|
| Status |
Public on Jun 01, 2021 |
| Title |
T5.WGBS.ML |
| Sample type |
SRA |
| |
|
| Source name |
T. murrelli
|
| Organism |
Trichinella murrelli |
| Characteristics |
tag: ISS417
tag: Muscle larvae
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the phenol chloroform extraction method
Genomic DNA extracted from three life stages of all Trichinella species were selected for libraries construction of WGBS. Briefly, approx. two to five micrograms of gDNA were first fragmented by Covaris to an average size of ~200-300 bp. End-repair, A-tailing and ligation were conducted as the Illumina PE genomic DNA sample prep kit protocol, except that ligation was performed using methylated cytosine PE adapters provided by Illumina previously. Ligation products were purified and bisulfited converted using the EZ DNA Methylation-Gold KitTM (ZYMO) according to the manufacturer’s instructions. The libraries were sequenced using Illumina HiSeq 2,500 platform.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
T5
|
| Data processing |
Raw sequencing reads with more than 30% ‘N’s in over 10% of the sequences or smaller than 30 bp were discarded
Clean reads were aligned to the corresponding reference genome using BSMAP (v2.73) with a of maximal four mismatches and gap size up to 2 nucleotides
Methylation level of each cytosine was calculated as the number of reads ascertained methylated to the total number of reads for each covered CpG sites.
To accurately investigate the methylation levels in each sample, we used CpG sites with a minimal 5× sequencing depth per strand.
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: cout, bed format
|
| |
|
| Submission date |
Oct 28, 2019 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Yayan Feng |
| E-mail(s) |
[email protected]
|
| Phone |
13161164012
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Lab |
Genome Analysis Laboratory of the Ministry of Agriculture
|
| Street address |
No. 7 pengfei road, dapeng new district, shenzhen
|
| City |
Shenzhen,Guangdong Province,China |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
518000 |
| Country |
China |
| |
|
| Platform ID |
GPL27664 |
| Series (2) |
| GSE139486 |
12 single-base resolution methylomes of three life stages using WGBS |
| GSE140384 |
Three life stages |
|
| Relations |
| BioSample |
SAMN13140920 |
| SRA |
SRX7064721 |
