NBDC Research ID: hum0366.v1
SUMMARY
Aims: To analyze the immune response to the mRNA vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and pathophysiology of the coronavirus disease 2019 (COVID-19) and to provide insights into the clinical development.
Methods: single cell RNA-seq: Peripheral blood mononuclear cells from COVID-19 patients (with ARDS, n=8; without ARDS, n=8) and healthy controls (n=5) were analyzed by single cell RNA sequence.
RNA-seq: Total RNA extracted from monocytes derived from peripheral blood mononuclear cells of healthy subjects (n=4) was analyzed by RNA sequence.
ATAC-seq: DNA extracted from monocytes derived from peripheral blood mononuclear cells of healthy subjects (n=5) was analyzed by ATAC sequence.
Participants/Materials: single cell RNA-seq: patients with COVID-19 (with ARDS, n=8; without ADRS, n=8), healthy subjects (n=5)
RNA-seq: healthy subjects (n=4 per person, PBMC)
ATAC-seq: healthy subjects (n=4 or 5 per person, PBMC)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| E-GEAD-551 | NGS (scRNA-seq) | Unrestricted-access | 2023/03/16 |
| E-GEAD-552 | Unrestricted-access | 2023/03/16 |
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
COVID-19 (ICD10: U07.1): 16 cases patients with ARDS: 8 cases patients without ARDS: 8 cases healthy subjects : 5 individuals |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from a single cell isolated from PBMCs |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5′ Library & Gel Bead Kit v1.1, Chromium Next GEM Chip G Single Cell Kit, Single Index Kit T Set A |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
Read1: 26 bp Read2: 91 bp |
| Mapping Methods | STAR |
| Reference Genome Sequence | GRCh38 |
| Detecting method for read count (software) | dropEst |
| QC Methods | Cells with less than 1,000 UMIs or more than 20,000 UMIs, and cells containing more than 10% reads from mitochondrial or hemoglobin genes, were filtered. Furthermore, for each sample, doublets identified by Scrublet were removed. |
| Gene Number | 24,541 genes |
| Genomic Expression Archive ID | E-GEAD-551 |
| Total Data Volume | 2.3495 GB (txt) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | healthy subjects : 4 individuals (4 samples each) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | Total RNA extracted from monocytes derived from PBMCs |
| Cell Lines | - |
| Library Construction (kit name) | Nextera XT DNA Library Preparation Kit |
| Fragmentation Methods | Tagmentation (Nextera XT DNA Library Preparation Kit) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Mapping Methods | HISAT2 |
| Reference Genome Sequence | hg38 |
| Detecting method for read count (software) | featureCounts (version 1.6.3) |
| QC Methods | Low-quality (<20) bases and adaptor sequences were trimmed with Trimmomatic software (version 0.38) with the following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. |
| Gene Number | 31,706 genes |
| Genomic Expression Archive ID | E-GEAD-552 |
| Total Data Volume | 2.3495 GB (txt) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | healthy subjects : 5 individuals (4 or 5 samples each) |
| Targets | ATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNA extracted from monocytes derived from PBMCs |
| Cell Lines | - |
| Library Construction (kit name) | ATAC-Seq Kit |
| Fragmentation Methods | Tagmentation (ATAC-Seq Kit) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | Bowtie2 |
| Reference Genome Sequence | hg38 |
| Detecting method for open chromatin region (software) | featureCounts (version 1.6.3) |
| QC Methods | Low-quality (<20) bases and adaptor sequences were trimmed with Trimmomatic software (version 0.38) with the following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. |
| Peak Number | 33548 peaks |
| Genomic Expression Archive ID | E-GEAD-552 |
| Total Data Volume | 2.3495 GB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yasuhiro Kato
Affiliation: Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (S) | Pathological significance and regulation of guidance factors in neurology, immunity and metabolism. | 18H05282 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Consecutive BNT162b2 mRNA vaccination induces short-term epigenetic memory in innate immune cells | doi: 10.1172/jci.insight.163347 | E-GEAD-551 E-GEAD-552 |
| 2 |
