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Sample GSM994476 Query DataSets for GSM994476
Status Public on Jun 01, 2013
Title N2 F2
Sample type SRA
 
Source name C.elegans whole animal, young adult
Organism Caenorhabditis elegans
Characteristics strain/line: N2
tissue: whole animal
developmental stage: young adult
genotype/variation: wild type
generation: F2
Treatment protocol Synchronized worms were collected as young adults by washes in M9 and worm pellets were snap-frozen in liquid Nitrogen.
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). We used bleaching followed by starvation-induced L1 arrest to generate synchronized cultures. The wild-type strain was Bristol N2.
Extracted molecule total RNA
Extraction protocol cDNA libraries were prepared by Vertis Biotechnologie AG (Martinsried). Briefly total RNA was extracted using the mirVana miRNA isolation kit (Ambion). Small RNAs were size selected to ~18-30 nucleotides by denaturing polyacrylamide gel fractionation. cDNA libraries that did not depend on 5'-monophosphates were constructed by tobacco acid pyrophosphatase treatment using adapters recommended for Illumina sequencing as described previously (Das et al. 2008). Each sample was labelled with a unique four base pair barcode. cDNA was purified using the NucleoSpin Extract II kit (Macherey & Nagel).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Description Sample8.fa
Data processing Custom Perl scripts were used for processing and run with Perl v5.10.1. Fastq entries with missing bases or barcodes not matching any of the expected sequences were excluded. Reads were trimmed by removing 5' barcodes (if applicable) and any 3'As. Inserts with length outside the relevant size range (18-30 nucleotides) were excluded.
Supplementary_files_format_and_content: collapsed fasta files showing unique sequences.
 
Submission date Aug 29, 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 GPL13657
Series (2)
GSE40457 Transgenerational profiling of small non-coding RNAs in C.elegans RSD mutants
GSE40460 RSD-2 and RSD-6 promote germ cell immortality by repressing spermatogenesis and repeat loci via small interfering RNAs
Relations
SRA SRX181334
BioSample SAMN01141255

Supplementary file Size Download File type/resource
GSM994476_Sample8.fa.gz 12.9 Mb (ftp)(http) FA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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