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GSE104500

GSE GEO
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RNA-Seq of L4 C. elegans

Organism: 6239
Platform: GPL18245
Samples: 3
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Oct 02 2017
Last Updated: May 15 2019
Status: Public on Oct 19 2017
Contact: Amy,,Pasquinelli (University of California, San Diego)

Relations

SubSeries of: GSE104502 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA412861 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP119250

Summary

RNA-seq libraries were generated for L4 wildtype worms to analyze RNA abundance at this point in development.

Overall Design

Three independent replicates of wildtype C. elegans were collected at the L4 stage for RNA.

Analysis (2 steps)

View Data Processing
Processing steps for GSE104500
  1. Read counts were quantified using kallisto.
  2. These were then aligned to C. elegans genome WS247.

Supplementary Files (1)

GSE104500_Abundance.csv.gz Download
GEO Samples (3)
GSM2802525 GSM2802526 GSM2802527

Dataset Citations (1)

Short poly(A) tails are a conserved feature of highly expressed genes.
PMID 29106412 · 2017 · Nature structural & molecular biology
Sarah Azoubel Lima, Laura B Chipman, Angela L Nicholson, Ying-Hsin Chen, Brian A Yee, Gene W Yeo, Jeff Coller, Amy E Pasquinelli

SRA Experiments (3) and Runs (3)

Total: 4202 MB
SRX3237804 SRP119250 RNA-Seq SINGLE
GSM2802525: WT rep1 (RNA-Seq); Caenorhabditis elegans; RNA-Seq
Sample: SRS2561531
BioProject: PRJNA412861
BioSample: SAMN07730912
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Caenorhabditis elegans
Sample attributes
source_name: whole organism
developmental stage: L4
genotype: wildtype N2
tissue: whole organism
Original files (1)
whole organism
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6125151 42897159 4289715900 1520.77 Rep1.fastq.gz, SRR6125151, SRR6125151.sralite SRA
SRX3237805 SRP119250 RNA-Seq SINGLE
GSM2802526: WT rep2 (RNA-Seq); Caenorhabditis elegans; RNA-Seq
Sample: SRS2561532
BioProject: PRJNA412861
BioSample: SAMN07730914
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Caenorhabditis elegans
Sample attributes
source_name: whole organism
developmental stage: L4
genotype: wildtype N2
tissue: whole organism
Original files (1)
whole organism
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6125152 36780262 3678026200 1301.29 Rep2.fastq.gz, SRR6125152, SRR6125152.sralite SRA
SRX3237806 SRP119250 RNA-Seq SINGLE
GSM2802527: WT rep3 (RNA-Seq); Caenorhabditis elegans; RNA-Seq
Sample: SRS2561533
BioProject: PRJNA412861
BioSample: SAMN07730913
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Caenorhabditis elegans
Sample attributes
source_name: whole organism
developmental stage: L4
genotype: wildtype N2
tissue: whole organism
Original files (1)
whole organism
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6125153 38903561 3890356100 1380.02 Rep3.fastq.gz, SRR6125153, SRR6125153.sralite SRA

Linked Publications (1)

Short poly(A) tails are a conserved feature of highly expressed genes.
Nature structural & molecular biology · 2017

Data Files (3)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— Rep1.fastq.gz RNA-Seq 1.5 GB link
— Rep2.fastq.gz RNA-Seq 1.3 GB link
— Rep3.fastq.gz RNA-Seq 1.3 GB link