|
| Status |
Public on Jan 10, 2022 |
| Title |
W2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
W2.0_apical meristem
|
| Organism |
Triticum turgidum subsp. durum |
| Characteristics |
variety: Kronos
waddington stage: W2.0
tissue: apical meristem
|
| Growth protocol |
Plants were grown in controlled conditions in PGR15 growth chambers (Conviron, Manitoba, Canada) under a long day photoperiod (16 h light/8 h dark) at 23 ℃ day/17 ℃ night temperatures and a light intensity of ~260 µM m-2 s-1. Developing apical meristems were harvested under a dissecting microscope using a sterile scalpel and placed immediately in liquid nitrogen. All samples were harvested within a one-hour period of the day 4 h after the lights were switched on (+/- 30 min) to account for possible differences in circadian regulation of gene expression.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were ground into a fine powder in liquid nitrogen and total RNA was extracted using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO).
Libraries were barcoded to allow multiplexing and all samples were sequenced using the 100 bp single read module across two lanes of a HiSeq3000 sequencer at the UC Davis Genome Center.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
RNA-seq reads were trimmed and checked for quality Phred scores above 30 using Fastp v0.20.1
Trimmed reads were aligned to a version of the IWGSC RefSeq v1.0 genome assembly consisting of A and B chromosome pseudomolecules and Unanchored scaffolds not assigned to any chromosome (ABU) using STAR 2.7.5 aligner (outFilterMismatchNoverReadLmax = 0.04, alignIntronMax = 10,000)
Transcript levels were quantified by featureCounts using 190,391 gene models from the ABU IWGSC RefSeq v1.1 annotations
Genome_build: IWGSC RefSeq v1.0, ABU
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jan 06, 2022 |
| Last update date |
Jan 10, 2022 |
| Contact name |
Carl VanGessel |
| Organization name |
Colorado State University
|
| Street address |
Colorado State University
|
| City |
Fort Collins |
| State/province |
CO |
| ZIP/Postal code |
80523 |
| Country |
USA |
| |
|
| Platform ID |
GPL31178 |
| Series (1) |
|
| Relations |
| SRA |
SRX13632335 |
| BioSample |
SAMN24670007 |
