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Sample GSM8379870 Query DataSets for GSM8379870
Status Public on Jul 17, 2024
Title pup-4(om141)_sRNA-seq_rep3
Sample type SRA
 
Source name whole animal
Organism Caenorhabditis elegans
Characteristics tissue: whole animal
cell line: NA
cell type: NA
genotype: pup-4(om141)
developmental stage: 1-day adult
gender: hermaphrodite
Growth protocol 1-day old adult hermaphrodites raised at 22°C
Extracted molecule other
Extraction protocol RNA was isolated from whole animals using the TRIzol (Invitrogen) method.
Treated with RNA 5' polyphosphatase; libraries generated with NEBNext Small Library Prep Kit.
 
Library strategy ncRNA-Seq
Library source other
Library selection size fractionation
Instrument model Illumina MiSeq
 
Description pup4_sRNA_rep3
Data processing Read were trimmed and quality-controlled using cutadapt with the parameters ‘-a AGATCGGAAGAGCACACGTCTGAACTCCAGTC -q 20 -m 15 -M 26’. Mapping was performed with HISAT2 using the c_elegans.PRJNA13758.WS284.genomic.fa reference genome and sorted BAM files were used as input into smalldisco. miRNAs and piRNAs were extracted from c_elegans.PRJNA13758.WS272.canonical_geneset.gtf and the file was converted into a BED file using BEDOP’s gft2bed command. The sorted BAM files, BED reference, and c_elegans.PRJNA13758.WS284.genomic.fa reference were used as input for smalldisco’s tail function using the ‘--tails-all’ to map the reads as sense to strand for miRNAs and piRNAs. For siRNAs, the sorted BAM files and c_elegans.PRJNA13758.WS272.canonical_geneset.gtf reference were supplied for the sirna function (smalldisco) with the parameter ‘-f CDS’. The output of this was used as input with smalldisco’s tail function, along with the c_elegans.PRJNA13758.WS284.genomic.fa reference. Counts tables were imported into R and processed to produce a matrix that combines the miRNA, piRNA, and siRNA counts (regardless of tail type).
Assembly: C. elegans WS284
Supplementary files format and content: Total counts (not parsed by tail type or sRNA biotype) in a matrix
 
Submission date Jul 05, 2024
Last update date Jul 17, 2024
Contact name Eleanor Maine
E-mail(s) [email protected]
Organization name Syracuse University
Department Biology
Street address 107 College Place
City Syracuse
State/province New York
ZIP/Postal code 13210
Country USA
 
Platform ID GPL15716
Series (1)
GSE271568 Sequencing experiments on poly(U) polymerase mutants in C. elegans [srna]
Relations
BioSample SAMN39507816
SRA SRX23314843

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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