|
| Status |
Public on Mar 24, 2023 |
| Title |
Embryo,E16,RNA_batch3 |
| 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 |
total RNA |
| 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.
An RNA-seq library was prepared by following the instruction manual of the NEBNext UltraII DNA Library Prep Kit for Illumina (New England Biolabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
20210303-YHY-1-3
|
| Data processing |
Processing of the single-cell RNA-seq data ：The raw data was trimmed with Cutadapt (v1.15). Clean reads for individual cells were then classified according to the cell barcodes on Read#2. Then, Read#1 was mapped to the mf5 genome using STAR (v2.6.0a) with the default parameters. The transcript copy number of each gene was determined with HTseq (v0.10.0) after de-duplication based on unique molecular identifiers (UMIs). Then, cells with low complexity (fewer than 500 detected genes) were excluded. High-quality data containing 3,682 cells from scChaRM-seq were retained for further analyses.
Genome_build: mf5
Supplementary_files_format_and_content: counts.csv: Count matrix in tab-separated value files; meta.csv: annotations of cells processed by scChaRM-seq.
Assembly: mf5
Supplementary files format and content: tab-delimited text files include counts for each cell
|
| |
|
| Submission date |
Nov 22, 2022 |
| Last update date |
Mar 24, 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) |
| GSE218523 |
Neurulation of the cynomolgus monkey embryo achieved from 3D blastocyst culture [RNA-Seq] |
| GSE218525 |
Neurulation of the cynomolgus monkey embryo achieved from 3D blastocyst culture |
|
| Relations |
| BioSample |
SAMN31833330 |
| SRA |
SRX18343954 |
