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Series GSE60635 Query DataSets for GSE60635
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
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.
 
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).
 
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 sppearce@ucdavis.edu
Organization name UC Davis
Department Plant Sciences
Street address One Shields Avenue
City Davis
State/province California
ZIP/Postal code 95616
Country USA
 
Platforms (1)
GPL19107 Illumina HiSeq 2000 (Triticum turgidum subsp. durum)
Samples (36)
GSM1483983 WT_HD_Rep_1
GSM1483984 WT_HD_Rep_2
GSM1483985 WT_HD_Rep_3
Relations
BioProject PRJNA259173
SRA SRP045697

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE60635_Additional_file_2.xlsx 93.9 Mb (ftp)(http) XLSX
GSE60635_GPC_RNA-seq_IWGSC_A_B_gene_loci.gff.gz 2.2 Mb (ftp)(http) GFF
GSE60635_GPC_RNA-seq_raw_counts_08_21_2014.txt.gz 4.1 Mb (ftp)(http) TXT
Raw data are available in SRA
Processed data is available on Series record

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