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| Status |
Public on Oct 25, 2022 |
| Title |
IDA007_S2 |
| Sample type |
SRA |
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| Source name |
Brushing of bronchial epithelium
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Brushing of bronchial epithelium
subject: IDA007
Sex: Female
age: 62
smoking status: Former
race: Black or African American
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| Treatment protocol |
N/A
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
The tissue obtained from bronchial brushings was treated with 0.25% Trypsin/EDTA for epithelial sheet dissociation and cells were sorted using a BD FACSAria II. FACS was used to isolate singlet events based on forward scatter height vs. forward scatter area (FSH-H vs. FSH-A). Dead cells (PI+) and red blood cells (GYPA/CD235a+) are stained and excluded. For each donor, single live cells (Hoechst 33342+ Prodium Iodide- CD235a-) were sorted into 2 96-well PCR plates per patient sample.
Cells were resuspended and sorted into 96-well PCR plates before being processed using the CEL-Seq2 RNA library preparation protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Gene expression data from bronchial brushing IDA007, replicate 2.
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| Data processing |
Initial sample-level demultiplexing and creation of FASTQ files was performed using BaseSpace.
Quality metrics and gene-level counts were generated for the single-cell RNA-sequencing samples using Scruff.
In the bronchial scRNA-seq data, cells had a median UMI of 4580, a median number of genes detected of 1870, median predicted contamination of 0.168 %, and the percentage of predicted doublets of 7.51%. Poor quality cells were identified if they met any of the following criteria: 1) bottom quantile for a total number of genes detected, 2) bottom quantile for total library size and 3) top quantile for the percentage of counts mapped to the mitochondrial genome. Overall, 1189 cells (including 34 empty wells) were filtered and 2075 cells were kept for further analysis.
Cells were defined by examining the relative expression level of knowledge-based gene markers. Transitional cells were named based on their relative location on the UMAP plot and expression of a combination of marker genes.
In the bronchial scRNA-seq data, markers included KRT5 (basal cells), CEACAM5 (peri-goblet cells), SCGB1A1 (club cells), MUC5AC (goblet cells), FOXJ1 (ciliated cells), FOXI1 (ionocytes), CD3D (T cells), GNLY (NK cells), KIT (mast cells), CXCR2 (neutrophil and macrophages).
Assembly: hg19
Supplementary files format and content: IDA_bronchial_single_cell_counts.tsv: Tab-separated value (TSV) file containing count matrix for 24138 features (rows) x 2075 cells (columns).
Supplementary files format and content: IDA_bronchial_single_cell_barcodes.tsv: Tab-separated value (TSV) file containing the barcode sequence for each of the 96 CEL-Seq2 wells.
Supplementary files format and content: IDA_bronchial_single_cell_labels.tsv: Tab-separated value (TSV) file containing the subject ID, barcode, and cell-type label for each of the 2075 cells (rows).
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| Submission date |
Aug 08, 2022 |
| Last update date |
Oct 25, 2022 |
| Contact name |
Adam C Gower |
| E-mail(s) |
agower@bu.edu
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| Phone |
617-358-7138
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| Organization name |
Boston University School of Medicine
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| Department |
Department of Medicine
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| Lab |
Division of Computational Biomedicine
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| Street address |
72 East Concord Street, E632
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE210661 |
Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways |
| GSE210694 |
Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways (IDA bronchial brushings) |
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| Relations |
| BioSample |
SAMN30190394 |
| SRA |
SRX16976865 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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