NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE112442 Query DataSets for GSE112442
Status Public on Aug 08, 2019
Title Gene expression profiling (RNA-seq) in wild-type and bdrs triple mutant Arabidopsis seedlings in response to light or to a heat shock
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary We analyzed by RNA-seq the modulation of the transcriptome in response to light or a heat shock in wild-type and bdrs triple mutant Arabidopsis thaliana seedlings (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We showed that the overall changes in the transcriptome were very similar in the two genotypes. However, when studying specifically gene pairs organized in tandem and with short intergenic distances, we showed that the rapid and strong regulations of upstream genes was associated with bdrs-dependent changes on the downstream gene expression that are consistent with bdrs-dependent transcriptional interferences.
 
Overall design mRNA profiles in seedlings from wild-type (Col0), or bdr triple mutant were generated by deep sequencing, in triplicates, on Illumina NextSeq500. In the photomorphogenesis experiment, seedlings were grown for 5 days in the dark and exposed or not (DARK) to 2h (LIGHT2h) or 4h (LIGHT4h) of white light. In the heat shock experiment, seedlings were grown for 12 days in the cold (12°C) and exposed (HEAT) or not (COLD) to a heat shock of 4h at 27°C.
 
Contributor(s) Michaels SD, Martin PG, Yu X, Huang J, Ford JB
Citation(s) 31554790
Submission date Mar 28, 2018
Last update date Nov 07, 2019
Contact name Pascal GP Martin
E-mail(s) pascal.martin@inrae.fr
Organization name INRAE
Department UMR1332 BFP
Lab FDFE
Street address 71 avenue Edouard Bourlaux
City Villenave d'Ornon
ZIP/Postal code 33140
Country France
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (30)
GSM3070178 wt_DARK_rep1
GSM3070179 wt_DARK_rep2
GSM3070180 wt_DARK_rep3
This SubSeries is part of SuperSeries:
GSE112443 RNA-seq, ChIP-seq and MNase-seq in WT, fpa mutant and bdr1,2,3 mutant Arabidopsis seedlings
Relations
BioProject PRJNA446045
SRA SRP136641

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
GSE112442_GSF1377_NormalizedCounts_heatshock.txt.gz 1.7 Mb (ftp)(http) TXT
GSE112442_GSF1377_NormalizedCounts_photomorphogenesis.txt.gz 2.6 Mb (ftp)(http) TXT
GSE112442_GSF1377_RawCounts_heatshock.txt.gz 532.2 Kb (ftp)(http) TXT
GSE112442_GSF1377_RawCounts_photomorphogenesis.txt.gz 727.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap