 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 24, 2023 |
| Title |
Embryo_10 PS and derivative [DNA_batch2_sc12] |
| Sample type |
SRA |
| |
|
| Source name |
in vitro
|
| Organism |
Macaca fascicularis |
| Characteristics |
cell line: in vitro
cell type: Embryo
genotype: WT
time: E16
|
| Growth protocol |
The creation of cynomolgus monkey embryos including oocyte retrieval, intracytoplasmic sperm injection, and pre-implantation embryo culture were performed as described by Yamasaki et al (Nakamura et al., 2016). Briefly, female cynomolgus monkeys 7-10 years old with a successful reproductive history were used for mature oocyte collection by super-ovulation with follicle-stimulation hormone. The day collected oocytes were artificially fertilized by sperm injection was designated as embryonic day (E) 0. When the embryos developed to E6-E7, embryos with an expanded blastocoel (>75% volume of the embryo) were selected for further culture .
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The single-cell isolation procedures were performed according to the protocol previously described (Ma et al., 2019a). In brief, the pIVC cynomolgus embryos were dissected by removing the extraembryonic tissues, then the inner embryonic bodies were digested with 500 μL of 1 × TrypLE for 15 min at 37°C and dissociated into single cells by mouth pipetting. Advanced DMEM/F12 containing 10% FBS was added to terminate the enzymatic reaction and the cells were centrifuged at 300 g for 5 min at room temperature, followed by the resuspension with 100 μL pre-cold 0.1% BSA/PBS.
Single cells were individually picked into ice-cold lysis buffer under stereoscopic microscope. single cells were picked of each stage and then the subjected to construct scChaRM-seq library. The method of library construction was described in our recently published method (Yan et al., 2021). In brief, in vitro CpG methylation was performed by M.CviPI (New England Biolabs, NEB) supplemented with S-adenosyl-methionine (SAM;NEB) and terminated by adding RLT buffer (QIAGEN). Then the genome DNA and mRNA were separated by capturing mRNA with oligo(dT) primers conjugated beads (Invitrogen), the supernatant containing genomic DNA was transferred into another PCR tube to bisulfite conversion (Zymo Research) and DNA library construction using previously descried TAILS method (Gu et al., 2019). The captured mRNA was subjected correspondingly to cDNA synthesis, PCR amplification and library construction (Gu et al., 2019).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
20211020-YR-1-2_sc12
|
| Data processing |
Processing of the scChaRM-seq DNA data:Trim Galore (v0.4.4) was used to remove random primer sequences, low-quality bases and adaptor sequences from the single-cell bisulfite data. Only reads longer than 50 bp after trimming were retained for alignment. Then, clean reads were mapped to the monkey reference genome mf5 by Bismark (v0.7.6) in paired-end mode, and unmapped reads were re-aligned to the reference genome in single-end mode. Duplicate reads from PCR were removed by the SAMtools (v0.1.18) command “samtools rmdup”, and only nonduplicate reads were used to perform the downstream analysis. The GCH (G=A, T or C) and WCG (W=A or T) sites (≥1× sequencing depth) in each single cell were summed. Then, the chromatin accessibility and DNA methylation level were calculated as the average GCH or WCG level, respectively.
Genome_build: mf5
Supplementary_files_format_and_content: bedgraph files；RNAid_DNAid_celltype.csv
Assembly: mf5
Supplementary files format and content: bedgraph files;csv files
|
| |
|
| Submission date |
Nov 22, 2022 |
| Last update date |
Mar 26, 2023 |
| Contact name |
Fan Guo |
| E-mail(s) |
guofan@ioz.ac.cn
|
| Organization name |
Institute of Zoology, Chinese Academy of Sciences
|
| Department |
The State Key Laboratory of Stem Cell and Reproductive Biology
|
| Lab |
Group of Reproductive Epigenetics
|
| Street address |
1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL23096 |
| Series (2) |
| GSE218524 |
Neurulation of the cynomolgus monkey embryo achieved from 3D blastocyst culture [Bisulfite-Seq] |
| GSE218525 |
Neurulation of the cynomolgus monkey embryo achieved from 3D blastocyst culture |
|
| Relations |
| BioSample |
SAMN31833357 |
| SRA |
SRX18344008 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6749487_DNA_batch2_sc12.GCH.bedGraph.gz |
10.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM6749487_DNA_batch2_sc12.WCG.bedGraph.gz |
1.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
