|
| Status |
Public on Mar 20, 2019 |
| Title |
Day9_1001_1000_cells |
| Sample type |
SRA |
| |
|
| Source name |
HS1001 from Dr. Hovatta’s laboratory (Rodin et al., 2014)
|
| Organism |
Homo sapiens |
| Characteristics |
cellline: HS1001
biological replicate: 1
time: day 9
|
| Treatment protocol |
At day 4, medium was supplemented with 10 mg of CHIR99021 and at day 7, medium was supplemented with 5 mg IWP2
|
| Growth protocol |
Cells were cultured in wells coated with LN-521 and LN-221. Cells at day 0 were cultured with Nutristem medium. Cells at Day 5 and 7 were cultured in RMPI 1640 with B27 without insulin supplement and CHIR99021. Cells at day 9 were cultured in RMPI 1640 with B27 without insulin supplement and IWP2. Cells at day 11 were cultured in RMPI 1640 with B27 without insulin supplement.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
A chromium instrument (10x Genomics) was used to partition viable cell suspensions into single cell droplets using Single Cell 3’ library and gel bead kit version 2 (10x Genomics, Cat.#120237) as per manufacturer’ protocol. Illumina Hi-Seq3000 sequencing platform in a single sequencing lane.
The samples were loaded into single cell chip (10x Genomics, Cat.No.120236) to capture 1000 cells in each of the four sets of cells
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Cells maintained on LN-521 for four days and then five days on LN-521+LN-221
|
| Data processing |
The reads were mapped to the human genome (Ensembl version 90) and quantified using Cell Ranger 2.1.1 (10x Genomics).
Cell Ranger was run with the expect number of cells parameter (expect-cells) set to 1,000, which resulted in 713, 841, 591 and 636 cells for the day9_HS1001, day9_H1, day11_HS1001 and day11_H1 samples respectively.
Reads were quantified using RSEM 1.2.31. Cell Ranger output matrices (i.e. genes.tsv and barcodes.tsv) were then input into R, the four 10x data runs were merged and genes with zero counts in all cells were discarded.
Genome_build: Human genome (Ensembl version 90). We provided to Cell Ranger a custom-built reference transcriptome generated by filtering the Ensembl transcriptome for the gene biotypes: protein coding, lincRNA and antisense.
Supplementary_files_format_and_content: CVPs_single_cell_sequencing_gene_raw_counts.txt: tab separated file with raw gene expression counts for each gene and cell sequenced
|
| |
|
| Submission date |
Mar 06, 2019 |
| Last update date |
Mar 20, 2019 |
| Contact name |
Aida Moreno-Moral |
| Organization name |
Duke-NUS Medical School
|
| Street address |
8 College Road
|
| City |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE100725 |
In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors |
| GSE127955 |
Single-cell RNA-seq of human cardiovascular progenitor cells generated with a chemically defined, xeno-free laminin based differentiation protocol |
|
| Relations |
| BioSample |
SAMN11078380 |
| SRA |
SRX5486259 |
