|
| Status |
Public on Aug 05, 2020 |
| Title |
Patient_1-2 |
| Sample type |
SRA |
| |
|
| Source name |
Sorted macrophages and T cells
|
| Organism |
Homo sapiens |
| Characteristics |
individual: Patient_1
disease state: COVID-19 Positive
time: 2 days after intubation
sample type: BAL
cell type: Sorted macrophages and T cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared with 10x Genomics 5' gene expression (GEX) reagents according to the manufacturer protocol (CG000086_RevM).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample 6
main.h5ad
supplement.h5ad
|
| Data processing |
Reads were demultiplexed using with cellranger mkfastq command (v3.1.0). Reads were aligned to a custom built genome (human GRCh38.93 and SARS-CoV-2 NC_045512.2) and counted by gene by cell with cellranger count command (v3.1.0), producing raw and filtered gene expression matrices.
Doublets were identified and removed with scrublet v0.2.1. Ambient RNA was corrected with FastCAR (https://github.com/LungCellAtlas/FastCAR).
Samples were processed with scanpy v1.5.1, low-quality cells were removed and samples were integrated with BBKNN v1.3.12
Sample 16 contained cells from patients A and B. To assign cells to correct patients, we used souporcell v2.0 with the list of common variants for GRCh38 genome, provided on the souporcell page (https://github.com/wheaton5/souporcell) on samples 14, 15 and 16 with the number of clusters k=2. We used Pearson correlation between genotypic clusters in samples 14 & 16 and 15 & 16 to determine which genotypic clusters come from the same patients. Genotypic doublets and unassigned cells were discarded.
Genome_build: custom (human GRCh38.93 and SARS-CoV-2 NC_045512.2)
Supplementary_files_format_and_content: gene expression count matrices; anndata objects; cell metadata
|
| |
|
| Submission date |
Jul 28, 2020 |
| Last update date |
Oct 23, 2020 |
| Contact name |
Alexander V Misharin |
| E-mail(s) |
a-misharin@northwestern.edu
|
| Organization name |
Northwestern University
|
| Street address |
303 E Superior
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE155249 |
Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia |
|
| Relations |
| BioSample |
SAMN15659772 |
