|
Status |
Public on Oct 19, 2022 |
Title |
Day 21 wild type AEP organoid RNAseq |
Sample type |
SRA |
|
|
Source name |
Lung
|
Organism |
Mus musculus |
Characteristics |
tissue: Lung time: Day 21 cell type: AEP organoid genotype: wild type
|
Growth protocol |
Lung alveolar organoids in 3D matrix
|
Extracted molecule |
total RNA |
Extraction protocol |
Lung alveolar epithelial progenitor derived organoids were digested into a single cell suspension and analyzed by scRNAseq. Nuclei were prepared from this single cell suspension for separate analysis by scATACseq
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
Cellranger pipeline from 10x genomics used for alignment RNA alignment to spliced/nonspliced genome via Velocyto RNA analysis in Seurat for clustering and differential gene expression ATAC analysis in ArchR for clustering and analysis
|
|
|
Submission date |
Oct 14, 2022 |
Last update date |
Oct 20, 2022 |
Contact name |
William Zacharias |
E-mail(s) |
william.zacharias@cchmc.org
|
Organization name |
Cincinnati Children's Hospital Medical Center
|
Street address |
3333 BURNET AVE
|
City |
CINCINNATI |
State/province |
OH |
ZIP/Postal code |
45229-3026 |
Country |
USA |
|
|
Platform ID |
GPL21103 |
Series (1) |
GSE215824 |
Alveolar epithelial progenitor cells drive lung regeneration via dynamic changes in chromatin topology modulated by lineage-specific Nkx2-1 activity |
|
Relations |
BioSample |
SAMN31289114 |
SRA |
SRX17897203 |