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| Status |
Public on May 31, 2023 |
| Title |
Lung Nb day 45 |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
cell type: CD45 enriched cells
strain: C57BL/6
treatment: Day 45 Nb
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| Treatment protocol |
Animals were infected with 500 third stage N. brasilienesis larvae by subcutaneous injection.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lung lobes were diced into small pieces and incubated in RPMI containing 0.33mg/mL Liberase TL and 0.1mg/mL DNase I (both from Sigma Aldrich) at 37°C for 45 minutes under agitation (150rpm). Enzymatic activity was stopped by adding FCS. Digested lung was filtered through a 70µm cell strainer and washed with RPMI. Red blood cells were lysed with the addition of ammonium-chloride-potassium buffer (Gibco) for 3 minutes at room temperature. Cells were then washed with RPMI supplemented with 10% FCS. Enrichment for CD45+ immune cell was done from lung single cell suspension using the EasySepTM Mouse CD45 positive selection kit (Stemcell Technologies) according to the manufacturer’s instruction. The nuclei isolation was done using the Chromium Nuclei Isolation Kit (10x Genomics) according to the manufacturer’s instruction. 10,000 nuclei from each group were loaded on a 10X Genomics Next GEM chip and single cell GEMs were generated on a 10X Chromium Controller. Subsequent steps to generate the scRNA-seq libraries were prepared according to the manufacturer protocol (10x Genomics). Libraries were sequenced on an Illumina NovaSeq 6000 run. The sequenced data were processed using Cell Ranger ATAC 2.0.0 software. The reads were aligned to Mus musculus mm10 genomes to generate count tables that were further analyzed using Seurat (version 4.1.2). Dimension reduction was performed with UMAP, and individual clusters were annotated based on expression on markers and gene sets from the single cell RNAseq analyzed data. Integration of scRNA-seq and scATAC-seq was performed from the Seurat package.
10X Genomics Next GEM chip. All samples have sequencing yields of more than 422 million read per sample. The sequencing run was setup as a 50 cycles + 49 cycles non-symmetric run. Demultiplexing was done allowing 1 mismatch in the barcodes. Sequencing quality is good, over 86.55% of bases in the barcode regions have Q30 or above and at least 91.02% of bases in the read have Q30 or above, and 87.32% or more of bases in the sample index have Q30 or above. The analysis was performed with the Cell Ranger ATAC 2.0.0 software using the default parameters. The number of cells captured ranges from 2,703 to 5,424. The median fragments per cell ranged from 15,891 to 22,856. The percentage of reads mapped confidently to genome (>30 mapq) is above 91.33% for all the samples. The fraction of fragments (that passed all filters) overlapping TSS is above 47.48% and overlapping peaks is above 73.63%.
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| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Primary Cells
Sample_C
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| Data processing |
Demultiplexing was done allowing 1 mismatch in the barcodes. The analysis was performed with the Cell Ranger ATAC 2.0.0 software using the default parameters.
Assembly: mm10
Supplementary files format and content: Processed data sets are submitted as zipped files - *tar for each individual sample; Embedded within each zipped file for each sample are the various h5, matrix and tsv files
Supplementary files format and content: h5, matrix and tsv files for individual files are provided under A, B, C subfolders
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| Submission date |
Mar 29, 2023 |
| Last update date |
May 31, 2023 |
| Contact name |
Oyebola Oyesola |
| E-mail(s) |
oyebola.oyesola@nih.gov
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| Phone |
607-379-7745
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| Organization name |
National Institute of Health
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| Department |
Type 2 Immunity Section
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| Lab |
LPD
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| Street address |
Building 4, Room B1 05 4 Memorial Drive Bethesda, MD 20892
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| City |
Maryland |
| ZIP/Postal code |
20852 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE228504 |
Exposure to lung-migrating helminth protects against murine SARS-CoV-2 infection through macrophage-dependent T cell activation |
| GSE228507 |
Exposure to lung-migrating helminth protects against murine SARS-CoV-2 infection through macrophage-dependent T cell activation |
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| Relations |
| BioSample |
SAMN33971477 |
| SRA |
SRX19811453 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7122878_C_count.tar.gz |
33.3 Gb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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