|
| Status |
Public on Sep 05, 2022 |
| Title |
stage E18 embryo 2 section 3 sector 4 |
| Sample type |
SRA |
| |
|
| Source name |
Crab-eating macaque embryonic cells
|
| Organism |
Macaca fascicularis |
| Characteristics |
developmental stage: E18
tissue: embryo
|
| Treatment protocol |
Sample from sections were laser-microdissected and collected for single-cell based RNA sequencing.
|
| Growth protocol |
Embryos of gastrulating Crab-eating macaque embryos were embedded with OCT and subjected to cryosection.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using Vayzme TD503 DNA sample preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
E18S2_3-4
|
| Data processing |
Sequencing quality of raw sequencing data was evaluated by fastp
The genome sequence Macaca_fascicularis_5.0 for Crab-eating macaque (Macaca fascicularis)) were obtained from the Ensemble (https://asia.ensembl.org/index.html). Reads were mapped to the Macaca_fascicularis_5.0 genome assemblies by HISAT2 using default settings.
All mapped reads were processed by StringTie to quantify gene expression levels (measured by TPM , Transcripts Per Kilobase per Million mapped reads) using default parameters.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each samples
|
| |
|
| Submission date |
Aug 26, 2021 |
| Last update date |
Sep 05, 2022 |
| Contact name |
Cui Guizhong |
| E-mail(s) |
cui_guizhong@gzlab.ac.cn
|
| Organization name |
Guangzhou Laboratory
|
| Department |
Center of Cell Lineage and Atlas
|
| Lab |
Center of Cell Lineage and Atlas
|
| Street address |
188 KaiYuan Road, Huangpu District
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510530 |
| Country |
China |
| |
|
| Platform ID |
GPL28212 |
| Series (1) |
| GSE182838 |
Geography and molecular anatomy of germ layers in the gastrulating primate embryo |
|
| Relations |
| BioSample |
SAMN20990140 |
| SRA |
SRX11919163 |
