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Sample GSM7670821 Query DataSets for GSM7670821
Status Public on Aug 01, 2023
Title ICSI-TE-WGBS-rep1
Sample type SRA
Source name trophoblast
Organism Macaca fascicularis
Characteristics tissue: trophoblast
cell line: trophoblast
cell type: embryo trophoblast cells
genotype: wild type
treatment: ICSI
Extracted molecule genomic DNA
Extraction protocol ICSI and SCNT trophoblast cells were seeded into lysis buffer by mouth pipette and subjected to bisulfite conversion using the EZ DNA Methylation Direct Kit.
Each replicates containing trophoblast cells obtained from 6~8 blastocysts were collected for the library construction. A small amount of unmethylated Lambda DNA (Promega, D152A) was added to each sample before bisulfite conversion to serve as spike-in controls for evaluating bisulfite conversion efficiency. After column-based purification, DNA was complemented with the random primer Preamp and Klenow polymerase (Enzymatics, P7010-HC-L). This random priming was repeated five times in total. Second strands were synthesized using another random primer, Adapter 2. Final libraries were generated after PCR amplification with the Illumina universal PCR primer and Illumina indexed primer, and were then purified using SPRI beads. Final libraries were subjected to paired-end 150 bp sequencing on a NovaSeq 6000 sequencer (Illumina) with PhiX spike-in control.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model MGISEQ-2000RS
Description ICSI
Data processing The raw sequencing reads were trimmed by trim_galore with default parameters to remove low-quality bases and adapters in paired-end reads.
The remaining reads of were aligned to the Macaca fascicularis genome (macFas5) using Bismark with the parameter “--non_directional”.
After merging the pair end bam files of each sample into a single bam file, the single bam file was sorted.
Then, deduplication was performed using bismark.
The methylation level and coverage depth of each cytosine were extracted from the aligned reads with bismark_methylation_extractor.
The bedGraph files resulted from bismark_methylation_extractor was converted to BW files using bedGraphToBigWig software.
The resulted CpG_report.txt files containing DNA methylation levels were used to subsequent analysis in R.
Assembly: macFas5
Supplementary files format and content: The tab-delimited txt files containing the DNA methylation peaks of CpGs of the corresponding samples.
Submission date Aug 01, 2023
Last update date Aug 01, 2023
Contact name Liao Zhaodi
Phone 17521632708
Organization name Chinese Academy of Sciences
Department Institute of Neuroscience
Street address 500, Qiangye Road
City Shanghai
ZIP/Postal code 2016000
Country China
Platform ID GPL33633
Series (2)
GSE239742 A somatic cell cloned rhesus monkey obtained by trophoblast replacement [WGBS II]
GSE239746 A somatic cell cloned rhesus monkey obtained by trophoblast replacement
BioSample SAMN36780576
SRA SRX21206137

Supplementary file Size Download File type/resource
GSM7670821_ICSI1.merge.sort.deduplicated.CpG_report.txt.gz 247.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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