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Sample GSM1429751

Query DataSets for GSM1429751

Status

Public on Jun 26, 2017

Title

EM-mRNA-1

Sample type

SRA

Source name

hydatid cyst

Organism

Echinococcus multilocularis

Characteristics

larvel stage: protoscoleces

Extracted molecule

total RNA

Extraction protocol

Total RNA from the parasites was purified with Trizol reagent and contaminating gemomic DNA was removed by the RNase-Free DNase Set. Polyadenylated RNA were isolated from total RNA.
The mRNA was interrupted into short fragments by adding fragmentation buffer as described (Illumina RNA-seq kit, part no. 1004898). Taking these short fragments as templates, random hexamer primers were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified and double strand cDNAs were end-repaired according to manufacturer-recommended protocols (https://icom.illumina.com/), and then were connected with Illumina adapters (Illumina RNA-seq kit, part no. 1004898). The fragments were first amplified by PCR. Purified cDNA fragments were pooled and indexed and were loaded onto one lane of an Illumina HiSeq™ 2000 instrument. Pair-end 100 sequencing cycles were carried out.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

Sample 3

Data processing

For mRNA sequencing,low quality and adapter sequences were removed from the Illumina reads by an in-house Perl script.
For mRNA sequencing,high-quality reads were mapped onto the E. granulosus and E. multilocularis genome v3 downloaded from http://www.sanger.ac.uk/ by tophat v2.0.4.
mRNA transcript sequences were assembled by Cufflinks v2.0.2. Then Cuffdiff was used to find significant changes of expression.
Functional annotation and classification were analysed by using KEGG and Gene Ontology databases.
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 FPKMs.

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