|
| Status |
Public on Dec 25, 2019 |
| Title |
H6.IBMEC.Day 6 |
| Sample type |
SRA |
| |
|
| Source name |
hPSC-Derived
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hPSC-Derived cell
differentiation condition: n/a
|
| Growth protocol |
Cells were grown in 10cm coated tissue culture dishes using media specific for each cell type.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A single-cell suspension was loaded into the Bio-Rad ddSEQ Single-Cell Isolator on which cells were isolated, lysed and barcoded in droplets.
Libraries were generated with direct tagmentation followed by 3’ enrichment and sample indexing using Illumina Nextera library prep kit.
ddSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Analyses were performed using the Seurat package in R (version 3.0.3).
UMI counts files that had been knee-filtered were downloaded from the Illumina BaseSpace Sequence Hub.
Following best practices in the package suggestions UMI counts were log-normalized and after the most highly variable genes selected the data matrices were scaled using a linear model with variation arising from UMI counts mitigated for.
Principal component analysis was subsequently performed on this matrix and after reviewing principal component heatmaps and jackstraw plots Uniform Manifold Approximation and Projection (UMAP) visualization was performed using the top 30 components and clustering resolution was set at 0.8.
|
| |
|
| Submission date |
Sep 25, 2019 |
| Last update date |
Dec 26, 2019 |
| Contact name |
Tyler Lu |
| E-mail(s) |
[email protected]
|
| Phone |
9089383803
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
1300 York Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE138025 |
Vascular fate in misidentified pluripotent-derived blood-brain-barrier endothelial cells rescued by transcriptional reprogramming. |
|
| Relations |
| BioSample |
SAMN12846506 |
| SRA |
SRX6907063 |
