Open Access Highly Accessed Research article

Genome wide expression profiling of two accession of G. herbaceum L. in response to drought

Alok Ranjan1, Deepti Nigam1, Mehar H Asif1, Ruchi Singh1, Sanjay Ranjan1, Shrikant Mantri2, Neha Pandey1, Ila Trivedi1, Krishan Mohan Rai1, Satya N Jena1, Bhupendra Koul1, Rakesh Tuli2, Uday V Pathre1 and Samir V Sawant1*

Author Affiliations

1 Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, UP, India

2 National Agri-Food Biotechnology Institute, Department of Biotechnology, C-127, Industrial Area, S.A.S. Nagar, Phase 8, Mohali-160071, Punjab, India

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BMC Genomics 2012, 13:94  doi:10.1186/1471-2164-13-94

Published: 16 March 2012

Additional files

Additional file 1:

List of primers for QGE assay. Excel file containing all primer sequences used for the QGE experiment.

Format: XLS Size: 23KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

Annotation and fold change (fold change > = 2) of up-regulated unique genes in Vagad during irrigated condition. Excel file containing the list of unique up-regulated genes of Vagad during irrigated condition.

Format: XLS Size: 107KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

Annotation and fold change (fold change > = 2) of up-regulated unique genes in RAHS-14 during irrigated condition. Excel file containing the list of unique up-regulated genes of RAHS-14 during irrigated condition.

Format: XLS Size: 90KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 4:

Annotation and fold change (fold change > = 2) of up-regulated unique genes in Vagad during drought stress. Excel file containing the list of unique up-regulated genes of Vagad during drought condition.

Format: XLS Size: 77KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 5:

Annotation and fold change (fold change > = 2) of up-regulated unique genes in RAHS-14 during drought stress. Excel file containing the list of unique up-regulated genes of RAHS-14 during drought condition.

Format: XLS Size: 80KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 6:

Phenylpropanoid biosynthesis pathways analysis by KEGG using differentially up-regulated genes in Vagad in drought condition. JPEG image file containing the pathways mapping of phenylpropanoid biosynthesis from differentially up-regulated genes in Vagad in drought condition. Red color highlighted steps in pathways show involvements of genes in pathways from input gene list.

Format: JPEG Size: 157KB Download file

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Additional file 7:

Flavonoid biosynthesis pathways analysis by KEGG using differentially up-regulated genes in Vagad in drought condition. JPEG image file containing the pathway mapping of flavonoid biosynthesis from differentially up-regulated genes in Vagad in drought condition. Red color highlighted steps in pathways show involvements of genes in pathways from input gene list.

Format: JPEG Size: 186KB Download file

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Additional file 8:

Analysis of differentially expressed TFs. Excel file containing the summary result of expressed TFs number in both the accessions under drought and irrigated condition. Arabidopsis homolog IDs were mapped from TAIR10.

Format: XLSX Size: 11KB Download file

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Additional file 9:

Histogram of frequency of the number of reads assembled in contigs. In JPEG image file, X-axis represents the number of reads, and Y-axis represents the number of genes. The color code indicates the contigs of Vagad and RAHS-14.

Format: JPEG Size: 18KB Download file

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Additional file 10:

BlastN analysis of both transcriptome contigs and singlets against the NCBI NR database. Excel file containing summary result of BLAST analysis and short description.

Format: XLS Size: 4.6MB Download file

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Additional file 11:

BlastN analysis of both transcriptome contigs and singlets against publicly available Cotton EST sequences. Excel file containing summary of BLAST analysis from cotton EST.

Format: XLSX Size: 3.7MB Download file

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Additional file 12:

Percentage of contigs passing the ESTScan model in both libraries. JPEG image showed the total number of EST that has passed through the ESTScan model.

Format: JPEG Size: 15KB Download file

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Additional file 13:

Uniprot analyses of Vagad and RAHS-14. Excel file containing uniprot analysis of Vagad in worksheet 1 and RAHS-14 in worksheet 2.

Format: XLS Size: 6.3MB Download file

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Additional file 14:

Differentially expressing contigs that were filtered by an R value of 9. Excel file containing differentially expressed contigs in Vagad and RAHS-14 and EST counts.

Format: XLS Size: 205KB Download file

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Additional file 15:

Fold change gene analysis by digital transcriptome of both the accessions. Excel file containing short description and fold change of both the accessions. Worksheet 1 showed up-regulated contigs, and worksheet 2 showed down-regulated contigs in Vagad compared with RAHS-14.

Format: XLS Size: 127KB Download file

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Additional file 16:

Correlation analysis between differentially expressed genes obtained in microarray and contigs obtained from transcriptome sequencing. PPT file containing Pearson correlation graph between microarray and contigs of transcriptome sequencing. For each contigs the counts were converted to transcripts per million which was then converted to log2 counts and their ratio was calculated for fold change between Vagad and RAHS-14.

Format: PPT Size: 149KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

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Additional file 17:

Annotation analysis of 167 gene obtained in correlation analysis of microarray and transcriptomic contigs. Excel file contacting detail analysis of differentially expressed genes obtained in microarray correlated with transcriptomic contigs.

Format: XLS Size: 88KB Download file

This file can be viewed with: Microsoft Excel Viewer

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