GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3519086 Query DataSets for GSM3519086
Status Public on Aug 02, 2020
Title Oocyte_1 [CLEVER-seq]
Sample type SRA
Source name Oocyte
Organism Homo sapiens
Characteristics developmental stage: MII oocyte
Extracted molecule genomic DNA
Extraction protocol The CLEVER-seq experiment was carried out according to the previous study with slight modification. The single cells of human early embryo were transferred into lysis buffer (20 mM Tris, 2 mM EDTA, 20 mM KCl, and 0.3% TritonX-100, 1 mg/ml QIAGEN protease) by mouth pipette. After centrifugation (1 min at 7,000 r.p.m., 4°C), the sample was incubated at 50°C for 3 hr to release the genomic DNA followed by 70°C for 30 min to inactive the protease. Then trace mount of spike-in oligo DNA contain 5fC modification was added into sample. In order to label the 5fC, 150 mM malononitrile (J&K) was used. Mineral oil (15 μl) was add onto the surface of the sample to prevent evaporation. The sample was incubated at 37°C for 20 hr with constant shaking at 850 r.p.m. in the Thermomixer (Eppendorf). Then the single cell genome was amplified by MALBAC (Yikon Genomics) according to the user guide.
The genomic DNA was fragment into ~300 by by covaris S2. The library construction was performed using KAPA Hyper Prep Kit (Kapa Biosystems). The libraries were sequenced on Illumina Hiseq 4000 platform in pair-end 150 bp model (Novogene).
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
Data processing Library strategy: CLEVER-seq
Illumina CASAVA version 1.8 were used to the basecalling.
We used Trim Galore (v0.3.3) to remove adaptors and low quality bases.
Next, reads passed quality control were mapped to human reference genome (version: hg19) using Bismark (v0.13.0). After alignment, PCR duplicates were removed with the command ‘samtools rmdup’ (v0.1.18).
Genome_build: hg19
Supplementary_files_format_and_content: The processed bed files include chromosome, start position, end position, reference genotype, regular CpG ("0") or 5fCpG ("1"), strand.
Submission date Dec 18, 2018
Last update date Aug 02, 2020
Contact name Lin Li
Organization name Southern Medical University
Department Pathophysiology
Street address Shatai South Road
City Guangzhou
ZIP/Postal code 510515
Country China
Platform ID GPL20301
Series (1)
GSE124035 5-Formylcytosine Landscapes of Human Preimplantation Embryos at Single-cell Resolution
BioSample SAMN10611259

Supplementary file Size Download File type/resource
GSM3519086_Oocyte_1.bed.gz 34.3 Mb (ftp)(http) BED
Processed data provided as supplementary file
Raw data not provided for this record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap