|
| Status |
Public on Apr 15, 2021 |
| Title |
E11-C-18 |
| Sample type |
SRA |
| |
|
| Source name |
embryo cell
|
| Organism |
Macaca fascicularis |
| Characteristics |
tissue: embryo
development stage: E11
lineage: TE
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The single-cell was washed in 30µL micro-drop of PBS-BSA solution and individual cells were picked into 0.2mL PCR tubes by micropipette for modified Smart2-seq,all the cDNA were quantified on a 2100 Bioanalyzer (Agilent) and Qubit 3.0.
The scRNA-seq libraries were generated using the TruePrepTM DNA Library Prep Kit V2 for Illumina®(Vazyme) . Briefly, we use 5-50ng cDNA constructing the libraries according to the manufacturer’s instructions. cDNA molecules were preamplified and pooled followed by library construction. All libraries were quantified on a 2100 Bioanalyzer (Agilent) and realtime quantitative PCR, and then subjected to 150 bp paired-end sequencing on an Illumina Xten platform (sequenced by Novogene and Annoroad).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Chimera embryo cell of Macaca fascicularis
|
| Data processing |
fastp was used to cut adapters and quality control
human and monkey cells were identified by two ways using the clean data. One way is to compare the number of identical hits of sequencing reads from each cell by blastp with the random selected 10000 reads against the human and monkey genome (Ensembl Homo_sapiens.GRCh38 and Macaca_fascicularis_5.0), respectively. Another way is to compare the reads counts of sequencing reads mapped to tdTomato vector.
hisat2 was used to map sequencing reads to the human or monkey genome with the default parameters.
The program stringtie with default parameters was used to assembly alignments into potential transcripts
Quantify the gene expression as transcripts per million mapped reads (TPM) value by the program stringtie
Genome_build: Homo_sapiens.GRCh38 and Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text file include TPM matrix for all samples
|
| |
|
| Submission date |
Jul 29, 2020 |
| Last update date |
Apr 15, 2021 |
| Contact name |
shaoxing Dai |
| E-mail(s) |
daishx08@gmail.com
|
| Phone |
15287145159
|
| Organization name |
Kunming University of Science and Technology
|
| Street address |
No.1 boda road chenggong, Kunming 650500 Yunnan,China
|
| City |
昆明市 |
| State/province |
云南 |
| ZIP/Postal code |
650500 |
| Country |
China |
| |
|
| Platform ID |
GPL28212 |
| Series (1) |
| GSE155381 |
Chimeric contribution of human extended pluripotent stem cells to monkey embryos |
|
| Relations |
| BioSample |
SAMN15671334 |
| SRA |
SRX8846349 |
