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Sample GSM1867444 Query DataSets for GSM1867444
Status Public on Sep 07, 2015
Title WT_L2_TotalRNA_rep1
Sample type SRA
 
Source name Total RNA
Organism Caenorhabditis elegans
Characteristics strain: Wild type
developmental stage: L2
Growth protocol C. elegans culture was performed using standard nematode growth conditions, except the HB101 Escherichia coli strain was used as the food source. All strains were grown at 20 °C. Because of their strong heterochronic phenotypes, alg-1(anti) mutant animals often burst through the vulva during the L4-adult molt (31). Therefore, alg-1(anti) mutations were maintained in a lin-31(n1053) genetic background that impairs vulva development and thereby suppresses the bursting phenotype of alg-1 mutants, while leaving their heterochronic phenotypes intact. The adult-specific col-19::gfp reporter transgene is also present in all of the strains. Therefore, the alg-1(anti) strains used here contain lin-31; col-19::gfp, and in all experiments the wild-type controls were lin-31(n1053); col-19::gfp
Extracted molecule total RNA
Extraction protocol Whole animal pellets were dounced, the resulting lysates were clarified. Total RNA or RNA that co-immunoprecipitated with anti-ALG-1 antibody was subsequently used for library preparations.
Libraries were prepared according to Gu W, Claycomb J, Batista P, Mello C, Conte D (2011) in Methods in Molecular Biology, eds Hobman TC, Duchaine TF (Humana Press), pp 251–280–280 using the primers appropriate for each sequencing instrument (Illumina GAIIx or Illumina Nextseq500)
Total small RNA or ALG-1 co-immunoprecipitated small RNA
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Description small RNA profiling
Data processing Sequencing files in FastQ format were processed using the Fastx toolkit to remove the 3' adapter sequences (CTGTAGGCACCATCAAT) and split the reads according to the 5' 4 nt barcode sequences.
Reads shorter than 17 nt ang longer then 40 nt were removed.
Reads with identical sequences were combined.
Reads were than aligned to the Caenorhabditis elegans genome (WormBase release WS215) using bowtie with arguments, -v 3 -f -B 1 -a–best –strata
Alignments were then filtered based on the length of the read and the number of mismatches as follows: for sequence lengths 17, 18–19, 20–24, or >24: zero, one, two, or three mismatches were allowed, respectively.
Genome_build: WS215
Supplementary_files_format_and_content: The tab delimeted text files contain unique sequence reads of smallRNA with counts for each sequence.
 
Submission date Sep 02, 2015
Last update date May 15, 2019
Contact name Isana Veksler-Lublinsky
Organization name University of Massachusetts Medical School
Department Molecular Medicine
Lab Ambros
Street address 373 Plantation Street
City Worcester
State/province MA
ZIP/Postal code 01655
Country USA
 
Platform ID GPL19757
Series (1)
GSE72659 Caenorhabditis elegans ALG-1 antimorphic mutations uncover functions for Argonaute in microRNA guide strand selection and passenger strand disposal
Relations
BioSample SAMN04027340
SRA SRX1178649

Supplementary file Size Download File type/resource
GSM1867444_WT_L2_TotalRNA_rep1.txt.gz 21.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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