|
| Status |
Public on Sep 01, 2022 |
| Title |
hPSC-SHF-DAY3 |
| Sample type |
SRA |
| |
|
| Source name |
HES2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SHF mesoderm
source: hPSC-derived
|
| Treatment protocol |
Distinctively patterned mesoderm populations are treated with 2 uM IWP2 and 10 ng/mL VEGF (day 3 to day 5) for the generation of cardiac progenitors. At the progenitor stage, aSHF cells are treated with 2 uM retinol and 10 ng/mL BMP4, and pSHF cells are treated with 2 uM of retinol for 3 days (day 5 to day 8). The treated progenitors were cultured to day 20 for the differentiation of cardiomyocytes.
|
| Growth protocol |
FHF mesoderm is specified with 16 ng/mL BMP4, 5ng/mL bFGF and 8 ng/mL ActivinA from HES2-WT-hPSCs, and the SHF mesoderm is generated with 3 ng/mL BMP4, 5ng/mL bFGF and 1.5 ng/mL
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10X Genomics Single Cell 3ʹ Reagent Kits v3 protocols
10X Genomics 3ʹ Gene Expression Library Construction (fragmentation Mix, purified cDNA for Library Construction, and adaptor ligation mix)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw data of Illumina's base call files (Cell Ranger to process 10x Genomics data)
Bam files and read count matrix (QC by Cell Ranger)
Updated read count matrix and imputed it
Genome_build: GRCH38
Supplementary_files_format_and_content: Cell Ranger output files
|
| |
|
| Submission date |
Apr 28, 2021 |
| Last update date |
Sep 01, 2022 |
| Contact name |
Gordon Keller |
| E-mail(s) |
Gordon.Keller@uhnresearch.ca
|
| Organization name |
University of Toronto
|
| Department |
McEwen stem cell institute
|
| Lab |
Gordon Keller lab
|
| Street address |
101 College Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE173486 |
Single-cell transcriptomic profiles of hPSC-derived cardiac cells of various lineages and stages |
|
| Relations |
| BioSample |
SAMN18905842 |
| SRA |
SRX10697653 |
