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| Status |
Public on Dec 23, 2014 |
| Title |
Regulation of Zn and Fe transporters by the GPC1 gene during wheat monocarpic senescence |
| Organism |
Triticum turgidum subsp. durum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
TaGPC1 and TaGPC2 are NAC-domain transcription factors which accelerate the onset of senescence and facilitate nutrient translocation in wheat. We developed knockout mutants of these genes in tetraploid wheat and used RNA-seq to identify the effect of these mutations on the wheat flag leaf transcriptome during monocarpic senescence. Several transporter-related genes were identified which were upregulated during senescence and differentially expressed between genotypes.
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| Overall design |
Illumina cDNA libraries were constructed from four biological replicates of three genotypes (WT, gpc-a1 and gpc-a1/gpc-b2) at three timepoints (Heading date, 12 days after anthesis and 22 days after anthesis). Reads were aligned to a collection of assembled genomic contigs from flow-sorted chromosome arms (A and B genomes only) provided by the International Wheat Genome Sequencing Consortium. A custom GTF file was generated to identify 139828 gene loci corresponding to transcribed regions of this reference sequence.
Please note that the contig names provided by URGI (http://wheat-urgi.versailles.inra.fr/Seq-Repository) were used in the analysis. Most, but not all, of these loci are present in Ensembl (With a modified name, but the same basic information, chromosome arm and unique contig ID) at ftp://ftp.ensemblgenomes.org/pub/plants/release-22/fasta/triticum_aestivum/dna/
Therefore, the contig IDs from URGI (which are available for all our sequences) were used in the processed data file (i.e. the count table and GFF file) and an additional file describing the corresponding Ensembl names for these was provided (Additional_file_2.xlsx).
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| Contributor(s) |
Pearce S, Dubcovsky J |
| Citation(s) |
25524236 |
| |
| Submission date |
Aug 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Pearce |
| E-mail(s) |
[email protected]
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| Organization name |
Rothamsted Research
|
| Department |
Sustainable Soils and Crops
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| Street address |
West Common
|
| City |
Harpenden |
| State/province |
Hertfordshire |
| ZIP/Postal code |
AL52JQ |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL19107 |
Illumina HiSeq 2000 (Triticum turgidum subsp. durum) |
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| Samples (36)
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| Relations |
| BioProject |
PRJNA259173 |
| SRA |
SRP045697 |
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