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Sample GSM1577170 Query DataSets for GSM1577170
Status Public on Feb 09, 2015
Title PSG1 rep2
Sample type SRA
 
Source name Fertile hydatid cyst from the liver of naturally infected sheep
Organism Echinococcus granulosus
Characteristics genotype: G1
developmental stage: protoscoleces
extracted molecule: small RNAs (<200 nt)
Extracted molecule total RNA
Extraction protocol Protoscoleces and cyst walls were carefully recovered from fertile hydatid cysts obtained from the livers of naturally infected swine and sheep. Samples were frozen in liquid nitrogen and stored at -80ºC until RNA extraction. RNA enriched in small RNAs (<200 nt) was purified from protoscoleces and cyst walls using mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s instructions.
Libraries were prepared for sequencing using a NEBNext Small RNA Library Prep Set for Illumina (NEB) following the instruction’s manual with 1.5 μg of RNA enriched in small RNAs (<200 nt) as starting material.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer IIx
 
Data processing Base-calling performed with Illumina Casava 1.8 software.
small RNA-seq reads were trimmed for adaptor sequence and low quality reads were discarded. Then reads were mapped to E. multilocularis genome assembly v4 using bowtie (mapper module of miRDeep2 software package) with parameters -c -j -l 18 -m –p.
miRNA prediction was performed with the core algorithm of miRDeep2 software package using as input all metazoan mature miRNAs and hairpins along with mapped reads from the previous step.
Data were filtered using the following criteria: i) miRDeep2 score ≥ 4 ii) significant randfold p-value < 0.05 iii) mature reads in more than one library iv) presence of star strand v) rRNAs, tRNAs and CDS were removed.
Genome_build: Echinococcus multilocularis genome assembly version 4
Supplementary_files_format_and_content: tab-delimited text file include raw miRNA counts for each sample
 
Submission date Jan 06, 2015
Last update date May 15, 2019
Contact name Natalia Macchiaroli
Organization name IMPaM
Street address Paraguay 2155, 13th floor
City Buenos Aires
ZIP/Postal code C1121ABG
Country Argentina
 
Platform ID GPL18185
Series (1)
GSE64705 microRNA profiling in the zoonotic parasite Echinococcus canadensis using a high-throughput approach
Relations
BioSample SAMN03275920
SRA SRX831388

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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