|
| Status |
Public on Oct 17, 2023 |
| Title |
TO_3084 |
| Sample type |
SRA |
| |
|
| Source name |
Bilaminoid D9 (Blimp1-tdTomato+/TFAP2C-GFP+)
|
| Organism |
Homo sapiens |
| Characteristics |
analysis method: scRNA-seq
cell line: 585B1 iPSCs
cell type: Bilaminoid Day9
transgenes: Blimp1-tdTomato, TFAP2C-EGFP
protocol: FACS:Blimp1-tdTomato and TFAP2C-EGFP+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bilaminoids (D6) were manually picked. Each bilaminoid was transferred in a drop of Accutase and incubated at 37℃ for 15-20 min, then dissociated into single cells by repeated pipetting using glass capillaries. Each single cell was transferred into individual PCR tubes and immediately frozen in Smart-seq HT lysis buffer. To collect amnion-like cells(AMLCs), PGC-like cells(PGCLCs), and hematoendothelial progenitor-like cells(HEPLCs), CER1-GFP+ anterior visceral endoderm-like cells(AVELCs) were sorted as single-cells and immediately frozen in Smart-seq HT lysis buffer.
The libraries for scRNA-seq were prepared using the SMART-seq HT kit (Z4436N, Takara), following the manufacture’s instruction. The libraries were then sequenced on an NovaSeq 6000 or NextSeq 2000 with paired-end sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
The sequenced data were preprocessed and quantified for gene expression using STAR aligner (v2.5.1b) and RSEM (v1.3.1) tool.
Assembly: GRCh38-3.0.0
Supplementary files format and content: text file includes TPM values for each sample.
|
| |
|
| Submission date |
May 30, 2023 |
| Last update date |
Oct 18, 2023 |
| Contact name |
Yasuhiro Takashima |
| E-mail(s) |
y.takashima@cira.kyoto-u.ac.jp
|
| Phone |
0081-75-366-7193
|
| Organization name |
Kyoto University
|
| Street address |
53 Kawahara-cho, Shogoin, Sakyo-ku
|
| City |
Kyoto |
| ZIP/Postal code |
606-8507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE131747 |
Hypoblast from human pluripotent stem cells regulates epiblast development |
| GSE233715 |
Hypoblast from human pluripotent stem cells regulates epiblast development [scRNA-seq] |
|
| Relations |
| BioSample |
SAMN35528620 |
| SRA |
SRX20539268 |
