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Sample GSM1022811 Query DataSets for GSM1022811
Status Public on Jun 01, 2013
Title N2_2
Sample type SRA
 
Source name C.elegans whole animal, Orsay virus infected, mixed stage
Organism Caenorhabditis elegans
Characteristics 5' end dependence: 5' Independent (RNA treated with 5' RNA polyphosphatase (Epicentre) for 30 minutes at 37C)
genotype: N2 (Bristol)
tissue: whole animal
Treatment protocol RNA was extracted from worms 4 days after infection with the Orsay virus using Trizol.
Growth protocol C. elegans were grown under standard conditions at 20C The food source used was E. coli strain HB101 (Caenorhabditis Genetics Center, University of Minnesota, Twin Cities, MN, USA). Uninfected animals were picked as L4s and virus laid onto the plates after 24hrs.
Extracted molecule total RNA
Extraction protocol cDNA libraries were prepared from total RNA using the Illumina Truseq protocol according to the manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina MiSeq
 
Data processing Adaptors were removed with Cutadapt ver 1.0
Fastq files were converted to fasta files using a custom perl script run in Perl version 5.8.12
Fasta files were collapsed using FastX toolkit
Collapsed fasta files were trimmed so that only reads with length of 15 nucleotides or above were included, using a custom perl script run in Perl version 5.8.12
Supplementary_files_format_and_content: collapsed fasta files with adaptors removed with the header sequence number-read count_sequence
 
Submission date Oct 18, 2012
Last update date May 15, 2019
Contact name Eric A. Miska
E-mail(s) e.miska@gurdon.cam.ac.uk
Phone 44-1223-767221
Organization name University of Cambridge
Department Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We
Lab Miska
Street address Tennis Court Rd
City Cambridge
ZIP/Postal code CB2 1QN
Country United Kingdom
 
Platform ID GPL15716
Series (1)
GSE41693 Analysis of small RNA response to viral infection in C.elegans
Relations
SRA SRX197345
BioSample SAMN01768069

Supplementary file Size Download File type/resource
GSM1022811_cutN2-3_S1_L001_R1_001.fasta.gz 9.1 Mb (ftp)(http) FASTA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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