Open Access Highly Accessed Research article

Comparative transcriptomic analysis of roots of contrasting Gossypium herbaceum genotypes revealing adaptation to drought

Alok Ranjan, Neha Pandey, Deepika Lakhwani, Neeraj Kumar Dubey, Uday V Pathre and Samir V Sawant*

Author Affiliations

CSIR-, National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India

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BMC Genomics 2012, 13:680  doi:10.1186/1471-2164-13-680

Published: 29 November 2012

Additional files

Additional file 1:

List of primer used in RT-PCR Description: Word file containing list of primer sequences used for RT-PCR.

Format: XLS Size: 78KB 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 RAHS-14 under control condition. Description: Excel file containing the list of unique up regulated genes and their annotation of RAHS-14 under control condition.

Format: XLS Size: 165KB 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 under drought stress. Description: Excel file containing the list of unique up regulated genes and their annotation of RAHS-14 under drought stress.

Format: XLS Size: 521KB 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 genes (probe sets) in Vagad under control condition. Description: Excel file containing the list of unique up regulated genes and their annotation of Vagad under control condition.

Format: XLS Size: 113KB 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 Vagad under drought stress. Description: Excel file containing the list of unique up regulated genes and their annotation of Vagad under drought stress.

Format: XLSX Size: 5.8MB Download file

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Additional file 6:

Contigs analysis by R-statistics of GujCot-21 and RAHS-IPS-187 genotypes. Description: Excel file containing detail analysis of contigs in both genotypes. Worksheet 1 containing total differential contigs, worksheet 2 is up-regulated contigs in RAHS-IPS-187, worksheet 3 is up-regulated contigs in GujCot-21, worksheet 4and 5 are agriGO of RAHS-IPS-187 and GUjCot-21 respectively. Worksheet 6 and 7 are KOBAS analysis of RAHS-IPS-187 and GUjCot-21 respectively.

Format: DOCX Size: 12KB Download file

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Additional file 7:

BLASTX analysis of contigs and singlets against NCBI NR database. Description: Excel file containing BLASTX (TAIR database) results of supercontigs (worksheet1), super singleton (worksheet2), contigs of GujCot-21 (worksheet3), singletone of GujCot-21 (worksheet4), contigs of RAHS-IPS-187 (worksheet 5) and singletone of RAHS-IPS-187 (worksheet 6).

Format: PPT Size: 248KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

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Additional file 8:

BLASTX analysis of both transcriptome contigs and singlets against TAIR database. Description: Excel file containing BLASTX (NCBI NR database) results of supercontigs (worksheet1), super singleton (worksheet2), contigs of GujCot-21 (worksheet3), singletone of GujCot-21 (worksheet4), contigs of RAHS-IPS-187 (worksheet 5) and singletone of RAHS-IPS-187 (worksheet 6).

Format: XLSX Size: 6.9MB Download file

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Additional file 9:

BLASTN analysis of both transcriptome contigs and singlets against publicly available cotton EST sequences. Description: Excel file containing BLASTN (Cotton EST) results of supercontigs (worksheet1), super singleton (worksheet2), contigs of GujCot-21 (worksheet3), singletone of GujCot-21 (worksheet4), contigs of RAHS-IPS-187 (worksheet 5) and singletone of RAHS-IPS-187 (worksheet 6).

Format: XLSX Size: 598KB Download file

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Additional file 10:

Venn diagram of contigs obtained after BLASTX in NCBI-NR, TAIR and Cotton EST database (BLASTN). Contigs of (A) Drought tolerant genotype (GujCot-21) (B) Sensitive genotype (RAHS-IPS-187) (C) Supercontigs Description: PPT contains a figures of venn diagram representing unique and common contigs in different database.

Format: XLSX Size: 5.4MB Download file

Open Data