|
| Status |
Public on Jan 07, 2014 |
| Title |
Naïve 1 (transcript-level) |
| Sample type |
RNA |
| |
|
| Source name |
Dorsal root ganglia, L5
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Dorsal root ganglia, L5
strain: Wistar
treatment: SNT or naïve: Naïve
|
| Treatment protocol |
Spinal nerve transection (SNT) of the L5 spinal nerve was performed. Dorsal root ganglia (DRG) were harvested 7 days after surgery fresh dissection
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extracted using the miRNEasy kit (QIAGEN) according to manufacturer’s instructions. RNA concentration was measured using the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA).
|
| Label |
biotin
|
| Label protocol |
Standard protcol performed by UCL genomics, following Affymetrix instructions
|
| |
|
| Hybridization protocol |
Standard protcol performed by UCL genomics, following Affymetrix instructions
|
| Scan protocol |
Standard protcol performed by UCL genomics, following Affymetrix instructions
|
| Data processing |
CEL files were processed in R using the oligo Bioconductor package. Background correction, normalisation and summarisation were performed using robust multi-array average (RMA), quantile normalisation and median polish respectively. Summarisation was performed at the exon level (where each probeset corresponds to an exon, with some exons being probed by more than one probeset) or the transcript cluster/gene level, where all probesets from different exons belonging to the same gene were summarised to produce a single transcript cluster measurement.
|
| |
|
| Submission date |
Jan 02, 2014 |
| Last update date |
Jan 07, 2014 |
| Contact name |
James R Perkins |
| E-mail(s) |
jimrperkins@gmail.com
|
| Organization name |
Hospital Carlos Haya
|
| Department |
Hospital Civil
|
| Lab |
Research Laboratory for Allergic Diseases
|
| Street address |
Pl. Hosp. Civil
|
| City |
Malaga |
| ZIP/Postal code |
29009 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6543 |
| Series (2) |
| GSE53764 |
Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix transcript-level) |
| GSE53861 |
Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths |
|
