|
| Status |
Public on Aug 14, 2019 |
| Title |
SC284 |
| Sample type |
SRA |
| |
|
| Source name |
mix of hashtagged upper lobe + hashtagged lower lobe lung_scleroderma patient
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: scleroderma patient
tissue: lung
lung section/portion: mix of hashtagged upper lobe + hashtagged lower lobe lung
10x genomics chemistry: 10X Genomics 3 Prime V3 chemistry + Cell Hashing HTO + CITE-Seq Feature Barcoding with BioLegend Total-Seq A antibodies
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Explanted lungs were finely diced and digested for 45 minutes in a mix of Liberase DL/DNAse I. A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 2%FBS. Cells were labeled with TotalSeq-A Cell Hashing HTO and CITE-Seq ADT antibodies according to the New York Genome Center's CITE-Seq and Cell Hashing protocol. Follwing antibody-hashtag labeling, cells were resuspended in PBS containing 0.04% BSA and loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v3 User Guide; Cell Hashing HTO and CITE-Seq ADT libraries measuring surface protein expression were generated according to the New York Genome Center's CITE-seq & Cell Hashing Protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
poly-adenylated RNA, surface protein expression with TotalSeq-A antibodies
SSC 11/12
This sample was sequenced twice-- once on the NextSeq 500 and once on the NovaSeq 6000. The output .h5 file contains the combined data from both of these instruments following alignment to the GRCh38 reference genome.
|
| Data processing |
10X Genomics' Cell Ranger 3.0.2 software's mkfastq command was used for basecalling. It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38 transcriptome using 10X Genomics' Cell Ranger 3.0.2 software's cellranger count function
Cell Ranger output of raw_feature_bc_matrix.h5 files 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. Cell Ranger 3.0.2's Feature Barcoding
Genome_build: GRCh38
Supplementary_files_format_and_content: The .h5 files contain gene expression and antibody capture counts for each donor or patient
|
| |
|
| Submission date |
Jun 27, 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 |
SAMN12151586 |
