GSM2220782: merged_Hyl-2-G3; Caenorhabditis elegans; RNA-Seq - SRA

SRX1889677: GSM2220782: merged_Hyl-2-G3; Caenorhabditis elegans; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 31.6M spots, 1.6G bases, 996.5Mb downloads

Submitted by: NCBI (GEO)

Study: Glucose or Altered Ceramide Biosynthesis Mediate Oxygen Deprivation Sensitivity Through Novel Pathways Revealed by Transcriptome Analysis in Caenorhabditis elegans

PRJNA327375 • SRP077649 • All experiments • All runs

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RNA-Seq analysis was performed to assess how a glucose-supplemented diet and/or a hyl-2 mutation altered the transcriptome. Comparison analysis of transcripts associated with anoxia sensitive animals (hyl-2(tm2331) mutation or a glucose diet) revealed 199 common transcripts encoded by genes with known or predicted functions involving innate immunity, cuticle function (collagens) or xenobiotic and endobiotic phase I and II detoxification system. Overall design: mRNA profiles of OP50-fed C. elegans, glucose-fed C. elegans (N2 strain), OP50-fed C. elegans altered in ceramide metabolism (due to a hyl-2(tm2031) mutation), and glucose-fed C. elegans altered in ceramide metabolism were generated by RNA-Seq, in triplicate, using an Illumina HiSeq2000. Transcriptome data were then used for a comprehensive quantitative analysis of differential gene regulation in hyl-2(tm2031) and glucose-fed C. elegans.

Sample: merged_Hyl-2-G3

SAMN05332106 • SRS1532791 • All experiments • All runs

Organism: Caenorhabditis elegans

Library:

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Construction protocol: 4 volumes of Trizol per volume of animals were added. The tubes were immediately frozen in liquid nitrogen, thawed and briefly vortexed; this step was repeated and then followed by a 5-minute incubation at room temperature. To each tube 0.2 ml of chloroform per 1 ml of Trizol was added, mixed gently, for 15 seconds, incubated at room temperature for 2-3 minutes, and then centrifuged at 12,000g for 15 minutes at 4ºC. The colorless upper phase was transferred to an RNase free tube. RNA was then purified using an Ambion PureLink RNA Mini Kit (Cat#12183018A). Following RNA purification, the RNA was treated with DNase I (Life Technologies Cat# 12185010), quantified using a NanoDrop Spectrophotometer and stored at -80ºC. RNA libraries were prepared for sequencing using standard Illumina protocols

Experiment attributes:

GEO Accession: GSM2220782

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 31.6M spots, 1.6G bases, 996.5Mb

Run	# of Spots	# of Bases	Size	Published
SRR3733903	31,563,788	1.6G	996.5Mb	2016-12-22

ID:: 2734676

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