnostic Splice Site Discovery for CNS Transcriptomics Tested in Chronic Pain |
|
| Relations |
| SRA |
SRX020088 |
| BioSample |
SAMN00012542 |
