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Sample GSM2267046 Query DataSets for GSM2267046
Status Public on Aug 10, 2016
Title N2-L4440-1
Sample type SRA
 
Source name mixed stage early embryos
Organism Caenorhabditis elegans
Characteristics range of embryonic cell stages: 1cell to 350 cell stage
strain: N2
genotype/variation: control
Growth protocol Synchronized L1 worms were fed on OP50 bacteria for 72 hrs, then adult worms were treated with standard bleaching solution to collect embryos in utero
Extracted molecule total RNA
Extraction protocol Total RNAs were purified using Trizol/chloroform extraction protocol.
1µg of total RNA was used as starting material, and a sequencing library was prepared using TruSeq Stranded Total RNA Sample Prep Kit after treatment with Ribo-Zero (Human/Mouse/Rat) for rDNA depletion.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing RNA-seq reads were quality-checked using FastQC version 0.5.2
FastQ Quality Trimmer version 1.0 was used to trim reads with less than optimal quality scores.
The DE analysis protocol outlined in Trapnell et. al. was used to perform the DE analysis
The quality filtered reads were mapped to C. elegans (ce10) reference genome using TopHat2 version 0.5.
Cufflinks version 2.1.1 was used to assemble transcripts and estimate their abundance. The transcript assembly outputs from Cufflinks were merged into a unified list of transcripts using Cuffmerge.
Cuffdiff version 2.0.2 was then used to quantify gene and transcript expression levels and test them for significant differences. Default parameters were utilized for all steps.
Genome_build: ce10
Supplementary_files_format_and_content: .txt files, cuffdiff differential expression output (gene-level, isoform-level, primary transcript)
 
Submission date Aug 10, 2016
Last update date May 15, 2019
Contact name Susan Strome
E-mail(s) sstrome@ucsc.edu
Organization name UC Santa Cruz
Department MCD Biology
Street address 1156 High St
City Santa Cruz
State/province CA
ZIP/Postal code 95064
Country USA
 
Platform ID GPL13657
Series (2)
GSE85442 Comparison of transcriptomes of sig-7 (RNAi) vs WT C. elegans early stage embryos by RNA-seq
GSE85445 HTS comparison of sig-7 (RNAi) vs WT C. elegans early stage embryos
Relations
BioSample SAMN05559056
SRA SRX2011752

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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