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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 07, 2021 |
| Title |
Monkey_Cerebellum_mCG |
| Sample type |
SRA |
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| Source name |
Cerebellum
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| Organism |
Macaca fascicularis |
| Characteristics |
tissue: Cerebellum
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The methylome extraction is majorly based on post-bisulfite adaptor tagging (PBAT). DNA from tissues are extracted by phenol/chloroform/isoamylalcohol followed by isopropanol precipitation. Then extracted DNA was mixed with lambda DNA (1:200) and subjected to sodium bisulfite conversion using the Zymo EZ DNA Methylation-Direct Kit (Zymo Research) following the manufacturer’s instruction. The eluted bisulfite-converted DNA was then subject to preamplification by Klenow exo- with adaptor-marked oligos on both strands. Then, the double-tagged DNA was purified by SPRIbeads and amplified using KAPA HiFi Uracil+ ReadyMix (Kapa Biosystems) and NEBNext Multiplex Oligos for Illumina (New England BioLabs).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
genome build: macFas5
For PBAT libraries, the paired-end sequenced reads were mixed and processed as single-end sequenced reads. Adaptors were firstly trimmed by Trim Galore with parameters --dont_gzip --clip_R1 9 --three_prime_clip_R1 9. Adaptor trimmed reads were mapped to macFas5 using Bismark (v0.20.0) using parameters --fastq -L 30 -N 1 --non_directional. Duplicated reads were removed using Picard MarkDuplicates and methylated CpGs were interpreted by bismark_methylation_extractor with parameters -s --no_overlap --report --bedGraph. For calculating of 5mC levels at base resolution, a cutoff of minimal 3× coverage was required for each CpG site. The 5mC levels for certain CpG was calculated using the number of methylated CpGs to divide the number of total CpGs detected on this CpG site.
Tab-delimited text files for bisulfite-seq including the average mCG level in 200bp bins.
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| Submission date |
Oct 10, 2020 |
| Last update date |
Sep 08, 2021 |
| Contact name |
Wenhao Zhang |
| E-mail(s) |
zwhonep2@gmail.com
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| Phone |
+1 617-784-1683
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| Organization name |
Harvard Medical School
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| Department |
Genetics
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| Lab |
Yi Zhang
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| Street address |
Warren Alpert Bldg, Rm 160, 200 Longwood Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL20302 |
| Series (1) |
| GSE159347 |
Analysis of developmental imprinting dynamics in primates using SNP-free methods to identify imprinting defects in cloned placenta |
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| Relations |
| BioSample |
SAMN16410210 |
| SRA |
SRX9275492 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4827043_Monkey_Cerebellum_mCG.txt.gz |
73.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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