|
| Status |
Public on Nov 26, 2019 |
| Title |
WT_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Fully-extended third leaf
|
| Organism |
Triticum turgidum subsp. durum |
| Characteristics |
tissue: Fully-extended third leaf
genotype: WT
|
| Growth protocol |
Plants were grown in a Conviron PGR15 growth chamber at UC Davis, CA, in 8hr light/16hr dark conditions with a light intensity of 260µM m-2 s-1 and 20 °C day/ 18 °C night temperatures.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the youngest fully-expanded leaf of eight-week-old plants using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO).
RNA-seq libraries were constructed using the TruSeq™ RNA library prep kit v2 (Illumina, San Diego, CA) according to the manufacturer's instructions and their quality determined by running samples on a high-sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Triticum turgidum L. subsp. durum (Desf.)
|
| Data processing |
Bases were called at the UC Davis Genome Center using CASAVA1.5
Raw reads were trimmed for adapter contamination using "Scythe" (Default options, https://github.com/vsbuffalo) and for quality using “Sickle” (Default options except –l 25 –q 25, https://github.com/najoshi/sickle).
Trimmed reads were mapped to A and B homoeolgous chromosomes from the IWGSC RefSeqv1.0 wheat genome assembly from the hexaploid wheat variety ‘Chinese Spring’. Reads were aligned using GSNAP(l) (version 03-06-2016, default parameters except -m 4 -n 1 -N 1 -A sam).
Uniquely mapped reads were counted with ht-seq count (-m union) (http://www-huber.embl.de/users/anders/HTSeq/doc/index.html) using high confidence and low confidence gene models extracted from IWGSC RefSeqv1.0 annotations.
Gene loci with no raw count values greater than or equal to three in any replicate of any of the three genotypes were excluded from subsequent analyses.
Genome_build: IWGSC RefSeqv1.0
ftp://ftp.ensemblgenomes.org/pub/plants/release-45/fasta/triticum_aestivum/dna/
GFF3 files for annotations of all genes can be downloaded at the following link: https://urgi.versailles.inra.fr/download/iwgsc/IWGSC_RefSeq_Annotations/v1.0/
Supplementary_files_format_and_content: Tabular raw count and processed Transcripts Per Million (TPM) for each gene locus.
|
| |
|
| Submission date |
Nov 25, 2019 |
| Last update date |
Nov 27, 2019 |
| Contact name |
Stephen Pearce |
| E-mail(s) |
stephen.pearce@rothamsted.ac.uk
|
| Organization name |
Rothamsted Research
|
| Department |
Sustainable Soils and Crops
|
| Street address |
West Common
|
| City |
Harpenden |
| State/province |
Hertfordshire |
| ZIP/Postal code |
AL52JQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL27807 |
| Series (1) |
| GSE141000 |
PHYB and PHYC–mediated transcriptomic responses to short and long day photoperiods in wheat |
|
| Relations |
| BioSample |
SAMN13385932 |
| SRA |
SRX7214187 |
