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Series GSE181565 Query DataSets for GSE181565
Status Public on Sep 23, 2022
Title Circadian Clock-Controlled Translation of Specific mRNAs in Neurospora crassa Requires Rhythmic eIF2α Activity and P-body Sequestration [Ribo-seq]
Organism Neurospora crassa
Experiment type Other
Summary We report the genome-wide impact of rhythmic P-eIF2α levels in vivo by performing ribosome profiling and RNA-seq in Neurospora crassa samples grown over a circadian time course. We identified candidate genes which showed rhyhmic ribosome occupancy in WT cells but lost rhythms in mRNA levels and ribosome occupancy in the clock mutant Dfrq, eIF2α kinase knockout Dcpc-3, and constitutively active kinase mutant cpc-3c cells. Select mRNAs harbor a P-body localization motif identified by MEME and MEME Suite's GOMo function. P-body localization of the target mRNAs provides an attractive mechanism for explaining translational rhythms from otherwise arrhythmic mRNAs.
 
Overall design Ribosome profiling (ribo-seq) (done in parallel with RNA-seq) of Neurospora crassa WT, clock mutant Dfrq, eIF2α kinase knockout Dcpc-3, and constitutively active kinase mutant cpc-3c mycelia, grown over a circadian time course. Each time point has a duplicate.
 
Contributor(s) Castillo KD, Wu C, Ding Z, Sachs MS, Bell-Pedersen D
Citation(s) 36577368, 37841830
Submission date Aug 06, 2021
Last update date Oct 26, 2023
Contact name Deborah Bell-Pedersen
E-mail(s) dpedersen@bio.tamu.edu
Organization name Texas A&M University
Department Biology
Street address 3258 TAMU
City College Station
State/province Texas
ZIP/Postal code 77840
Country USA
 
Platforms (2)
GPL20660 Illumina NextSeq 500 (Neurospora crassa)
GPL30082 Illumina HiSeq 3000 (Neurospora crassa)
Samples (80)
GSM5506265 Ribo-seq wild-type DD12 rep1
GSM5506266 Ribo-seq wild-type DD16 rep1
GSM5506267 Ribo-seq wild-type DD20 rep1
This SubSeries is part of SuperSeries:
GSE181566 Circadian Clock-Controlled Translation of Specific mRNAs in Neurospora crassa Requires Rhythmic eIF2α Activity and P-body Sequestration
Relations
BioProject PRJNA752584
SRA SRP331348

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
GSE181565_RAW.tar 4.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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