|
| Status |
Public on Jul 01, 2020 |
| Title |
CTRL002 |
| Sample type |
SRA |
| |
|
| Source name |
Sputum cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: control
tissue: Sputum cells
subject: CTRL002
group: CTRL
age: 42
Sex: M
smoking: no
fev1 % predicted: NA
platform: 10x Genomics
technology: Chromium Single Cell 3' Kits (v3 Chemistry)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sputum cell were obtained from spontaneous (CF) and induced sputum (CTRL)
Single-cell libraries were prepared using the standard 10x Genomics single cell 3' reagent kits v3 processing workflow.
Standard10x genomics single cell 3' reagent kits v3 library preparation. Sequencing on Illumina HiSeq 4000 sequencer, aiming for 150 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Raw data to be made available through dbGaP
|
| 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 25 bp long were discarded.
Downstream processing was conducted with STAR v2.7.3a and its single cell seq implementation "STARsolo".
Cells being accepted had to pass the following filters: at least 750 transcripts profiled, having at least 10% of transcripts arising from intron spanning or unspliced reads, less than 15% of their transcriptome of mitochondrial origin
Genome_build: GENECODE release 31 (GRCh38.p12)
Supplementary_files_format_and_content: gene vs barcode sparse matrix (raw counts and normalized data) of all samples
Supplementary_files_format_and_content: Sputum.raw.counts.processed.mtx: sparse matrix file of processed raw counts
Supplementary_files_format_and_content: Sputum.data.processed.mtx: sparse matrix file of processed normalized data
Supplementary_files_format_and_content: Sputum.processed.genes.tsv: gene IDs to sparse matrix files of processed raw counts and normalized data
Supplementary_files_format_and_content: Sputum.processed.barcodes.tsv: barcode IDs to sparse matrix files of processed raw counts and normalized data
Supplementary_files_format_and_content: Sputum.processed.meta.data.txt: meta data to sparse matrix files of processed raw counts and normalized data
|
| |
|
| Submission date |
Feb 16, 2020 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Naftali Kaminski |
| E-mail(s) |
naftali.kaminski@yale.edu
|
| Phone |
2037374612
|
| Organization name |
YALE UNIVERSITY
|
| Department |
PCCSM
|
| Lab |
Kaminski
|
| Street address |
300 Cedar Street
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE145360 |
Single Cell sequencing of human Sputum cells in cystic fibrosis and healthy controls |
|
| Relations |
| BioSample |
SAMN14117679 |
