|
| Status |
Public on Aug 14, 2019 |
| Title |
SC108SSCLOW |
| Sample type |
SRA |
| |
|
| Source name |
lower lobe lung_scleroderma patient
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: systemic sclerosis- associated interstitial lung disease (SSc-ILD) patient
tissue: lung
lung section/portion: lower lobe lung
10x genomics chemistry: 10X Genomics 3 Prime V2 chemistry
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Explanted lungs were finely diced and digested for 1 hour in a mix of collagenase A/DNAse I. A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA. Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v2 User Guide
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SSC 6
|
| Data processing |
10X Genomics' Cell Ranger 2.0 software's mkfastq command was used for basecalling. It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38 whole genome using 10X Genomics' Cell Ranger 2.0 software's cellranger count function
Cell Ranger output of raw_gene_bc_matrices were utilized for further downstream analysis in R with the package Seurat 2.3.4, only cells expressing at least 200 genes were kept for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample
|
| |
|
| Submission date |
Mar 12, 2019 |
| Last update date |
Aug 14, 2019 |
| Contact name |
Tracy Tabib |
| Organization name |
University of Pittsburgh
|
| Department |
Department of Medicine
|
| Lab |
Laboratory of Robert Lafyatis
|
| Street address |
200 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE128169 |
Single-cell analysis reveals fibroblast heterogeneity and myofibroblasts in systemic sclerosis-associated interstitial lung disease |
|
| Relations |
| BioSample |
SAMN11106028 |
