Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (RNA-Seq)

ABSTRACT: Poly(A) enriched RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to RNA-seq analysis at different sequencing depths 6 biological replicates (3 case – SNT subjected L5-DRG tissue, 3 control – naïve L5-DRG tissue). Each biological replicate was divided B46into 3 technical replicates; each of the technical replicates for a given sample was sequenced to a depth of 17M, 25M or 50M reads. Reads were single stranded and 34bps in length. Multiplexing was used in order to generate the read depths of different sizes. The gene expression values and fold changes in expression between naive and SNT samples were compared to those generated by a microarray experiment carried out on further technical replicates of the same samples, details in the manuscript (submitted - under revision).

ORGANISM(S): Rattus norvegicus

SUBMITTER: James Perkins

PROVIDER: E-GEOD-53762 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix exon-level)

Project description:RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level 6 biological replicates (3 case – SNT subjected L5-DRG tissue, 3 control – naïve L5-DRG tissue). Each sample was made from pooling 4 distinct animals. Sample preparation and hybridization were performed by UCL genomics, following Affymetrix instructions. The 6 replicates were also used for RNA-seq, see GSE53762.

2014-01-07 | E-GEOD-53860 | biostudies-arrayexpress

Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix transcript-level)

2014-01-07 | E-GEOD-53764 | biostudies-arrayexpress

Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (RNA-Seq)

Project description:Poly(A) enriched RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to RNA-seq analysis at different sequencing depths

2014-01-07 | GSE53762 | GEO

Transcription profiling of dorsal root ganglia from rats with and without traumatic neuropathic pain from sciatic nerve transection to identify genes responsible for mechanical hypersensitivity

Project description:Comparison of L5 DRG gene expression profiles at day 14 from SNT treated animals vs. sham controls. This experiment is part of larger study, where the expression profiles of three disparate models of neuropathic pain (SNT, VZV infection and gp120+ddC) are compared in order to find genes that are responsible for mechanical hypersensitivity

2008-07-14 | E-MEXP-976 | biostudies-arrayexpress

Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix exon-level)

Project description:RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level

2014-01-07 | GSE53860 | GEO

Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix transcript-level)

Project description:RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level

2014-01-07 | GSE53764 | GEO

Rice lab_rat model of HIV related neuropathy

Project description:Comparison of L5 DRG gene expression profiles at day 14 from gp120+ddC treated animals vs sham (SA + saline) treated animals.<br>This experiment is part of larger study, where the expression profiles of three disparate models of neuropathic pain (SNT, VZV infection and gp120+ddC) are compared in order to find genes that are responsible for mechanical hypersensitivity formation/maintenance.

2008-01-01 | E-MEXP-974 | biostudies-arrayexpress

A novel functional role for the serine protease inhibitor SerpinA3N and its substrate leukocyte elastase in neuropathic pain

Project description:Two out-bred rat selection lines were separated to produce different hypersensitivity phenotypes following nerve injury. These lines were termed High Pain and Low Pain (HP or LP). Each sub-strain was either subject to a Sham surgery or a Spinal Nerve Ligation (SNL) surgery to the L4 and L5 spinal nerves. Three days following surgery L4/L5 Dorsal Root Ganglia (DRG) were dissected from these animals. For the rat line separation protocol see: Devor M, Raber P (1990) Heritability of symptoms in an experimental model of neuropathic pain. Pain 42:51-67. 12 Hybridizations, 3 per condition; Sham HP DRG; 3 day SNL HP DRG; Sham LP DRG; 3 day SNL LP DRG.

2015-02-19 | E-GEOD-63442 | biostudies-arrayexpress

MicroRNA profiling in dorsal root ganglion after sciatic nerve injury

Project description:Changes in microRNA (miRNA) expression in the mouse L4 and L5 dorsal root ganglion following unilateral sciatic nerve transection. The timepoint of 7 days post-axotomy was chosen to capture miRNA expression profiles at a time when the injured neurons were beginning to regenerate. Two condition experiment, paired control DRG vs axotomised DRG following unilateral sciatic nerve transection. 3 biological replicates, one replicate per array. Dye swap in Replicate 2.

2011-05-06 | E-GEOD-29096 | biostudies-arrayexpress

RNA-seq of rat dorsal root ganglia after ligation to investigate central nervous system transcriptomics in chronic pain using agnostic splice site discovery methods

Project description:The study pursued dual goals: To advance mRNA-seq bioinformatics towards unbiased transcriptome capture and to demonstrate its potential for discovery in neuroscience by applying the approach to an in vivo model of neurological disease. We found that 12.4% of known genes were induced and 7% were suppressed in the dysfunctional (but anatomically intact) L4 dorsal root ganglion (DRG) 2 weeks after L5 spinal Nerve Ligation (SNL). A new algorithm for agnostic mapping of pre-mRNA splice junctions (SJ) achieved a precision of 97%. mRNA-seq of L4 DRG 2 weeks and 2 months after L5 spinal nerve ligation. CONTROL and SNL were used to identify differential gene expression between chronic pain and standard conditions in Rattus norvegicus. CONTROL and SNL and PILOT were used to perform 'agnostic splice site discovery' in the nervous system transcriptome in Rattus norvegicus

2010-05-01 | E-GEOD-20895 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data