Transcriptomics,Multiomics

Dataset Information

5

Chickpea Small RNA Atlas - Development


ABSTRACT: In this study, we sequenced small RNA content from seven major tissues/organs employing Illumina technology. More than 154 million reads were generated using Illumina high-throughput sequencing GAII platform, which represented more than 20 million distinct small RNA sequences. After pre-processing, several conserved and novel miRNAs were identified in chickpea. Further, the putative targets of chickpea miRNAs were identified and their functional categorization was analyzed. In addition, we identified miRNAs exhibitng differential and specific expression in various tissues/organs. We collected different tissue samples used in this study and total RNA isolated was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were pre-processed using modified perl script provided in the miRTools software. After quality control, the identical reads were collapsed into a unique read and read count for each sequence was recorded. All the filtered unique reads from each sample were screened stepwise against annotated non-coding RNA sequences, including plant snoRNA, tRNA and rRNA. The remaining reads were screened against repeat sequences from RepBase and chickpea chloroplast sequence. Conserved miRNAs were identified based on similarity with miRBase database and novel miRNAs were identified using miRDeep-P pipeline. For differential expression analysis, the read count for each miRNA was normalized using DESeq software. The genes preferentially and specifically expressed in various tissues/organs were identified.

OTHER RELATED OMICS DATASETS IN: PRJNA222362

ORGANISM(S): Cicer arietinum  

TISSUE(S): Root, Mature Leaf, Flower Bud, Mature Flower, Young Pod, Shoot, Stem

SUBMITTER: Mukesh Jain   Rohini Garg  Narayana V Chevala 

PROVIDER: E-GEOD-51300 | ArrayExpress | 2014-09-08

SECONDARY ACCESSION(S): GSE51300SRP030647PRJNA222362

REPOSITORIES: GEO, ArrayExpress, ENA

Dataset's files

Source:
Action DRS
E-GEOD-51300.idf.txt Idf
E-GEOD-51300.processed.1.zip Processed
E-GEOD-51300.processed.2.zip Processed
E-GEOD-51300.sdrf.txt Txt
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Publications

Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing.

Jain Mukesh M   Chevala V V S Narayana VV   Garg Rohini R  

Journal of experimental botany 20140823 20


MicroRNAs (miRNAs) are essential components of complex gene regulatory networks that orchestrate plant development. Although several genomic resources have been developed for the legume crop chickpea, miRNAs have not been discovered until now. For genome-wide discovery of miRNAs in chickpea (Cicer arietinum), we sequenced the small RNA content from seven major tissues/organs employing Illumina technology. About 154 million reads were generated, which represented more than 20 million distinct sma  ...[more]

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