|
| Status |
Public on Oct 19, 2022 |
| Title |
Day 28 wild type AEP organoid ATACseq |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
time: Day 28
cell type: AEP organoid
genotype: wild type
|
| Growth protocol |
Lung alveolar organoids in 3D matrix
|
| Extracted molecule |
genomic DNA |
| 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 |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| 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 |
SAMN31289108 |
| SRA |
SRX17897209 |
