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Sample GSM4320006 Query DataSets for GSM4320006
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

Supplementary file Size Download File type/resource
GSM4320006_BCP1.barcodes.tsv.gz 53.4 Kb (ftp)(http) TSV
GSM4320006_BCP1.genes.tsv.gz 118.0 Kb (ftp)(http) TSV
GSM4320006_BCP1.idents.tsv.gz 155.0 Kb (ftp)(http) TSV
GSM4320006_BCP1.raw.data.mtx.gz 61.3 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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