|
| Status |
Public on Dec 31, 2023 |
| Title |
HyM_2 |
| Sample type |
SRA |
| |
|
| Source name |
Stem Internode
|
| Organism |
Sorghum bicolor |
| Characteristics |
tissue: Middle internode
developmental stage: Milky stage
cultivar: CSH22SS
|
| Growth protocol |
Hybrid Sweet Sorghum CSH22SS plants were raised in an open field
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using a modified trizol method
Libraries were prepared using TruSeq® Stranded Total RNA kit using manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Low-quality reads with Phred score<30 were filtered
Adapter triming using cutadapt 1.8.1
ribosomal RNA sequences removal by aligning thea reads with silva database using bowtie2 (2.2.9)
read alignment o the genome using Hisat2 program (version 2.0.5)
estimation of gene expression and transcript abundance using String_Tie program (version 1.3.3b)
pairwise differential expression analysis using cuffdiff
Genome_build: Phytozome v3.3.2
Supplementary_files_format_and_content: FPKM values in excel format
|
| |
|
| Submission date |
Jun 28, 2020 |
| Last update date |
Dec 31, 2023 |
| Contact name |
Manoj K. Sharma |
| E-mail(s) |
mksharma@jnu.ac.in
|
| Phone |
01126738895
|
| Organization name |
Jawaharlal Nehru University
|
| Lab |
Manoj K. Sharma
|
| Street address |
133
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110067 |
| Country |
India |
| |
|
| Platform ID |
GPL21615 |
| Series (1) |
| GSE153418 |
Stem transcriptome of sweet sorghum hybrid CSH22SS during development and in response to water limiting conditions. |
|
| Relations |
| BioSample |
SAMN15394718 |
| SRA |
SRX8627458 |
