Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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

ORGANISM(S): Rattus norvegicus

SUBMITTER: Peter Beyerlein 

PROVIDER: E-GEOD-20895 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain.

Hammer Paul P   Banck Michaela S MS   Amberg Ronny R   Wang Cheng C   Petznick Gabriele G   Luo Shujun S   Khrebtukova Irina I   Schroth Gary P GP   Beyerlein Peter P   Beutler Andreas S AS  

Genome research 20100507 6

mRNA-seq is a paradigm-shifting technology because of its superior sensitivity and dynamic range and its potential to capture transcriptomes in an agnostic fashion, i.e., independently of existing genome annotations. Implementation of the agnostic approach, however, has not yet been fully achieved. In particular, agnostic mapping of pre-mRNA splice sites has not been demonstrated. The present study pursued dual goals: (1) to advance mRNA-seq bioinformatics toward unbiased transcriptome capture a  ...[more]

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