Gene expression profiling in different organs of chickpea
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ABSTRACT:
PROVIDER: PRJNA401922 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this study, global transcriptome profiling was performed for different organs of ICC 4958 (leaves, roots, flowers and young pod) and leaves of wild chickpea, PI 489777. More than 50 million high-quality reads were obtained from each sample using Illumina platform. A consensus reference-guided assembly was generated for the transcriptome data from all samples and gene expression was analysed.
2018-07-15 | GSE103561 | GEO
Project description:In this study, we have elucidated the DNA methylation patterns in different organs of a cultivated chickpea genotype ICC 4958 (leaf, root, flower and young pod) and leaf of wild chickpea PI 489777 using bisulphite sequencing. Approximately 108 million read pairs were analyzed per sample. The extent of methylation along-with the context and genomic location of methylated Cs was identified. Further processing was performed to identify the differentially methylated regions among samples with leaves of ICC 4958 as the reference sample. The high resolution methylome maps of different organs and differentially methylated regions will serve as reference for understanding the epigenetic regulation in chickpea.
2018-07-15 | GSE103575 | GEO
Project description:Single-base resolution DNA methylome maps of different organs in chickpea
| PRJNA401936 | ENA
Project description: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.
2014-09-08 | E-GEOD-51300 | biostudies-arrayexpress
Project description:In this study, we aim to present a global view of transcriptome dynamics in different tissues/organs/developmental stage in chickpea. We generated about ~31-95 million reads from each of 94 libraries representing 32 different tissues/organs using Illumina platform. We generated a hybrid assembly of these data along with PacBio data to produce full-length transcriptome assembly. We mapped the reads to the transcriptome assembly for estimation of the abundance of coding and long non-coding transcripts in different tissue samples. The transcriptome dynamics was studied by differential and tissue-specific expression analyses, and co-expression network and transcriptional regulatory network analyses.
2022-10-26 | GSE147831 | GEO
Project description: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.
2014-09-08 | GSE51300 | GEO
Project description:We generated the global transcriptome profile of the two chickpea genotypes under control and drought conditions. Approximately 12 million high-quality reads were obtained for each cultivar and different conditions using the Illumina platform. Reference-based assembly was generated for each cultivar and condition. Differentially expressed genes were identified between drought and control conditions for each cultivar.
2023-05-20 | GSE193077 | GEO
Project description:In this study, we aim to present a global view of transcriptome dynamics during flower development in chickpea. We generated around 234 million high-quality reads for eight flower development stages (ranging from 16 to 40 million reads for each stage) and 91 million high-quality reads from three vegetative tissues using Illumina high-throughput sequencing GAII platform. Because of non-availability of reference genome sequence, we mapped the reads to chickpea transcriptome comprised of 34,760 transcripts for estimation of their transcriptional activity in different tissue samples. The transcriptome dynamics was studied by comparison of gene expression during flower development stages with vegetative tissues. 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 mapped to 34760 chickpea transcripts and reads per kilobase per million (RPKM) was calculated for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using DESeq software. The genes preferentially expression during various stages of flower development as compared to vegetative stages and those with speciifc expression were identified.
2014-01-09 | E-GEOD-42679 | biostudies-arrayexpress
Project description:Microarrays have increasingly become a powerful tool for high throughput gene-expression studies and discovery of novel biomarker genes. Developed for a large number of organisms, including plants, microarrays are commonly performed for species that have sequenced data, for performing gene expression analysis, miRNA profiling, comparative genomic hybridization (CGH), ChIP-on-chip and SNP analysis. Genomic resources are still very limited for chickpea, a very important food legume crop. Here, we report the design and comprehensive validation of Next Generation Sequencing transcriptome data for chickpea through microarray technology to develop a high-throughput resource for studying the expression of all the transcripts in different biological samples to help functional genomics and breeding programs. This microarray design was developed and validated jointly by Genotypic Technology Private Limited and National Institute of Plant Genome Research. First, we designed 400k probes using reads covering 35k assembled contigs and 100k singletons chickpea transcripts. The 400k chip was hybridized with DNA and RNA samples of chickpea and microarray analysis was carried out. A total of 73,922 probes were found to be specific to chickpea transcripts. Best probes were filtered from the analyzed data and a total of 61,659 probes were selected to develop the final microarray design in 60k gene-expression microarray format. The probes represented 51,444 unique transcripts. The probes were annotated based on their corresponding chickpea transcript and similarity with other plants species. Microarray results were concordant with previous results from the NGS studies. The design of custom oligonucleotide probes for microarrays have varied functional genomic applications and this approach represents a valuable resource for chickpea.
2017-01-05 | GSE76972 | GEO
Project description:In this study, we aim to present a global view of transcriptome dynamics during salinity stress in different chickpea genotypes. We generated about 600 million high-quality reads from 16 libraries (control and stress samples for two chickpea genotypes for salinity stress at two developmental stages) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample for each genotype.
2016-07-08 | GSE70377 | GEO