|
| Status |
Public on Apr 12, 2022 |
| Title |
SCA1+ Organoid co-culture 3 |
| Sample type |
SRA |
| |
|
| Source name |
Lung organoid co-cultures
|
| Organism |
Mus musculus |
| Characteristics |
cell type: dsRED+
|
| Treatment protocol |
Cells from organoid co-cultures were delivered intratracheally into murine lungs after pre-treatment with bleomycin. Native SCA1+ cells were collected from untreated mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lungs from untreated or organoid transplanted mice were extracted, single cell suspensions generated, and native or transplanted (dsRed+) cells were collected using FACS. Cells from organoid co-cultures were also collected. Cells were encapsulated and libraries generated using the 10X Genomics Single Cell 3' pipeline. Pooled libraries were sequenced using an Illumina NextSeq500.
10X Genomics 3' Single Cell RNA Sequencing Protocol Version 2 or 3
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SCA1+ murine lung epithelial organoids co-cultured with lung stromal cells
SL11
|
| Data processing |
10X Genomics Cell Ranger 3.1.0 Pipeline was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz for each library.
|
| |
|
| Submission date |
Dec 09, 2021 |
| Last update date |
Apr 12, 2022 |
| Contact name |
Aaron L. Moye |
| Organization name |
Boston Children's Hospital
|
| Department |
Stem Cell Program
|
| Lab |
Carla Kim lab
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
Massachusetts |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE190565 |
Single cell transcriptional profiling of native, transplanted, or organoid SCA1+ and SCA1- lung epithelial cells |
|
| Relations |
| BioSample |
SAMN23822535 |
| SRA |
SRX13364078 |
