|
| Status |
Public on Dec 31, 2017 |
| Title |
Himchana 1_S1 - Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Mature plants
|
| Organism |
Cicer arietinum |
| Characteristics |
cultivar: Himchana 1
tissue: Seed
developmental stage: seed stage 1
|
| Treatment protocol |
Leaves were collected from the field-grown chickpea plants during mid maturation stage of seed development. Seven different stages of seeds (whole seed) representing the major events occurring within the seed, were collected from the field-grown plants. The tissues were collected in at least three biological replicates.
|
| Growth protocol |
Plants were grown in the field.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma of modified protocol proposed by Wang et al (2011, Phytochemical Analysis).
Libraries were prepared using mRNA-Seq Sample Prep kit (Illumina) according to the manufacture’s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data: HS1_FPKM.txt
|
| Data processing |
Illumina 1.5/1.8 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Fragments per exon kilobase per million (FPKM) value was calculated for all the genes in each tissue sample
Genome_build: Kabuli chickpea genome (http://www.icrisat.org/gt-bt/ICGGC/genomedata.zip); Genome visualization at: http://cicar.comparative-legumes.org/gb2/gbrowse/Ca1.0/
Supplementary_files_format_and_content: tab delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Mar 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mukesh Jain |
| Phone |
91-11-26704686
|
| Organization name |
Jawaharlal Nehru University
|
| Street address |
New Mehrauli Road
|
| City |
New Delhi |
| State/province |
New Delhi |
| ZIP/Postal code |
110067 |
| Country |
India |
| |
|
| Platform ID |
GPL20619 |
| Series (1) |
| GSE79720 |
Transcriptome dynamics during seed development in chickpea (Himchana) |
|
| Relations |
| BioSample |
SAMN04590571 |
| SRA |
SRX1670140 |
