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Sample GSM1429729

Query DataSets for GSM1429729

Status

Public on Jun 26, 2017

Title

EM-smallRNA-1

Sample type

SRA

Source name

hydatid cyst

Organism

Echinococcus multilocularis

Characteristics

larvel stage: protoscoleces

Extracted molecule

total RNA

Extraction protocol

For small RNA sequencing, an RNA preparation enriched in < 200nt RNAs was obtained from each sample using the mirVana miRNA Isolation Kit (Ambion, USA).
The 18-30nt fraction of total RNA was excised and purified following 15% Tris-Borate-EDTA (TBE) denaturing polyacrylamide gel electrophoresis (PAGE). Subsequently, proprietary adapters were ligated to the 5’ and 3’ termini of the RNA using T4 RNA ligase respectively. The adaptor-ligated small RNAs were subjected to RT-PCR amplification, and after the cDNA was further amplified, the PCR products (90bp, small RNA+ adaptors) were purified using PAGE. Two biological replicate small RNA libraries were constructed for each species and were sequenced on Illumina HiSeq™ 2000 Sequencing System at the Beijing Genomics Institute (BGI), Shenzhen, P.R.China.

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina HiSeq 2000

Description

Sample 3

Data processing

For small RNA sequencing, the unique reads were mapped onto the E.granulosus and E.multilocularis genomes respectively, using the program Bowtie."Contaminations" were removed by screening the unique reads against non-coding RNA database (Release 10), using Bowtie.
To identify potential conserved miRNA sequences, the remaining perfectly matched reads were Blast-searched against the Metazoa mature miRNA of Sanger miRBase(Release 20) using the program Patscan.
For novel miRNA prediction,software Einverted of Emboss (v6.5.7.0) was used to find the inverted repeats the secondary structure of the inverted repeat was predicted by RNAfold (ViennaRNA, v1.8.5). Unique reads in the inverted repeats were evaluated by MirCheck.
IDEG6 was used to identify miRNAs showing statistically significant difference in relative abundance (as reflected by total count of individual sequence reads) between the two small RNA libraries from E.granulosus and E.multilocularis.
Genome_build: E. granulosus and E. multilocularis genome v3 downloaded from http://www.sanger.ac.uk/
Supplementary_files_format_and_content: The .xlsx file reports abundance measurements.

Submission date

Jul 08, 2014

Last update date

May 15, 2019

Contact name

xiaosu zhou

E-mail(s)

xiaosu_joe@163.com

Organization name

Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

Street address

Dong Dan San Tiao 9