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| Status |
Public on Jun 01, 2021 |
| Title |
T11.WGS |
| Sample type |
SRA |
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| Source name |
T. zimbabwensis
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| Organism |
Trichinella zimbabwensis |
| Characteristics |
strain: ISS1029
passages: Muscle larvae
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the phenol chloroform extraction method.
High molecular DNA from 12 Trichinella genotypes were extracted from freshly collected muscle larvae. Qubit Fluorometer dsDNA HS Kit (Invitrogen) was used to determine total DNA amounts, followed by measurement of integrity by by agarose gel electrophoresis and using a BioAnalyzer (2100, Agilent). Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform, according to instructions provided by Illumina.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Library strategy: WGS
FastQC (v0.11.7) was used to assess the quality of sequence reads.
Adapters and low-quality reads were removed from raw sequencing reads by Trimmomatic (v0.36) using following paramaters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:75
Clean reads from each species were mapped to respective reference genome after quality control, and then conduct SNP calling using GATK workflow.
MUMmer (v3.0) was used to examine all the single nucleotide polymorphism (SNPs) between reference genomes of T. pseudospiralis and other eleven Trichinella species. SNPs from uniquely aligned regions and with homozygous genotypes constituted the final set of SNVs.
Genome_build: The genomic data resources of the twelve Trichinella species were downloaded from NCBI BioProject database with the following accession codes: PRJNA12603 for T. spiralis, PRJNA451013 for T. pseudospiralis, and PRJNA257433 for other ten Trichinella species.
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| Submission date |
Mar 23, 2021 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Yayan Feng |
| E-mail(s) |
[email protected]
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| Phone |
13161164012
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| Organization name |
Chinese Academy of Agricultural Sciences
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| Lab |
Genome Analysis Laboratory of the Ministry of Agriculture
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| Street address |
No. 7 pengfei road, dapeng new district, shenzhen
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| City |
Shenzhen,Guangdong Province,China |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
518000 |
| Country |
China |
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| Platform ID |
GPL29908 |
| Series (2) |
| GSE140384 |
Three life stages |
| GSE169404 |
WGS data to conduct phylogenetic analysis in Trichinella |
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| Relations |
| BioSample |
SAMN18437661 |
| SRA |
SRX10417622 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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