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Series GSE57993 Query DataSets for GSE57993
Status Public on May 25, 2015
Title POS-1 protects posterior gut specification by blocking GLD-3/2 polyadenylation of anterior factor neg-1
Organism Caenorhabditis elegans
Experiment type Expression profiling by high throughput sequencing
Summary The Poly(A)-Tail focused RNA-seq, or PAT-seq approach was utilised to determine the gene expression, poly(A)-site and polyadenylation state of the transcriptome of early C. elegans embryos having been depleated for a series of RNA binding proteins. Namely; pos-1 and mex-5 were independently knocked down using dsRNA expressing E. coli HT115(DE3) fed to ~100,000 starved/synchronized L1 larvae. When half of the population reached adulthood and half were still in the L4 stage, worms were bleached and embryos harvested and stored in Trizol. This ensured an enrichment of early embryos between 1 and 24 cell stage. mex-6(pk440) were synchronized and grown on OP50 until the same time point and embryos harvested in the same manner. Since prolonged gld-3 and gld-2 RNAi result in sterility, starved/synchronized L1 larvae were fed diluted OP50 (200uL of concentrated OP50 diluted in 2mL of M9 and starved L1s) for 16 hours. At that point the OP50 had been mostly consumed by the larvae and concentrated gld-3 or gld-2 dsRNA expressing E. coli were added to the plates. When half of the population reached adulthood and half were still in the L4 stage, worms were bleached and embryos harvested and stored in Trizol. Total RNA was isolated using standard procedures.
 
Overall design Analysis of poly(A) dynamics in early C. elegans embryos reponding to depletion of specific RNA binding proteins and adneylation state regulators
 
Contributor(s) Elewa A, Harrrison PF, Beilharz TH
Citation(s) 26096734
Submission date May 27, 2014
Last update date May 15, 2019
Contact name Traude Beilharz
E-mail(s) traude.beilharz@monash.edu
Organization name Monash University
Department Biomedicine Discovery Institute
Lab RNA Systems Biology Laboratory
Street address Wellington Rd
City Clayton
State/province VIC
ZIP/Postal code 3800
Country Australia
 
Platforms (1)
GPL18730 Illumina HiSeq 1500 (Caenorhabditis elegans)
Samples (12)
GSM1399287 N2 Rep1
GSM1399288 pos-1 (RNAi) rep1
GSM1399289 gld-3 (RNAi) rep1
Relations
BioProject PRJNA248658
SRA SRP042292

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
GSE57993_genes.gff.gz 776.4 Kb (ftp)(http) GFF
GSE57993_genewise-counts.csv.gz 379.0 Kb (ftp)(http) CSV
GSE57993_genewise-tails.csv.gz 617.9 Kb (ftp)(http) CSV
GSE57993_peaks.gff.gz 551.0 Kb (ftp)(http) GFF
GSE57993_peakwise-counts.csv.gz 242.5 Kb (ftp)(http) CSV
GSE57993_peakwise-tails.csv.gz 601.8 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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