|
| Status |
Public on Nov 16, 2021 |
| Title |
CF3 |
| Sample type |
SRA |
| |
|
| Source name |
Airway submucosal glands
|
| Organism |
Sus scrofa |
| Characteristics |
age: newborn
genotype: CFTR-/-
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tracheal segments from newborn wild-type and CFTR-/- pigs were collected and kept in cold 1x DPBS. Trachea were cut open at the ventral side in cold 1x DPBS with 0.1% gentamicin. Airway surface epithelial cells were scraped off and the remaining epithelial layer was separated from the cartilage layer of the trachea to explore SMGs. The peeled epithelial layer was transferred into a new dish with cold 1x DPBS with 0.1% gentamicin. Individual SMGs were then dissected off from the epithelial layer into the medium. Dissected SMG tissues were collected and successively dissociated with Collagenase/Hyaluronidase (30 min) and Pronase/DNase (2 hours) medium at 37 oC. After that, dissociation was terminated using cold 1 x DPBS with fetal bovine serum. Cells were further washed with cold 1 x DPBS and filtered with 40-µm tissue strainers. Single cells were spun down and resuspended in 1 x DPBS with 0.4 mg/ml bovine serum albumin at around 1000 cells/µl.
10x Genomics Chromium Single Cell 3’ Reagent Kits v2 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.
Raw FASTQ reads alignment, filtering, barcode counting, and UMI counting were performed using 10x CellRanger version 3.0.2.
Genome_build: Sscrofa11.1 from RefSeq database. The annotation of about 240 genes were improved based on references from Ensembl, Genbank mRNA databases.
Supplementary_files_format_and_content: HDF5 format files (including raw and filtered files) contain counts for each gene and cell barcode.
Supplementary_files_format_and_content: GTF format file is an improved version of the original Sscrofa11.1.gtf (date as 12/10/2019) file from RefSeq database
|
| |
|
| Submission date |
Oct 13, 2021 |
| Last update date |
Nov 16, 2021 |
| Contact name |
Michael J. Welsh |
| E-mail(s) |
michael-welsh@uiowa.edu
|
| Organization name |
The University of Iowa & Howard Hughes Medical Institute
|
| Department |
Internal Medicine
|
| Lab |
Michael Welsh
|
| Street address |
200 Hawkins Dr, 6330 PBDB
|
| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE185849 |
Single-cell RNA sequencing of airway submucosal glands in wild-type and cystic fibrosis Pigs |
|
| Relations |
| BioSample |
SAMN22247177 |
| SRA |
SRX12593951 |
