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Cellular and Molecular Neurobiology

, Volume 29, Issue 4, pp 533–548 | Cite as

Transcriptome Profiling of Neuronal Model Cell PC12 from Rat Pheochromocytoma

  • Ramasamy Saminathan
  • Arjunan Pachiappan
  • Luo Feng
  • Edward G. Rowan
  • Ponnampalam Gopalakrishnakone
Original Paper

Abstract

GeneChip® microarray is a cutting-edge technology being used to study the expression patterns of genes with in a particular cell type. In this study, the Affymetrix® RAE230A platform was used to profile stably expressed mRNA transcripts from PC12 cells at passage 5 and 15. The whole-cell PC12 transcriptome revealed that a total of 7,531 stable transcripts (P < 0.05), corresponding to 6,785 genes, were found to be consistently expressed between passage 5 and 15. The data analysis revealed 3,080 functional proteins, belonging to 13 families, which indicate that about 65% of the proteins expressed in PC12 cells are uncharacterized. By using our custom-built rat neuronal reference genome database, we mapped endogenously expressed stable neuronal transcripts from PC12 cells comprising about 765 genes responsible for neuronal function and disease. These neuronal transcripts were further analyzed to provide a genetic blueprint that can be used by neurobiologist to unravel the complex cellular and molecular mechanisms underlying biological functions and their associated signalling networks for diseases affecting the nervous system.

Keywords

PC12 cells Microarray Gene expression Rat pheochromocytoma PC12 transcriptome 

Abbreviations

ERK

Extracelular signal-regulated kinase

EST

Expressed sequence tag

GABA

γ-Aminobutyric acid

GAPDH

Glyceraldehyde-3-phosphate dehydrogenase

GCOS

GeneChip® operating software

GenMAPP

Gene map annotator and pathway profiler

GEO

Gene expression omnibus

IPA

Ingenuity® pathway analysis

JNK

c-Jun N-terminal kinase

KEGG

Kyoto encyclopaedia of genes and genomes

MAPK

Mitogen-activated protein kinase

NGF

Nerve growth factor

PACAP

Pituitary adenylate cyclase-activating polypeptide

PKA

Protein kinase A

qRT-PCR

Quantitative reverse transcription-polymerase chain reaction

RAE230A

Rat expression 230A

Notes

Acknowledgements

We are thankful to National University of Singapore for funding [R-181-000-089-112] and facilities to carry out this work. And, we are also grateful to Mr. Akira Niwayama, Director, Commercial Operations (Asia Pacific), Redwood City, CA, USA, for his extended support in providing IPA software (Ingenuity® Systems) and Mr. Len Sheng Wong, Genomax Technologies Pte Ltd, Singapore, for his technical support in analyzing Affymetrix® Genechip® expression data using GeneSpring GX 7.3.1 software.

Supplementary material

10571_2009_9345_MOESM1_ESM.pdf (53 kb)
Supplementary material 1 (PDF 52 kb)

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Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Ramasamy Saminathan
    • 1
    • 2
  • Arjunan Pachiappan
    • 1
  • Luo Feng
    • 1
  • Edward G. Rowan
    • 2
  • Ponnampalam Gopalakrishnakone
    • 1
  1. 1.Venom and Toxin Research Programme, Department of Anatomy, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
  2. 2.Division of Physiology and Pharmacology, Strathclyde Institute of Pharmacy and Biomedical SciencesUniversity of StrathclydeGlasgowUK

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