DNA Microarray Facility Back

( Prithviraj Chavan, Ch. Mohan Rao & M. B. Madhavi)

Microarray is a high-throughput technique for analyzing expression levels of thousands of genes or genotyping large numbers of SNPs in a single experiment.

Facility is equipped to do genome wide analysis with applications in basic research as well as in biomedicine and agro-biotechnology. Microarrays (also known as DNA/Gene chips) are generated by a technology that integrates molecular biology and information technology.  

We have both major array platforms:

  • Spotted Array
  • Affymetrix

Spotted Array System:

  • Generation III Array Spotter (can spot 9,216 features on 36 slides)
  • Axon Gene Pix 4000B Scanner
  • Instrument Control DELL Optiplex 755 (Pentium 1.8GHz, 2GB RAM, XP Prof. 2002-OS)
  • GenepixPro 7.0 (Image Analysis s/w)
  • Analysis HP xw8600 Wks (Xeon 2.0GHz, 8GB RAM, XP Prof. x64 2003-OS)
  • Acuity 4.0 (Data Analysis s/w)

 

(Hitendra Patel & P.Ramesh)

Affymetrix System:

It is being extensively used for genotyping applications and gene expression studies.

  • Hybridization Oven 640
  • Fluidics Station 450
  • Scanner 450
  • Instrument Control DELL Workstation (Xeon 3GHz, 2GB RAM, XP Prof. 2002-OS).
  • Affymetrix Genechip Command Console (Image/Data Analysis s/w)
  • Genespring 11.5 (Data Analysis s/w)
  • Analysis HP z600 Wks (Xeon 2.67GHz, 16GB RAM, x64 Win.Prof.7-OS).

Contact: 

In-charge: Dr.Ramesh V.Sonti sonti@ccmb.res.in, Ph.: 27192577

Staff: Room: C405, Ph.:27192628
M.B.Madhavi [Wet-Lab Analyst] madhavimb@ccmb.res.in
P.Ramesh [Data Analyst] rameshp@ccmb.res.in

 

Publications:

Prasad Mohit, Kalpana Makhijani, M.B. Madhavi, V. Bharathi, Ashish Lal, Gururaj Sirdesai, V. Ram Reddy, Palaparthi Ramesh, Ramakrishna Kannan, Jyotsna Dhawan and L.S. Shashidhara, Modulation of AP and DV Signaling pathways by the homeotic gene Ultrabithorax during haltere development in Drosophila, Developmental Biology, Volume 291, Issue 2, 15 March 2006, Pages 356-367.


Gopaljee Jha, Hitendra Kumar Patel, Madhumita Dasgupta, Ramesh Palaparthi and Ramesh V. Sonti, Transcriptional Profiling of Rice Leaves Undergoing a Hypersensitive Response Like Reaction Induced by Xanthomonas oryzae pv. oryzae Cellulase, Rice, Volume 3, Number 1, March 2010, Pages 1-21.

Rajeswari Jinka, Renu Kapoor, Sivapriya Pavuluri, Avinash T Raj, Mahesh J Kumar, Lakshmi Rao and Gopal Pande (2010) Differential gene expression and clonal selection during cellular transformation induced by adhesion deprivation, BMC Cell Biology, Vol 11:93.

Resource Links:

ArrayExpress - http://www.ebi.ac.uk/microarray-as/ae/ 
Gene Expression Omnibus - http://www.ncbi.nlm.nih.gov/geo/ 
Stanford Microarray Database - http://smd.stanford.edu/ 
Microarray databases - http://mybio.wikia.com/wiki/Microarray_databases 
NetAffxTM Analysis Center - http://www.affymetrix.com/analysis/index.affx 
DNA MICROARRAY VIRTUAL LAB -. http://learn.genetics.utah.edu/content/labs/microarray/
TIGR - http://www.tm4.org/midas.html 
DAVID Bioinformatics Resources - http://david.abcc.ncifcrf.gov/ 
Tools for Analysis of Data Sets - http://www.geneontology.org/GO.tools.microarray.shtml

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