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Series GSE57806 Query DataSets for GSE57806
Status Public on Jul 01, 2014
Title RNA Sequencing analysis of Wild Type and HID1 mutant Transcriptomes
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Seedling photomorphogenesis is a sophisticated developmental process that is controlled by both the transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis noncoding RNA, designated HIDDEN TREASURE 1 (HID1), as a new factor promoting photomorphogenesisin continuous red light (cR). We show that HID1 acts through PHYTOCHROME-INTERACTING FACTOR 3 (PIF3), a bHLH transcription factor known to be a key repressor of photomorphogenesis.
 
Overall design Total RNA was isolated from 5-day-old cR-grown WT and hid1(hidden treasure 1)seedlings using RNeasy Plant Mini Kits (Qiagen). Three biological replicates for each sample were subjected to RNA-seq. Poly (A) RNA from 1 μg total RNA was used to generate the cDNA library according to the TruSeq RNA Sample Prep Kit protocol. The library was then sequenced using a HiSeq 2000 system (Illumina). RNA-seq reads were mapped to TAIR10 using Tophat (version 2.0.9) (1). Differentially expressed genes were defined as those that differed by >2-fold with an adjusted P value ≤0.05 that was identified using Cuffdiff software (version 2.0.0)
 
Contributor(s) Wang Y, Zhu D, Deng X
Citation(s) 24982146
Submission date May 19, 2014
Last update date May 15, 2019
Contact name Xuncheng Wang
E-mail(s) scwwxc@163.com
Organization name Peiking University
Street address 5 Yiheyuan Road
City Beijing
ZIP/Postal code 100871
Country China
 
Platforms (1)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
Samples (6)
GSM1390693 WT rep1
GSM1390694 WT rep2
GSM1390695 WT rep3
Relations
BioProject PRJNA248132
SRA SRP042088

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

Supplementary file Size Download File type/resource
GSE57806_RAW.tar 840.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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