|
| Status |
Public on Jun 29, 2016 |
| Title |
PhyC_WT_rep1_3 |
| Sample type |
SRA |
| |
|
| Source name |
Fully-extended third leaf
|
| Organism |
Triticum turgidum subsp. durum |
| Characteristics |
genotype/variation: wild type
|
| Growth protocol |
Plants were grown in a Conviron PGR15 growth chamber at UC Davis, CA, in 16hr light/8hr 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 third fully-expanded leaf of four-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 2000 |
| |
|
| 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 reference set of genomic contigs from the hexaploid wheat variety ‘Chinese Spring’. This reference was assembled from flow-sorted A and B chromosomes and provided by the International Wheat Genome Sequencing Consortium (http://plants.ensembl.org/Triticum_aestivum/Info/Index, v2.2). Reads were aligned using GSNAP(l) (version 05-09-2013, default parameters except -m 2 -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 a custom-made GFF file describing 150,754 transcribed genomic loci.
Gene loci with a low number of counts were removed using the R script "noleaven" (http://topherconley.github.io/noleaven/).
|
| |
|
| Submission date |
Mar 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Pearce |
| E-mail(s) |
stephen.pearce@colostate.edu
|
| Organization name |
Colorado State University
|
| Department |
Plant Sciences
|
| Street address |
2785 Exmoor Lane
|
| City |
Fort Collins |
| State/province |
CO |
| ZIP/Postal code |
80525 |
| Country |
USA |
| |
|
| Platform ID |
GPL19107 |
| Series (1) |
| GSE79049 |
RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways |
|
| Relations |
| BioSample |
SAMN04545435 |
| SRA |
SRX1625744 |
