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Series GSE64958 Query DataSets for GSE64958
Status Public on Jun 26, 2015
Title Transcriptomics and Metabolomics of 10 - 28 day post anthesis cotton fiber from Gossypium hirsutum and Gossypium barbadense
Organisms Gossypium barbadense; Gossypium hirsutum
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goal of this experiment was to use RNA-seq to compare the two commercial cotton species Gossypium hirsutum and Gossypium barbadense and determine what transcripts may account for the better fiber quality in the latter.
Methods: RNA was extracted from Gossypium barbadense or Gossypium hirsutum fibers at 10, 15, 18, 21, and 28 days post anthesis. Paired-end, 100-bp RNA-seq was performed on an Illumina HiSeq2000 and the reads were mapped to the Gossypium raimondii genome at www.phytozome.net and non-homologous contig assemblies from Gossypium arboreum. Results from RNA-seq were combined with non-targeted metabolomics.
Results: Approximately 38,000 transcripts were expressed (RPKM>2) in each fiber type and approximately 2,000 of these transcripts were differentially expressed in a cross-species comparison at each timepoint. Enriched Gene Ontology biological processes in differentially expressed transcripts suggested that Gh fibers were more stressed.
Conclusions: Both metabolomic and transcriptomic data suggest that better mechanisms for managing reactive oxygen species contribute to the increased fiber length in Gossypium barbadense. This appears to result from enhanced ascorbate biosynthesis via gulono-1,4-lactone oxidase and ascorbate recycling via dehydroascorbate reductase.
 
Overall design See Bioproject PRJNA263926 and SRA accession SRP049330 for study design and raw sequencing data and Bioproject PRJNA269608 and TSA accession GBYK00000000 for Gossypium arboreum assembled contig sequences used for transcriptome mapping - Cotton fiber mRNA from 10,15,18,21 and 28 day post anthesis fiber from either Gossypium hirusutm or Gossypium barbadense was sequenced and differential gene expression analysis was conducted between species for each timepoint and between adjacent timepoints. Each timepoint was representative of fiber from 9 individual plants processed as 3 biological replicate pools (material from 3 individual plants per pool).
 
Contributor(s) Haigler C, Tuttle JR, Nah G, Duke M, Guan X, Song Q, Chen ZJ, Scheffler B
Citation(s) 26116072
Submission date Jan 14, 2015
Last update date May 15, 2019
Contact name Candace Hope Haigler
Organization name North Carolina State University
Department Crop Science
Lab Haigler Lab
Street address 101 Derieux Place
City Raleigh
State/province NC
ZIP/Postal code 27695
Country USA
 
Platforms (2)
GPL16485 Illumina HiSeq 2000 (Gossypium hirsutum)
GPL19651 Illumina HiSeq 2000 (Gossypium barbadense)
Samples (30)
GSM1584998 G. hirsutum 15 day post anthesis cotton fiber biological pool 1
GSM1584999 G. hirsutum 15 day post anthesis cotton fiber biological pool 2
GSM1585000 G. hirsutum 15 day post anthesis cotton fiber biological pool 3
Relations
SRA SRP049330
BioProject PRJNA272585

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE64958_Agenome2096.fa.gz 351.0 Kb (ftp)(http) FA
GSE64958_Gb10_vs_15_10up.xlsx 589.6 Kb (ftp)(http) XLSX
GSE64958_Gb10_vs_15_15up.xlsx 324.6 Kb (ftp)(http) XLSX
GSE64958_Gb10_vs_28_10up.xlsx 1.4 Mb (ftp)(http) XLSX
GSE64958_Gb10_vs_28_28up.xlsx 550.9 Kb (ftp)(http) XLSX
GSE64958_Gb15_vs_18_15up.xlsx 456.5 Kb (ftp)(http) XLSX
GSE64958_Gb15_vs_18_18up.xlsx 229.0 Kb (ftp)(http) XLSX
GSE64958_Gb18_vs_21_18up.xlsx 30.3 Kb (ftp)(http) XLSX
GSE64958_Gb18_vs_21_21up.xlsx 49.6 Kb (ftp)(http) XLSX
GSE64958_Gb21_vs_28_21up.xlsx 1.3 Mb (ftp)(http) XLSX
GSE64958_Gb21_vs_28_28up.xlsx 445.8 Kb (ftp)(http) XLSX
GSE64958_Gb_vs_Gh_10dpa_Gb-up.xlsx 532.9 Kb (ftp)(http) XLSX
GSE64958_Gb_vs_Gh_10dpa_Gh-up.xlsx 455.8 Kb (ftp)(http) XLSX
GSE64958_Gb_vs_Gh_15dpa_Gb-up.xlsx 713.7 Kb (ftp)(http) XLSX
GSE64958_Gb_vs_Gh_15dpa_Gh-up.xlsx 507.6 Kb (ftp)(http) XLSX
GSE64958_Gb_vs_Gh_18dpa_Gb-up.xlsx 472.2 Kb (ftp)(http) XLSX
GSE64958_Gb_vs_Gh_18dpa_Gh-up.xlsx 471.2 Kb (ftp)(http) XLSX
GSE64958_Gb_vs_Gh_21dpa_Gb-up.xlsx 520.5 Kb (ftp)(http) XLSX
GSE64958_Gb_vs_Gh_21dpa_Gh-up.xlsx 415.8 Kb (ftp)(http) XLSX
GSE64958_Gb_vs_Gh_28dpa_Gb-up.xlsx 370.7 Kb (ftp)(http) XLSX
GSE64958_Gb_vs_Gh_28dpa_Gh-up.xlsx 362.2 Kb (ftp)(http) XLSX
GSE64958_Gh10_vs_15_10up.xlsx 686.5 Kb (ftp)(http) XLSX
GSE64958_Gh10_vs_15_15up.xlsx 384.1 Kb (ftp)(http) XLSX
GSE64958_Gh10_vs_28_10up.xlsx 1.3 Mb (ftp)(http) XLSX
GSE64958_Gh10_vs_28_28up.xlsx 485.4 Kb (ftp)(http) XLSX
GSE64958_Gh15_vs_18_15up.xlsx 380.9 Kb (ftp)(http) XLSX
GSE64958_Gh15_vs_18_18up.xlsx 271.0 Kb (ftp)(http) XLSX
GSE64958_Gh18_vs_21_18up.xlsx 29.4 Kb (ftp)(http) XLSX
GSE64958_Gh18_vs_21_21up.xlsx 11.7 Kb (ftp)(http) XLSX
GSE64958_Gh21_vs_28_21up.xlsx 448.0 Kb (ftp)(http) XLSX
GSE64958_Gh21_vs_28_28up.xlsx 448.0 Kb (ftp)(http) XLSX
GSE64958_RAW.tar 55.7 Mb (http)(custom) TAR (of XLSX)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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