|
| Status |
Public on Nov 03, 2022 |
| Title |
BAL sample patient 9, healthy control |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
cell type: Bronchoalveolar lavage
covid status: negative, healthy
sample type: citeSeq
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction method explained in Loss of evolutionary conserved GM-CSF-dependent signature in pulmonary macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment. Cell Reports Medicine. 2022
Library construction explained in Loss of evolutionary conserved GM-CSF-dependent signature in pulmonary macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment. Cell Reports Medicine. 2022
All samples are CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
filtered_feature_bc_matrix_sampleName.h5 = count matrix of genes and antibodies; metaData_allBAL-umap.csv = metadata of umap in fig 2A; metaData_zoomMF-umap.csv = metadata of umap in fig 1B; metaData_zoomMF-diffMap.csv = metadata of diffusion map in fig1F; usedABs.csv = list of ABs used for TotalVI analysis
|
| Data processing |
Pre-processing of sequencing results to generate count matrices (gene expression, ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline (v4.0) and aligning to the GRCh38 genome build. For more detail, see Loss of evolutionary conserved GM-CSF-dependent signature in pulmonary macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment. Cell Reports Medicine. 2022
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files:h5 files
|
| |
|
| Submission date |
Oct 27, 2022 |
| Last update date |
Nov 03, 2022 |
| Contact name |
Liesbet Martens |
| E-mail(s) |
liesbet.martens@irc.vib-ugent.be
|
| Organization name |
VIB-University of Ghent
|
| Department |
VIB Inflammation Research Center
|
| Street address |
Technologiepark 927
|
| City |
Zwijnaarde |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE216704 |
Loss of GM-CSF-dependent instruction of alveolar macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment (RNA-Seq) |
| GSE216705 |
Loss of GM-CSF-dependent instruction of alveolar macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment |
|
| Relations |
| BioSample |
SAMN31488923 |
| SRA |
SRX18046689 |
