Open Access Highly Accessed Research article

De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments

Parul Gahlan1, Heikham Russiachand Singh2, Ravi Shankar2*, Niharika Sharma1, Anita Kumari1, Vandna Chawla2, Paramvir Singh Ahuja1 and Sanjay Kumar1*

Author Affiliations

1 Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), P.O. Box No. 6, Palampur 176 061, Himachal Pradesh, India

2 Studio of Computational Biology & Bioinformatics, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), P.O. Box No. 6, Palampur 176 061, Himachal Pradesh, India

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BMC Genomics 2012, 13:126  doi:10.1186/1471-2164-13-126

Published: 31 March 2012

Additional files

Additional file 1:

Pooled transcriptome data of P. kurrooa. Due to large amount, data is divided into Additional file 1 and Additional file 2.

Format: TXT Size: 16.2MB Download file

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Additional file 2:

Pooled transcriptome data of P. kurrooa. File contains the remaining data of Additional file 1.

Format: TXT Size: 16.5MB Download file

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Additional file 3:

Dissimilar sequence groupings for assembled transcriptome sequences. The grouped sequences are dissimilar from each other, and belong to different regions of common genes. This helps reducing the over-representation of total transcripts, usually missed in assembling.

Format: XLS Size: 4.2MB Download file

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Additional file 4:

Top highly represented functional conserved domains found in unknown sequences.

Format: TIFF Size: 1.3MB Download file

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Additional file 5:

Experimentally validated expressed sequence tags (ESTs) of P. kurrooa available at dbEST NCBI. Methods section has details including URL used in the present analysis.

Format: XLS Size: 46KB Download file

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Additional file 6:

Guanine-cytosine (GC) content analysis of P. kurrooa transcripts. The average GC content of each transcript was calculated and highest proportion of transcripts belongs to the GC content range of 40-49%.

Format: TIFF Size: 288KB Download file

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Additional file 7:

Simple sequence repeats (SSRs) identified in transcripts of P. kurrooa.

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Additional file 8:

Comparative plots for top ten highest represented molecular function (A) and biological process (B) categories in A. thaliana and P. kurrooa.

Format: TIFF Size: 3.9MB Download file

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Additional file 9:

Reads per exon kilobase per million (RPKM) based gene expression at 15°C and 25°C in different expression categories ranging from > 10 fold increment to 0.5 fold or lower.

Format: XLS Size: 20KB Download file

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Additional file 10:

Details on all the transcription factor (TF) families analyzed in P. kurrooa.

Format: XLS Size: 22KB Download file

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Additional file 11:

Top 20 most abundant transcription factor (TF) families analyzed in P. kurrooa. Details of all the TFs are mentioned in Additional file 10.

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Additional file 12:

Reads per exon kilobase per million (RPKM) based expression of transcription factors analysed for P. kurrooa transcriptome at 15°C and 25°C.

Format: XLS Size: 324KB Download file

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Additional file 13:

Reads per exon kilobase per million (RPKM) based expression of targeted genes of mevalonate (MVA), 2-C-methyl-D-erythritol 4-phosphate (MEP) and phenylpropanoid (PP) pathway (pathways associated with picrosides biosynthesis) at 15°C and 25°C.

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Additional file 14:

Reads per exon kilobase per million (RPKM) based expression of annotated cytochrome P450s (CYPs) in P. kurrooa transcriptome.

Format: XLS Size: 28KB Download file

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Additional file 15:

Reads per exon kilobase per million (RPKM) based expression of annotated glycosyltransferases in P. kurrooa transcriptome.

Format: XLS Size: 69KB Download file

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Additional file 16:

Oligonucleotide sequences and polymerase chain reaction (PCR) conditions used in reverse transcriptase (RT-PCR) based expression analysis.

Format: DOC Size: 60KB Download file

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