NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE67303 Query DataSets for GSE67303
Status Public on Sep 01, 2016
Title RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae
Organism Cyanidioschyzon merolae strain 10D
Experiment type Expression profiling by high throughput sequencing
Summary Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red light were found to regulate 35% of the total genes in C. merolae. Blue light affected the transcription of genes involved protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae.
 
Overall design Identification of blue light and red light regulated genes by deep sequencing in biological duplicates. qRT-PCR was performed to verify the RNA-seq results.
 
Contributor(s) Tardu M, Dikbas UM, Baris I, Kavakli IH
Citation(s) 27614431
Submission date Mar 26, 2015
Last update date May 15, 2019
Contact name mehmet tardu
E-mail(s) mtardu@umich.edu
Organization name University of Michigan
Department Chemistry
Lab Koutmou Lab
Street address 930 N University Ave
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platforms (1)
GPL19949 Illumina MiSeq (Cyanidioschyzon merolae strain 10D)
Samples (4)
GSM1644066 Cm_BlueLight_Rep1
GSM1644067 Cm_BlueLight_Rep2
GSM1644068 Cm_Darkness_Rep1
Relations
BioProject PRJNA279462
SRA SRP056574

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
GSE67303_DEG_cuffdiff.xlsx 473.9 Kb (ftp)(http) XLSX
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