|
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.
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|
|
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
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|
|
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 |