|
| Status |
Public on Apr 23, 2020 |
| Title |
Non-human primate mTB infected granulomas and uninvolved lungs [28818_Array9] |
| Sample type |
SRA |
| |
|
| Source name |
mTB granulomas and lung lobes
|
| Organism |
Macaca fascicularis |
| Characteristics |
cell type: TB Granuloma and Adjacent Uninvolved Lung epithelial cells
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell RNA capture, barcoding, and multiplexing according to the Seq-Well S^3 method (Hughes et al., BioRxiv 2019)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Samples of several granulomas and uninvolved lung lobes from 10 mTB-infected monkeys
NHP_TB_Grans_and_Lung_dge.txt
|
| Data processing |
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
Normalization, variable gene selection, and clustering were performed using Leiden clustering in the Scanpy v1.4.5.2 (scanpy.readthedocs.io) package (Wolf et al., 2018). Cell type labels were assigned using known marker genes and epithelial cell clusters are included in these matrices.
Macaca_fascicularis_5.0
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)
|
| |
|
| Submission date |
Apr 21, 2020 |
| Last update date |
Aug 11, 2021 |
| Contact name |
Alex Shalek |
| E-mail(s) |
shalek@mit.edu
|
| Organization name |
MIT
|
| Department |
Chemistry
|
| Lab |
Shalek Lab
|
| Street address |
45 Carleton Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL28212 |
| Series (1) |
| GSE148829 |
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues |
|
| Relations |
| BioSample |
SAMN14670898 |
| SRA |
SRX11705973 |
