|
Status |
Public on Feb 20, 2020 |
Title |
BCP1 |
Sample type |
SRA |
|
|
Source name |
peBC at P1
|
Organism |
Rattus norvegicus |
Characteristics |
group: cultured cells protocol: collagen-coated TCP using a pharmacologic expansion media (Propagenix)
|
Treatment protocol |
peBC were differentiated on four in vitro culture platforms, including organoids in matrigel (BCO1), at air-liquid interface (BCALI), in engineered trachea (BCT1), and in engineered lung (BCL5). All differentiation was performed in Propagenix Airway Differentiation Medium (PADM).
|
Growth protocol |
Native rat tracheal epithelial scapings (TE1ep) were plated and peBC expanded on collagen-coated TCP using a pharmacologic expansion media (Propagenix)(BCP1, BCP3, BCP6).
|
Extracted molecule |
total RNA |
Extraction protocol |
Samples were rendered to a single cell suspension for sequencing enzymatically using platform-specific protocols (Greaney 2020). Single-cell libraries were prepared using the standard 10x Genomics v2 processing workflow. Cell loadings were designed to yield 5000-10000 cells per library. 10x genomics standard library preparation. Sequencing on Illumina HiSeq 4000 sequencers, indexed to a depth of 160-220 million reads per library. Read 1 sequencing was 26 bp long, read 2 sequencing was 98 bp long.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
10x Genomics
|
Data processing |
FASTQ read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 30 bp long were discarded. Downstream processing was conducted with zUMIs v 0.4 (44) with the default parameters; the top 10,000 cell barcodes ranked by reads were output for each sample. Genome_build: Ensembl Rnor6.0 release 92 was used to align the data to the rat transcriptome. Supplementary_files_format_and_content: sparse matrix of raw counts Supplementary_files_format_and_content: barcodes (column names for .mtx file) Supplementary_files_format_and_content: genelist (rownames for .mtx file)
|
|
|
Submission date |
Feb 19, 2020 |
Last update date |
Oct 02, 2020 |
Contact name |
Allison M Greaney |
E-mail(s) |
allison.greaney@yale.edu
|
Organization name |
Yale University
|
Department |
Biomedical Engineering
|
Street address |
10 Amistad St
|
City |
New Haven |
State/province |
CT |
ZIP/Postal code |
06511 |
Country |
USA |
|
|
Platform ID |
GPL22396 |
Series (2) |
GSE145517 |
Platform effects on regeneration by pulmonary basal cells as evaluated by single-cell RNA sequencing [RNA-seq] |
GSE145518 |
Platform effects on regeneration by pulmonary basal cells as evaluated by single-cell RNA sequencing |
|
Relations |
BioSample |
SAMN14134178 |
SRA |
SRX7747839 |