|
| Status |
Public on Jun 29, 2023 |
| Title |
RNA-Seq of Zincol-2016 roots |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: root
treatment: Control
|
| Treatment protocol |
No treatment was applied
|
| Growth protocol |
The wheat seedlings were grown under optimum growth conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using EasyPure Plant RNA Kit (ER301-01) following manufacturer instructions
mRNAs were isolated and fragmented from total RNA using the oligo (dT) method for cDNA synthesis. The single-end sequencing libraries were constructed, and sequencing was performed on BGISEQ-500 using standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
RNA-Seq using single end sequencing library
|
| Data processing |
Adapters with unknown bases (N’s > 5%) and low quality were removed from raw reads to produce ‘clean data’ as FastQ data files
High quality single-end reads were mapped to the reference genome of bread wheat
Alignment of the reference sequence with reads was performed
Quantification of the reads was performed using featureCounts software program and differentially expressed genes (DEGs) were identified using DeSEQ2
Assembly: IWGSC, INSDC AssemblyGCA_900519105.1
Supplementary files format and content: tab delimited text files include gene counts of each sample
Supplementary files format and content: tab delimited text files include tpm values of each sample
|
| |
|
| Submission date |
Jun 26, 2023 |
| Last update date |
Jun 29, 2023 |
| Contact name |
Saman Maqbool |
| Organization name |
Quaid-i-Azam University, Islamabad
|
| Department |
Plant Sciences
|
| Lab |
Plant Biology Lab
|
| Street address |
Shahdra Road
|
| City |
Islamabad |
| ZIP/Postal code |
45320 |
| Country |
Pakistan |
| |
|
| Platform ID |
GPL26077 |
| Series (1) |
| GSE235844 |
Leveraging RNA-seq of bread wheat transcriptome to reveal diversity of RSA-related transcripts and their expression in contrasting environments |
|
| Relations |
| BioSample |
SAMN30032926 |
| SRA |
SRX16727185 |
