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| Status |
Public on Sep 07, 2015 |
| Title |
WT_L2_TotalRNA_rep2 |
| Sample type |
SRA |
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| Source name |
Total RNA
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: Wild type
developmental stage: L2
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| 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
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| 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
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
small RNA profiling
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| 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.
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| Submission date |
Sep 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Isana Veksler-Lublinsky |
| Organization name |
University of Massachusetts Medical School
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| Department |
Molecular Medicine
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| Lab |
Ambros
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| Street address |
373 Plantation Street
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| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01655 |
| Country |
USA |
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| Platform ID |
GPL13776 |
| Series (1) |
| GSE72659 |
Caenorhabditis elegans ALG-1 antimorphic mutations uncover functions for Argonaute in microRNA guide strand selection and passenger strand disposal |
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| Relations |
| BioSample |
SAMN04027343 |
| SRA |
SRX1178652 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1867447_WT_L2_TotalRNA_rep2.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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