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Series GSE90935 Query DataSets for GSE90935
Status Public on Jun 13, 2017
Title Transcriptome Analyses of Two Hybrid Citrus Cultivars in Seedlings Etiolation
Organisms Citrus reticulata x Citrus sinensis; (Citrus unshiu x Citrus sinensis) x Citrus reticulata
Experiment type Expression profiling by high throughput sequencing
Summary Citrus species are among the most important fruit crops. However, gene regulation and signaling pathways related to etiolation in this crop remain unknown. Using Illumina sequencing technology, modification of global gene expression in two hybrid citrus cultivars—Huangguogan and Shiranuhi, respectively—were investigated. More than 834.16 million clean reads and 125.12 Gb of RNA-seq data were obtained, more than 91.37% reads had a quality score of Q30 (sequencing error rate, 0.1%). 124,952 unigenes were finally generated with a mean length of 1,189 bp. Of these unigenes, 98,904 (79.15%), 105,408 (84.35%), 42,016 (33.62%), 78,872 (63.12%), 72,068 (57.67%), 72,464 (57.99%), 72464 (57.99%) and 46,308 (37.06%) had been annotated in NR, NT, KO, SwissProt, PFAM, GO and KOG databases, respectively. Further, we identified 604 differentially expressed genes (DEGs) in multicoloured and etiolated seedlings of Shiranuhi, including 180 up-regulated genes and 424 down-regulated genes. While in Huangguogan, we found 1,035 DEGs, 271 of which were increasing and the others were decreasing. 7 DEGs were commonly up-regulated, and 59 DEGs down-regulated in multicoloured and etiolated seedlings of these two cultivars, suggesting that some genes play fundamental roles in two hybrid citrus seedlings during etiolation. Functional classification of the DEGs in two cultivars using GO term indicated that biological process, cellular component and molecular function were three major groups. Our study is the first to provide the transcriptome sequence resource for seedlings etiolation of Shiranuhi and Huangguogan, and advance our knowledge of the genes involved in the complex regulatory networks of seedling etiolation.
Overall design Examination of 3 different stages of etiolation leaves of Huangguogan and Shiranuhi.
Contributor(s) Xiong B, Wang Z
Citation(s) 28387303, 31666652
Submission date Dec 06, 2016
Last update date Nov 12, 2019
Contact name bo xiong
Organization name Sichuan Agricultural University
Street address NO.211 Huimin
City chengdu
ZIP/Postal code 611130
Country China
Platforms (2)
GPL22751 Illumina HiSeq 4000 ((Citrus unshiu x Citrus sinensis) x Citrus reticulata)
GPL22752 Illumina HiSeq 4000 (Citrus reticulata x Citrus sinensis)
Samples (18)
GSM2417757 Shiranuhi green seedlings, sample 1
GSM2417758 Shiranuhi green seedlings, sample 2
GSM2417759 Shiranuhi green seedlings, sample 3
BioProject PRJNA356402
SRA SRP094626

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Supplementary file Size Download File type/resource
GSE90935_merged_fpkm.xls.gz 3.4 Mb (ftp)(http) XLS
GSE90935_unigene_merged_fpkm_additional_file.fasta.gz 54.1 Mb (ftp)(http) FASTA
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Raw data are available in SRA

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