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Sample GSM847430 Query DataSets for GSM847430
Status Public on Dec 10, 2011
Title wild type, 68 h, untreated
Sample type SRA
 
Source name Whole worms, adult, untreated
Organism Caenorhabditis elegans
Characteristics strain: N2
genotype: wild type
tissue: whole body
developmental stage: adult
treatment: none
Growth protocol Animals were grown at 20˚C on E. coli strain OP50.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from synchronized animals, and small RNAs were size selected, either treated with sodium periodate followed by beta elimination or untreated, tobacco acid pyrophosphatase (TAP)-treated to remove 5' di- and triphosphate groups, ligated to 3' and 5' adapters and subjected to RT-PCR.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Description Small RNA
Data processing Raw datasets are fastq files generated using Illumina software. The sequence of the 3' adapter used during library preparation is 5'-TGGAATTCTCGGGTGCCAAGG. For processed datasets, small RNA sequences were parsed from fastq files using CASHX v. 2.0 with a Q value threshold of 20. Sequences were not filtered for alignment to a genome. Tab-delimited files containing unique sequences and corresponding read counts were generated using custom Perl scripts.
 
Submission date Dec 09, 2011
Last update date May 15, 2019
Contact name Taiowa Montgomery
E-mail(s) montgomery@molbio.mgh.harvard.edu
Phone (617) 643-3319
Organization name Massachusetts General Hospital
Department Molecular Biology
Lab Ruvkun
Street address 185 Cambridge Street, CPZN-7250
City Boston
State/province MA
ZIP/Postal code 02114-2790
Country USA
 
Platform ID GPL13657
Series (2)
GSE34321 Analysis of 3' 2'-O-methylated small RNAs in Caenorhabditis elegans
GSE35550 Analysis of 22G siRNA triggered siRNA amplification and 3' 2'-O-methylated small RNAs in Caenorhabditis elegans
Relations
SRA SRX111400
BioSample SAMN00765491

Data table header descriptions
SEQUENCE Sequence read
COUNT Read count

Data table
SEQUENCE COUNT
AAAAAAAAAAAAAAAAATTTTTTTTTT 1
AAAAAAAAAAAAAAAATTTTTTTTTTT 1
AAAAAAAAAAAAAAATTTTTTTTTTTGTATGCA 1
AAAAAAAAAAAAAATTTTTTGTTCCGAAAAAAA 1
AAAAAAAAAAAAAATTTTTTTTTTT 1
AAAAAAAAAAAAAATTTTTTTTTTTTTTTT 1
AAAAAAAAAAAAAATTTTTTTTTTTTTTTTT 1
AAAAAAAAAAAAAATTTTTTTTTTTTTTTTTT 1
AAAAAAAAAAAAACACACACGTTTTTTTTTTGA 1
AAAAAAAAAAAAATTTTTTTTTTTTTTTAA 1
AAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTT 1
AAAAAAAAAAAAGACGATCATGTTTGAC 1
AAAAAAAAAAAAGCTTTTTTTTTGAAAATTTTT 1
AAAAAAAAAAAATTTTTTTTTTTTATCCACTATT 1
AAAAAAAAAAAATTTTTTTTTTTTTTT 1
AAAAAAAAAAAATTTTTTTTTTTTTTTTCAACAT 1
AAAAAAAAAAACAATTTTTTTTTCGAAAGCGT 1
AAAAAAAAAAAGAATATTTTTTTTGAATCTAGT 1
AAAAAAAAAAAGTATTTTTTTCTTTTTTTTT 1
AAAAAAAAAAAGTTTTTTTTTTTTTTTTTT 1

Total number of rows: 4481545

Table truncated, full table size 108974 Kbytes.




Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data included within Sample table

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