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| Status |
Public on Mar 17, 2023 |
| Title |
CEF_2 |
| Sample type |
SRA |
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| Source name |
Embryonic fibroblasts
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| Organism |
Macaca fascicularis |
| Characteristics |
tissue: Embryonic fibroblasts
genotype: wildtype
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNAs were purified from 10,000 - 20,000 cells by using Nucleospin Tissue XS (Macherey-Nagel, 740901) and eluted in 10µL Elution buffer. DNA concentration was quantitated by using Qubit dsDNA HS assay kit (ThermoFisher Scientific) and 20-140 ng of gDNA were mixed with 1pg of pUP19 DNA and 20pg of unmethylated lambda DNA in 50µL total volume.
Genomic DNAs were fragmented by sonication using Covaris focused-sonicator E220 (peak incident power 140W, Duty factor 10%, Cycles per burst 200 and Treatment time 130 msec). The fragmented DNA samples were purified by two-rounds of Axygen beads purification (0.7×, then 0.9× volumes). Then, all fragments were applied to library construction using NEBNext Enzymatic Methy-seq Kit (New England Biolabs, E7120) according to manufacturer’s instructions. Library concentration and fragment size were evaluated with KAPA Library quantification kits (Nippon Genetics, KK4828) and Labchip GX Touch HT (Perkin Elmer).
Enzymatic Methyl-seq (EMseq)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
All reads were processed with Trim_galore v0.6.3 with default setting to remove adapter and low-quality sequences.
Processed reads were mapped on cynomolgus macFas5.0 or human GRCh38.p12 genome, using Bismark v0.22.1 and bowtie2 v2.3.4.1 with "-X 2000" option. Resulting BAM files were, then, processed with deduplicate_bismark to remove PCR duplicate, and methylation levels per CpG were calculated using bismark_methylation_extractor script, included in Biskmark package.
For allelic methylation analysis, EM-seq data were re-mapped on SNP masked macFas5.0 or GRCh38.p12 genome as described above.
BAM files after PCR duplicate removal were processed with SNPsplit v0.3.2 with "--paired" and "--bisulfite" options and masked macFas5.0 or GRCh38.p12 reference to split mapped reads into paternal and maternal alleles.
Resulting BAM files were processed with bismark_methylation_extractor script with "-p" and "--comprehensive" options
Assembly: macFas5.0 or GRCh38.p12
Supplementary files format and content: biskark report text
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| Submission date |
Oct 20, 2022 |
| Last update date |
Mar 17, 2023 |
| Contact name |
Yukihiro Yabuta |
| E-mail(s) |
yabyab@anat2.med.kyoto-u.ac.jp
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| Organization name |
Kyoto University, Graduate school of medicine
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| Department |
Anatomy and Cell Biology
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| Street address |
Yoshida-Konoe-cho, Sakyo-ku
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| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
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| Platform ID |
GPL28212 |
| Series (2) |
| GSE216202 |
Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys (EM-Seq) |
| GSE216206 |
Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys |
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| Relations |
| BioSample |
SAMN31390025 |
| SRA |
SRX17968954 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6661500_EMseq_CEF_2.CpG_report.txt.gz |
275.7 Mb |
(ftp)(http) |
TXT |
| GSM6661500_EMseq_CEF_2_maternal.CpG_report.txt.gz |
212.9 Mb |
(ftp)(http) |
TXT |
| GSM6661500_EMseq_CEF_2_paternal.CpG_report.txt.gz |
213.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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