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| Status |
Public on Dec 23, 2014 |
| Title |
WT_HD_Rep_3 |
| Sample type |
SRA |
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| Source name |
WT_HD
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| Organism |
Triticum turgidum subsp. durum |
| Characteristics |
genotype/variation: wild type
time point: heading date
tissue: Flag leaf
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| Growth protocol |
Plants were grown in a greenhouse at UC Davis, CA, under standard conditions.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from flag leaves using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO).
RNA-seq libraries were constructed using the TruSeq™ RNA sample preparation kit v1 (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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Bases were called at the UC Davis Genome Center using CASAVA1.5
Raw reads were trimmed for quality using fastq-quality-trimmer (http://hannonlab.cshl.edu/fastx_toolkit/, default options, except -t 20, -l 25).
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). 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 139,828 transcribed genomic loci.
Gene loci with a low number of counts were excluded using the R script "noleaven" (http://topherconley.github.io/noleaven/).
Genome_build: http://wheat-urgi.versailles.inra.fr/Seq-Repository
Genome_build: http://plants.ensembl.org/Triticum_aestivum/Info/Index
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| Submission date |
Aug 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Pearce |
| E-mail(s) |
stephen.pearce@colostate.edu
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| Organization name |
Colorado State University
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| Department |
Plant Sciences
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| Street address |
2785 Exmoor Lane
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| City |
Fort Collins |
| State/province |
CO |
| ZIP/Postal code |
80525 |
| Country |
USA |
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| Platform ID |
GPL19107 |
| Series (1) |
| GSE60635 |
Regulation of Zn and Fe transporters by the GPC1 gene during wheat monocarpic senescence |
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| Relations |
| BioSample |
SAMN03002447 |
| SRA |
SRX684880 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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