NYU Data Catalog

Description
To investigate immune responses to SARS-CoV-2 antigens under various inflammatory conditions, researchers collected blood samples from five adult patients seen at NYU Langone Health with lab-confirmed cases of acute COVID-19 and from nine healthy adults (seven who had received the BNT162b2 mRNA vaccine and two with no prior exposure to SARS-CoV-2). Samples were obtained at multiple time points. Patients with an active infection contributed longitudinal samples up to 28 days post-onset of symptoms. To assess the vaccine response in healthy patients, samples were collected at baseline and at approximately 1, 3, and 4 weeks after the first vaccine dose. Three of the vaccine recipients also provided samples 5 weeks post-vaccine, pre-booster, and 1 and 4 weeks post-booster. In total, 42 post-vaccination and 9 post-infection samples were collected. These were processed for a total of 195,634 peripheral blood mononuclear cells (PBMC): 36,906 cells (∼19%) from COVID-19 patients; 37,680 cells (∼19%) healthy control and pre-vaccine samples; 90,753 cells (∼46%) from post-vaccine samples; and 30,295 cells (∼15%) from booster samples.
Geographic Coverage
New York (State) - New York City
Subject of Study
Homo sapiens
Subject Domain
COVID-19
Genomics
Infectious Disease
Population Age
Adult (19 years - 64 years)
Senior (65 years - 79 years)
Keywords
Adaptive Immunity
Adults
Antibodies
B-Lymphocytes
Blood
Blood Buffy Coat
Blood Plasma
Blood Serum
Coronavirus
COVID-19
COVID-19 Vaccines
Gene Expression
Genomics
Immune System
Immunity
Immunization
Immunoglobulins
Infectious Diseases
Innate Immunity
Leukocytes
Lymphocytes
Memory B Cells
Monocytes
Mononuclear Leukocytes
Natural Killer T-Cells
RNA
RNA Sequencing
SARS-CoV-2
T Cells
Treatment Outcome
Vaccination

Access

Restrictions
Free to All
Instructions
Raw and processed sequencing data can be accessed through the CELLxGENE data repository and BioProject collection.
Access via CELLxGENE

SARS-CoV-2 infection and vaccination ECCITE-seq data

Access via BioProject

Sequencing data in GEO and BioSample
Accession #: PRJNA1040888

Associated Publications
Ivanova EN, Shwetar J, Devlin JC, Buus TB, Gray-Gaillard S, Koide A, Cornelius A, Samanovic MI, Herrera A, Mimitou EP, Zhang C, Karmacharya T, Desvignes L, Ødum N, Smibert P, Ulrich RJ, Mulligan MJ, Koide S, Ruggles KV, Herati RS, Koralov SB. mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection. iScience. 2023 Nov 24;26(12):108572.
Data Type
Genomic
Equipment Used
Illumina NextSeq 500

Next-generation sequencer

Illumina NovaSeq 6000

Whole-genome sequencer

Software Used
Cell Ranger

Set of analysis pipelines

GSVA v1.38

R package for gene set variation analysis (GSVA) with microarray and RNA-seq data

kallisto kb-count v0.24.1

Python package for single-cell RNA-seq pre-processing

scDblFinder

Transcriptome-based doublet detecting method

Seurat

Tools for single cell genomics

totalVI

Python package for probabilistic analysis of single-cell omics data

Study Type
Observational
Dataset Format(s)
RDS
Data Collection Instruments
WHO Clinical Progression Scale
Grant Support
P30 CA016087/NCI NIH
UM1 AI148574/NIAID NIH
R01 HL125816/NHLBI NIH
LF-OC-20-000351/LEO Foundation
K08 AI114852/NIAID NIH
R01 CA212608/NCI NIH
R01 CA194864/NCI NIH
U19 AI082630/NIAID NIH
R01 CA271245/NCI NIH
R44 AI136141/NIAID NIH
R21 AI158997/NIAID NIH
K08 AI163457/NIAID NIH
Other Resources
COVID-19 Cell Atlas

Haniffa COVID-19 single-cell RNA-seq dataset

IgBLAST

A tool for analysis of immunoglobulin (IG) and T cell receptor (TR) V domain sequences