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| Status |
Public on Jul 17, 2024 |
| Title |
pup-1(tm1021)_sRNA-seq_rep3 |
| Sample type |
SRA |
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| Source name |
whole animal
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| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole animal
cell line: NA
cell type: NA
genotype: pup-1(tm1021)
developmental stage: 1-day adult
gender: hermaphrodite
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| Growth protocol |
1-day old adult hermaphrodites raised at 22°C
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| 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.
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| Library strategy |
ncRNA-Seq |
| Library source |
other |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
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| Description |
pup1_sRNA_rep3
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| 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
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| Submission date |
Jul 05, 2024 |
| Last update date |
Jul 17, 2024 |
| Contact name |
Eleanor Maine |
| E-mail(s) |
[email protected]
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| Organization name |
Syracuse University
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| Department |
Biology
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| Street address |
107 College Place
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| City |
Syracuse |
| State/province |
New York |
| ZIP/Postal code |
13210 |
| Country |
USA |
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| Platform ID |
GPL15716 |
| Series (1) |
| GSE271568 |
Sequencing experiments on poly(U) polymerase mutants in C. elegans [srna] |
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| Relations |
| BioSample |
SAMN39507807 |
| SRA |
SRX23314852 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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