|
| Status |
Public on Mar 16, 2021 |
| Title |
S2_distal airway_CF_pig id 3882 |
| Sample type |
SRA |
| |
|
| Source name |
distal airway_CF
|
| Organism |
Sus scrofa |
| Characteristics |
animal id: 3882
genotype: CFTR-/-
tissue: lung
region: distal airway
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trachea and small airways from neonatal WT and CF pigs were dissected and kept in cold 1 x DPBS. Tracheal tissues were scraped off and small airways were chopped into short segments. Tissues were washed with 1xDPBS with dithiothreitol (2 mM), incubated with red blood cell lysis buffer for 5 minutes, and dissociated in DMEM medium with Pronase (1.4 mg/ml) and DNase (50 U/ml) for 2 hours. Dissociation mix was terminated by adding 1 volume of cold 1 x DPBS with 10% fetal bovine serum and filtered with 40-µm tissue strainers to collect single cells.
10x Genomics Chromium Single Cell 3’ Reagent Kits v3 system
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina software HCS HD version 3.4.0 was used for basecalling.
Alignment of raw fastq files to pig genome assembly Sscrofa11.1, filtering, barcode counting, and UMI counting were performed with 10x CellRanger software version 3.0.2 with the argument --expect-cells=5000.
Genome_build: susScr11
Supplementary_files_format_and_content: HDF5 format file containing counts for each gene (row) and cell barcode (column)
|
| |
|
| Submission date |
May 10, 2020 |
| Last update date |
Mar 16, 2021 |
| Contact name |
Alejandro A. Pezzulo |
| E-mail(s) |
alejandro-pezzulo@uiowa.edu
|
| Organization name |
Universty of Iowa
|
| Department |
Department of Internal Medicine
|
| Lab |
Pezzulo Lab
|
| Street address |
6316 Pappajohn Biomedical Discovery Building
|
| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE150211 |
Single cell RNA sequencing of large and small airway surface epithelium in newborn cystic fibrosis (CF) and non-CF pigs |
|
| Relations |
| BioSample |
SAMN14883486 |
| SRA |
SRX8299841 |
