|
Status |
Public on Oct 17, 2023 |
Title |
NKO_CP_D8_Rep1 |
Sample type |
SRA |
|
|
Source name |
Cardiac progenitor cells
|
Organism |
Homo sapiens |
Characteristics |
cell type: d8 hiPSC-derived cardiac progenitor cells cell line: NKX2.5-/- treatment: untreated
|
Treatment protocol |
Detailed in "characteristics: Treatment" to specify different treatments on samples.
|
Growth protocol |
Cardiac progenitors cells were differentiated from WTC11 hiPSC lines by the WNT modulation protocol. In brief, 6 uM CHIR were added for 48hours, followed by 5 uM IWP4 for 48 hours. Cells were then grown RPMI with B27 supplement minus insulin until day 10, then with RPMI with B27 plus insulin
|
Extracted molecule |
total RNA |
Extraction protocol |
Single cell suspensions were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation. Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN- 1000121) and Chromium i7 Multiplex Kit (PN-120262).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
scRNA-seq of total RNA in cell type
|
Data processing |
Illumina Casava v1.8 was used for base-calling. Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger Suite v3.1.0 from 10X genomics Additional filtering, quality control and doublet removal was done using Seurat v3 according to specifications in the tutorials (https://satijalab.org/seurat/pbmc3k_tutorial.html) Assembly: hg19 Supplementary files format and content: normalized gene-cellbarcode expression matrix in csv format
|
|
|
Submission date |
Jan 20, 2023 |
Last update date |
Oct 17, 2023 |
Contact name |
Deepak Srivastava |
Organization name |
J David Gladstone Institutes
|
Department |
GICD
|
Lab |
Deepak Srivastava
|
Street address |
1650 Owens St
|
City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94158 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (2) |
GSE195476 |
The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5 |
GSE223339 |
Single cell RNA-sequencing (scRNA-seq) of ISL1 knockout (KO) or knockdown and NKX2.5 KO compared to WT in cardiac progenitors (CPs); scRNA-seq of ISL1 KO compared to WT in motor neuron progenitors (MNPs) |
|
Relations |
BioSample |
SAMN32811731 |
SRA |
SRX19103443 |