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Sample GSM6642030 Query DataSets for GSM6642030
Status Public on Oct 19, 2022
Title Day 21 wild type AEP organoid ATACseq
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 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 SAMN31289109
SRA SRX17897208

Supplementary file Size Download File type/resource
GSM6642030_10X-Zacharias-Day-21-Ax2-20200206-ATACv1-1mm.arrow 2.9 Gb (ftp)(http) ARROW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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