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| Status |
Public on Dec 04, 2019 |
| Title |
Pig1 |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Sus scrofa |
| Characteristics |
age: 3.5 months
Sex: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Lungs were exracted and perfused/inflated with an enzyme mixture containing collagenase, elastase, dispase, and DNAse. Following a 20-40 minute incubation, tissue was pushed through a metal strainer to dissociate. All subsequent steps performed on ice. Total time from tissue perfusion to library preparation <2 hours.
Single-cell libraries were prepped using the standard 10x Genomics v3 processing workflow. Cell loadings were designed to yield ~5000 cells per library.
10x genomics standard library preparation. Sequencing on Illumina HiSeq 4000 sequencers, indexed to yield a mean read depth of ~88,000 reads per cell. Read 1 sequencing was 26 bp long, read 2 sequencing was 98 bp long.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
10x Genomics
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| 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.
Cells were accepted with greater than 500 and fewer than 10000 unique mapped genes. Analysis was performed on cells with less than 5% mitochondrial mapping for the mouse, rat, and pig samples and less than 8% for the human samples.
Genome_build: Ensembl GRCm38 release 92, Ensembl Rnor6.0 release 92, Ensembl Sscrofa11.1 release 92, and Ensembl GRCh38 release 91 were used to align the mouse, rat, pig, and human data respectively.
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| Submission date |
Jul 02, 2019 |
| Last update date |
Dec 05, 2019 |
| Contact name |
Micha Sam Brickman Raredon |
| E-mail(s) |
michasam.raredon@yale.edu
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| Organization name |
Yale University
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| Department |
Biomedical Engineering
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| Lab |
Niklason Laboratory
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| Street address |
10 Amistad Street
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| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| Platform ID |
GPL22475 |
| Series (1) |
| GSE133747 |
Single-cell connectomic analysis of adult mammalian lungs |
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| Relations |
| BioSample |
SAMN12204826 |
| SRA |
SRX6399245 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3926543_Pig1.barcodes.tsv.gz |
57.8 Kb |
(ftp)(http) |
TSV |
| GSM3926543_Pig1.genes.tsv.gz |
120.3 Kb |
(ftp)(http) |
TSV |
| GSM3926543_Pig1.raw.data.mtx.gz |
41.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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