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Sample GSM4693933 Query DataSets for GSM4693933
Status Public on May 14, 2021
Title pir1_tm3198_7day_rep1
Sample type SRA
 
Source name small RNA in 7-day pir-1 mutant
Organism Caenorhabditis elegans
Characteristics genotype: pir-1 (tm3198)
tissue: whole worm
rna fraction: All RNA
Treatment protocol For cloning ppp-RNAs, the sample is treated with 0.5 μM PIR-1 at 20 °C for 2 hours and for cloning only p-RNAs, no PIR-1 is required.
Growth protocol Worms were grown on NGM or Ivermectin-containing NGM plates with OP50 at 20 °C.
Extracted molecule total RNA
Extraction protocol RNAs were extracted with TRIzol
RNAs were linked with Truseq LT/V1/V2 linkers using the standard 5' and 3' ligation methods. Amplicons with ~20 nt inserts were selected for sequencing. The samples were multiplexed with 8 nt indexes in the 3' linker. Please refer to Li L et al. RNA. 2020 Feb;26(2):218-227.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer II
 
Data processing The samples are debarcoded using the 8 nt barcodes
The 3' AGATCGGAA and beyond are removed and only reads of size >16 are kept
Small RNAs are mapped to genome and cDNA using Bowtie 0.12.7 and at most 2 mismatches are considered
Genome_build: C. elegans WS215
Supplementary_files_format_and_content: tabbed txt file containing sequence and read number for the analysis
 
Submission date Jul 24, 2020
Last update date May 15, 2021
Contact name Weifeng Gu
Organization name University of California at Riverside
Department Molecular, Cell and Systems Biology
Lab Weifeng Gu
Street address 900 University Ave
City Riverside
State/province California
ZIP/Postal code 92521
Country USA
 
Platform ID GPL9269
Series (1)
GSE150690 The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans
Relations
BioSample SAMN15638036
SRA SRX8817765

Supplementary file Size Download File type/resource
GSM4693933_pir1_tm3198_7day_rep1_processed.txt.gz 2.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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