|
| Status |
Public on Oct 14, 2020 |
| Title |
CBRA-PNEX-DUAL-SMAD: BU3 NGPT Basal Cell Medium_1 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC derived
|
| Organism |
Homo sapiens |
| Characteristics |
sample name synonym: Day 46 BU3 NGPT Basal Cell Medium_1
tissue: iPSC-derived airway organoids
culture media: PneumaCult-Ex-Plus media supplemented with SMAD inhibitors and Y-27632
isolation method: Dispase followed by trypsin
|
| Growth protocol |
This protocol is based on previously described approaches to derive airway organoid from hPSCs (Hawkins et al. 2017; McCauley et al. 2017) including a detailed step-by-step protocol prior to basal cell medium (McCauley et al. 2018).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
single cells were captured for sequencing library prepration using a 10X Chromium
10X chromium chemistry
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCh38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: GRCh38
Supplementary_files_format_and_content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5 format
|
| |
|
| Submission date |
Dec 18, 2019 |
| Last update date |
Oct 14, 2020 |
| Contact name |
Carlos Villacorta-Martin |
| Organization name |
Center for Regenerative Medicine at Boston University
|
| Street address |
670 Albany St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE142246 |
Derivation of airway basal stem cells from human pluripotent stem cells |
|
| Relations |
| BioSample |
SAMN13620513 |
| SRA |
SRX7405708 |
