Open Access Highly Accessed Research article

Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress

Sonali Dubey1, Prashant Misra1, Sanjay Dwivedi1, Sandipan Chatterjee1, Sumit K Bag1, Shrikant Mantri12, Mehar H Asif1, Arti Rai1, Smita Kumar1, Manju Shri1, Preeti Tripathi1, Rudra D Tripathi1, Prabodh K Trivedi1*, Debasis Chakrabarty1* and Rakesh Tuli2

Author Affiliations

1 National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India

2 National Agri-Food Biotechnology Institute (Department of Biotechnology, New Delhi), Mohali, Punjab, India

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BMC Genomics 2010, 11:648  doi:10.1186/1471-2164-11-648

Published: 20 November 2010

Additional files

Additional File 1:

Table S1. List of genes up-regulated during Cr (VI) stress in rice.

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Additional File 2:

Table S2. List of genes down-regulated during Cr (VI) stress in rice.

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Additional File 3:

Figure S1. Expression profiles of differentially expressed GST during 100 μM Cr (VI) in rice roots. The microarray data from different rice tissues/organs and developmental stages including seedling root (R), mature leaf (ML), leaf (YL; leaf subtending the shoot apical meristem), shoot apical meristem (SAM), and various stages of panicle (P1-P6) and seed (S1-S5) development. The data were taken from (GSE6893), GSE7951 (expression profiling of stigma), GSE6901 (expression data for stress treatment), GSE7256 (expression data for virulent infection by Magnaporthe grisea), and GSE10373 (expression data for interaction with the parasitic plant Striga hermonthica) were selected for analysis of GST-probe sets that are differentially expressed in Cr-stress.

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Additional File 4:

Table S3. List of root-specific genes up-regulated during Cr (VI) stress in rice.

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Additional File 5:

Table S4. List of root-specific genes down-regulated during Cr (VI) stress in rice.

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Additional File 6:

Figure S2. The COSY spectrum of aqueous fraction of rice roots.

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Additional File 7:

Figure S3 a-e. K-means clustering and GO annotations of genes up-regulated during chromium stress. The clustering was done according to the presence of the motifs identified in this study. a(i) cluster1 a(ii) GO annotation of cluster1. b(i) cluster2 b(ii) GO annotation of cluster2 c(i) cluster3 c(ii) GO annotation of cluster3 d(i) cluster4 d(ii) GO annotation of cluster4 e(i) cluster5 e(ii) GO annotation of cluster5

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Additional File 8:

Figure S4 a-e. K-means clustering and GO annotations of genes down-regulated during chromium stress. The clustering was done according to the presence of the motifs identified in this study. a(i) cluster1 a(ii) GO annotation of cluster1. b(i) cluster2 b(ii) GO annotation of cluster2 c(i) cluster3 c(ii) GO annotation of cluster3 d(i) cluster4 d(ii) GO annotation of cluster4 e(i) cluster5 e(ii) GO annotation of cluster5

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Additional File 9:

Table S5. List of primers used for RT-PCR analysis of Cr (VI) stress responsive genes in rice roots.

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