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Research Article

A curated collection of transcriptome datasets to study the transcriptional response in blood and nasal samples following viral respiratory inoculation and vaccination

[version 1; peer review: awaiting peer review]
Zheng Lan
https://orcid.org/0000-0002-7439-110X
1, Tongli Zhang2, Yu Zhang1, [...] Xuejun Sun1, Chuwen Liu1, Pei Liu3, Muyao Tang1, Meng Fu1, James S. Hagood
https://orcid.org/0000-0003-3938-0330
4,5, Raymond J Pickles5,6, Fei Zou1, Xiaojing Zheng1,7
Zheng Lan
https://orcid.org/0000-0002-7439-110X
1, Tongli Zhang2, [...] Yu Zhang1, Xuejun Sun1, Chuwen Liu1, Pei Liu3, Muyao Tang1, Meng Fu1, James S. Hagood
https://orcid.org/0000-0003-3938-0330
4,5, Raymond J Pickles5,6, Fei Zou1, Xiaojing Zheng1,7
PUBLISHED 13 May 2025
Author details Author details
OPEN PEER REVIEW
REVIEWER STATUS AWAITING PEER REVIEW

Abstract

Background

Our understanding of the human immune system’s response to viral respiratory tract infections (VRTIs) and vaccines, including the molecular mechanisms and correlates of protection, remains incomplete. Extensive transcriptomic data from inoculation and vaccination studies have been deposited in publicly available databases. However, these studies are often separate and difficult to locate.

Methods

To bridge this research gap, we have systematically searched and reviewed publicly available datasets from NCBI Gene Expression Omnibus (GEO), Archive of Functional Genomics Data (ArrayExpress), Immunology Database and Analysis Portal (ImmPort), and Google using targeted queries. Inoculation study queries included terms related to humans, blood, PBMCs, nasal, respiratory challenges, and respiratory viral inoculations; while vaccination study queries focused on humans, blood, PBMCs, transcriptomes, and respiratory viral vaccines or vaccinations.

Results

This collection includes 18 datasets from inoculation of 5 respiratory viruses: H1N1, H3N2, RSV, HRV, and SARS-CoV-2 (14 from blood and 4 from nasal swabs) with 429 participants (ages 18 to 55 years) and 37 datasets from vaccination of influenza and COVID-19 with 2,084 participants (ages 0.5 to over 89 years). The duration and number of post-immunization time points range from 14 days before to 28 days after inoculation (1 to 20 time points) and from 28 days before to 360 days after vaccination (1 to 13 time points).

Conclusion

We provide a curated compendium of public gene expression data repositories for researchers to reanalyze transcriptomes from human whole blood, peripheral blood mononuclear cells (PBMCs), and nasal swab samples. This will facilitate studies of transcriptional responses to respiratory viral inoculation or vaccination.

Keywords

Transcriptomics, Bioinformatics, Vaccination, Inoculation, Respiratory viral infection, Influenza viruses, COVID, Respiratory syncytial viruses (RSV), Human rhinoviruses (HRV) Whole Blood, PBMC.

Corresponding authors: Fei Zou, Xiaojing Zheng
Competing interests: No competing interests were disclosed.
Grant information: This work is supported by National Institute of Allergy and Infectious Diseases (NIAID) of the National Institutes of Health (NIH) under grant [P01 AI178377]; National Heart Lung and Blood Institute(NHLBI) of the NIH under grant [R01 HL173044]
Copyright:  © 2025 Lan Z et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
How to cite: Lan Z, Zhang T, Zhang Y et al. A curated collection of transcriptome datasets to study the transcriptional response in blood and nasal samples following viral respiratory inoculation and vaccination [version 1; peer review: awaiting peer review]. F1000Research 2025, 14:493 (https://doi.org/10.12688/f1000research.162267.1) First published: 13 May 2025, 14:493 (https://doi.org/10.12688/f1000research.162267.1) Latest published: 13 May 2025, 14:493 (https://doi.org/10.12688/f1000research.162267.1)

Introduction

Viral respiratory tract infections (VRTIs) are widespread globally, causing significant illnesses and hospitalizations each year.1 The importance of studying VRTIs has grown in light of the global COVID-19 pandemic.2 VRTIs involve a range of viruses, including respiratory syncytial viruses (RSV), human rhinoviruses (HRV), and influenza and coronaviruses.3 Most VRTIs lack both effective antiviral therapies and approved vaccines.4

In-depth investigation of human immune responses to inoculation and vaccination is critically needed. To facilitate further research, we have compiled a curated dataset collection, which includes transcriptomic data from the blood and nasal swabs of volunteers who underwent inoculation and vaccination, specifically for influenza, COVID-19, RSV, and HRV.

Our curated dataset collection is divided into two categories: inoculation studies and vaccination studies. The inoculation collection includes 18 datasets with 429 participants, while the vaccination collection comprises 37 datasets with 2,084 participants. All datasets were sourced from GEO, ImmPort Shared Data, and the ArrayExpress Collection at EMBL-EBI.5–7 These datasets have been organized into a publicly accessible format for download and further analysis.

Methods

The datasets were gathered using specific search queries across GEO, ArrayExpress, ImmPort, and Google search. The queries for inoculation studies included terms related to humans, blood, PBMCs, nasal, respiratory challenges, and viral inoculations. The vaccination study queries followed similar criteria, focusing on humans, blood, PBMCs, transcriptomes, and vaccines or vaccinations. The search queries used for GEO, ArrayExpress, and Google search to find inoculation studies are as follows:

GEO and ArrayExpress Inoculation Search Query

(“humans”[MeSH Terms] OR “Homo sapiens”[Organism] OR Homo sapiens [All Fields]) AND ((“blood”[Subheading] OR “blood”[MeSH Terms] OR blood [All Fields]) OR PBMC [All Fields] OR PBMCs [All Fields]) AND respiratory [All Fields] AND (challenge [All Fields] OR “experimentally infected”[All Fields] OR inoculated [All Fields])

Google Inoculation Search Query

Homo sapiens AND (blood OR PBMC OR PBMCs) AND transcriptome AND respiratory AND (inoculation OR challenge OR “experimentally infected” OR inoculated)

The search queries used for GEO, ArrayExpress, and Google to find vaccination studies are as follows:

GEO and ArrayExpress Vaccine Search Query

(“humans”[MeSH Terms] OR “Homo sapiens”[Organism] OR Homo sapiens [All Fields]) AND ((“blood”[Subheading] OR “blood”[MeSH Terms] OR blood [All Fields]) OR PBMC [All Fields] OR PBMCs [All Fields]) AND respiratory [All Fields] AND ((“vaccination”[MeSH Terms] OR inoculation [All Fields]) OR (“vaccines”[MeSH Terms] OR vaccine [All Fields]) OR (“vaccines”[MeSH Terms] OR vaccines [All Fields]) OR (“vaccination”[MeSH Terms] OR vaccination [All Fields]))

Google Vaccine Search Query

Homo sapiens AND (blood OR PBMC OR PBMCs) AND transcriptome AND respiratory AND (vaccine OR vaccines OR vaccination)

For ImmPort, vaccine studies were located using the following filters:

  • • Species: Homo sapiens

  • • Research Focus: Vaccine Response

  • • Condition or Disease: COVID-19 AND Influenza

Results

The majority of datasets obtained were derived from human blood, PBMCs, and nasal swabs, generated using Illumina or Affymetrix platforms or through RNA sequencing. Every dataset identified through this search was carefully curated manually. This involved thoroughly reviewing the dataset descriptions, examining the study designs, and reading through the related original articles on PubMed. Ultimately, we only included studies that involved human whole blood, PBMCs, and nasal swabs linked to VRTI inoculation or vaccination for our dataset collection. According to these criteria, we retained 18 inoculation datasets and 37 vaccine-related datasets.

The data selection process for inoculation is summarized in Figure 1a. Using GEO and ArrayExpress inoculation query, 108 studies were found with Homo sapiens as the primary organism. Google search returned 92 inoculation studies. The data selection process for vaccination is summarized in Figure 1b. GEO and ArrayExpress Vaccine query identified 82 studies where Homo sapiens is the top organism. Google search produced 89 vaccination studies. ImmPort search yielded 99 vaccination studies.

dd5044fb-69fb-4a66-83f6-d0b70bd12cab_figure1.gif

Figure 1. Flowchart illustrating construction of inoculation (a) and vaccination (b) dataset compendium.

Figure 2 illustrates the distribution of participants over time in 18 inoculation studies, involving 429 participants aged 18 to 55 years, across five respiratory viruses: H1N1, H3N2, RSV, HRV, and SARS-CoV-2. There is a notable peak on day 0. The duration and number of post-immunization time points range from 14 days before to 28 days after inoculation, spanning 1 to 20 time points. Notably, 56 participants from four studies had both blood and nasal samples, and they were counted separately. Subsequent time points show smaller but consistent sample collections, with varying contributions from different pathogens. H1N1, H3N2, and HRV are the most frequently sampled pathogens, while SARS-CoV-2 and RSV contribute fewer samples to the dataset.

dd5044fb-69fb-4a66-83f6-d0b70bd12cab_figure2.gif

Figure 2. A collection of datasets covering transcriptional responses to inoculation over time across varying viruses.

Histogram of the time points pre- and post-inoculation available in our compendium. Each virus is indicated by a different color. The height of the bars represents the number of participants with available gene expression data.

Figure 3 summarizes the distribution of 2,084 participants, aged 0.5 to over 89 years, over time in 37 vaccination studies covering COVID-19 and influenza vaccines and their types. The peak occurred on day 0, with participant recruitment enriched during the first week. The duration and number of post-immunization time points range from 28 days before to 360 days after vaccination, spanning 1 to 13 time points.

dd5044fb-69fb-4a66-83f6-d0b70bd12cab_figure3.gif

Figure 3. A collection of datasets covering transcriptional responses to vaccination over time across COVID-19 and influenza.

Histogram of the time points pre- and post-vaccination is available in our compendium. Each vaccine and type are indicated by a different color. The height of the bars represents the number of participants with available gene expression data.

The complete list of inoculation datasets included in our collection can be found in Table 1.

Table 1. Complete list of inoculation datasets.

Pathogen Sample typeSample sizeProfiling platformTime pointAccession number Citation
HRVPeripheral blood50Microarray (Affymetrix)-0.88, 0, 0.21, 0.5, 0.88, 1.21, 1.5, 1.88, 2.21, 2.5, 2.88, 3.21, 3.5, 3.88, 4.21, 4.5, 4.92, 5.21, 5.92, 6.92GSE730728
RSV20
H3N238
H1N143
HRVPeripheral blood20Microarray (Affymetrix)0GSE171569
RSV20
H3N217
H3N2Peripheral blood17Microarray (Affymetrix)0, 0.21, 0.50, 0.88, 1.21, 1.50, 1.88, 2.21, 2.50, 2.88, 3.21, 3.50, 3.88, 4.21, 4.50GSE3055010
H3N2Whole blood11Microarray (Illumina)0,0.50,1,2GSE6175411
SARS-CoV-2Blood and nose swabs36RNA-seq 0, 0.25, 14, 28(blood) 0,1,3,5,7,10,14(nose swabs)E-MTAB-1299312
H3N2Blood and nose swabs20RNA-seq 0, 1, 2, 3, 7, 10, 14, and 28(blood) 0,1, 2,3,7,14(nose swabs)EGAD50000000956
HRVNose swabs17Microarray (Affymetrix)-14,0.33, 2.00GSE1134813
H1N1Whole blood21Microarray (Illumina)0, 1, 2, 3, 4GSE9073214
RSVNose swabs58RNA-seq 0,3GSE15523715
H1N1PBMC24Microarray (Affymetrix)0, 0.21, 0.50, 0.90, 1.21, 1.50, 1.90, 2.21, 2.50, 2.90, 3.21, 3.50, 3.90, 4.21, 4.50GSE5242816
H3N217

We have collected transcriptomes from 18 cohorts across 10 inoculation studies, totaling 429 participants. This collection covers inoculations of five respiratory viruses: H1N1, H3N2, RSV, HRV, and SARS-CoV-2. The time span ranges from -14 to 28 days before and post for inoculation. The sample source includes blood (n=14) and nasal swabs (n=4). The transcriptomic data types include microarrays from Illumina (n=2) and Affy (n=11); bulk RNA-seq (n=5) ( Figure 4).

dd5044fb-69fb-4a66-83f6-d0b70bd12cab_figure4.gif

Figure 4. Distribution of inoculation datasets across different profiling platforms.

The complete list of vaccination datasets included in our collection can be found in Table 2.

Table 2. Complete list of vaccine datasets.

PathogenVaccine type Sample type Sample size Profiling platformTime point Accession number Citation
InfluenzaTIVPBMC172Microarray (Illumina)0,2,7,28GSE10799017
InfluenzaLAIVWhole blood20Microarray (Illumina)0,1,7,30GSE5200518
InfluenzaTIVWhole blood17Microarray (Illumina)0,1,7,30
InfluenzaLAIVPBMC28Microarray (Affymetrix)0,3,7GSE2961919
InfluenzaTIVPBMC28Microarray (Affymetrix)0,3,7
InfluenzaLAIV and inactivatedBlood44RNA-seq 0,3,7,29,85,92,113GSE21777020
InfluenzainactivatedPBMC50RNA-seq 0,1,3,7,21,22,24,28GSE10201221
InfluenzaLAIVNasal epithelium40RNA-seq 0,3GSE23049422
InfluenzaLAIVNasal cells55RNA-seq 0,5,12GSE11758023
InfluenzaTIVNasal cells62RNA-seq 0,5,12
Influenzavetor viral virusWhole blood11Microarray (Illumina)0,0.5,1,2GSE6175411
InfluenzaInactivatedPBMC14RNA-seq -7,0,1,2,3,4,5,6,7,8,9,10,21GSE4576424
InfluenzaInactivatedWhole blood18Microarray (Illumina)-7,0,1,3,7,10,14,21,28GSE30101/GSE4876225
InfluenzaInactivatedPBMC212Microarray (Affymetrix)0,3,7,14GSE7481726
InfluenzaInactivatedWhole blood247Microarray (Illumina)0,1,3,14GSE48024
InfluenzaInactivatedWhole blood91Microarray (Illumina)0GSE41080
InfluenzaInactivatedPBMC5RNA-seq 0,1,2,3,4,5,6,7,8,9,10GSE45735
InfluenzaInactivatedPBMC60Microarray (Illumina)0,2,4,7,28GSE59743/GSE95584
InfluenzaInactivatedPBMC27Microarray (Affymetrix)0,3,7GSE29617/GSE29614
InfluenzaInactivatedPBMC64Microarray (Illumina)0,2,4,7,28GSE59654
InfluenzaInactivatedWhole blood51Microarray (Illumina)0,2,7,28GSE101709
InfluenzaInactivatedPBMC42Microarray (Illumina)0,4,7,28GSE59635
InfluenzaInactivatedWhole blood44Microarray (Illumina)0,2,7,28GSE101710
InfluenzaInactivatedPBMC63Microarray (Affymetrix)-7,0,1,7,70GSE47353
InfluenzaLAIVPBMC28Microarray (Affymetrix)0,3,7GSE29615
influenzaInactivatedWhole blood123Microarray (Affymetrix)−7,0,1,3,7,10,14,21,28SDY311/SDY312/SDY314/SDY315/SDY11227
InfluenzaTIVWhole blood34Microarray (Illumina) 0,7,14SDY272/SDY648/SDY739/SDY819/SDY62228
influenzaTIVWhole blood65RNA-seq 0,2,7,28SDY139329
InfluenzaTIV Whole blood6RNA-seq 1,3,60SDY300*
COVIDmRNAPBMC16scRNA0,7,21,28GSE24791730
COVIDmRNABlood23RNA-seq 0,1,2,3,4,5,6,7,8,9GSE19000131
COVIDmRNAPBMC214RNA-seq 0,22,90,180,360GSE22068232
COVIDmRNABlood6scRNA0,1,2,7,21,22,28,42GSE17196433
COVIDmRNABlood56RNA-seq 0,1,7,21,22,28GSE169159
COVIDmRNAPBMC8scRNA28,35,60,110,201GSE19567334
COVIDmRNAPBMC4scRNA0,7,30,90GSE21022935
COVIDvetor viral virusWhole blood36RNA-seq 0,50,57GSE22884236

* This data is available at ImmPort (https://immport.org/shared/home) under study accession SDY300: Healthy Human DC and monocyte subsets transcriptional regulations in response to Fluzone 2010-2011 and pneumococcal vaccinations.

We have gathered transcriptomes from 37 cohorts across 22 vaccine studies, totaling 2084 participants. This collection focuses on studying Influenza and COVID-19 vaccines. The time span ranges from -28 to 360 days. The data source includes blood (n=34) and nasal swabs (n=3). The transcriptomic data types include microarrays from Illumina (n=13) and Affy (n=7); bulk RNA-seq (n=13) and scRNA-seq (n=4) ( Figure 5). Vaccine types: TIV (n=22) and LAIV (n=6) were used for influenza vaccination, mRNA vaccine (n=7) was used for COVID-19 vaccination, and vector adenovirus (n=2) was used for both influenza and COVID-19, one of each.

dd5044fb-69fb-4a66-83f6-d0b70bd12cab_figure5.gif

Figure 5. Distribution of vaccine datasets across different profiling platforms.

Ethics and consent

Ethical approval and consent were not required.

Data availability

All datasets in our curated collection are also accessible to the public on the NCBI GEO website at https://www.ncbi.nlm.nih.gov/gds/ ArrayExpress at https://www.ebi.ac.uk/biostudies/arrayexpress/studies ImmPort at https://www.immport.org/shared/home, and the European Genome-phenome Archive (EGA)37 at https://ega-archive.org/datasets/ cited in the manuscript using its GEO number, ArrayExpress number, ImmPort study number or EGA study number. All these citation and accession numbers are listed in Table 1. The dataset can be found by searching for the accession number on the corresponding websites listed above. Note that downloading from ImmPort requires registering a personal account on their website.

Accession number

NCBI: Expression Omnibus (GEO): Transcriptome datasets of the transcriptional response in blood samples following HRV, RSV, H3N2 and H1N1 inoculation. Accession Number: GSE73072; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE730728

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets of the transcriptional response in blood samples following HRV, RSV and H3N2 inoculation. Accession Number: GSE17156; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171569

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets of the transcriptional response in blood samples following H3N2 inoculation. Accession Number: GSE30550; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3055010

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets of the transcriptional response in blood samples following H3N2 inoculation. Accession Number: GSE61754; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6175411

EMBL-EBI: ArrayExpress: Transcriptome datasets of the transcriptional response in blood and nasal samples following SARS-CoV-2 inoculation. Accession Number: E-MTAB-12993; https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-1299312

European Genome-Phenome Archive (EGA): Transcriptome datasets to study the transcriptional response in blood samples following H3N2 inoculation. Accession Number: EGAD50000000956; https://ega-archive.org/datasets/EGAD5000000095612 (Data available on request)

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in nasal samples following HRV inoculation. Accession Number: GSE11348; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1134814

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following H1N1 inoculation. Accession Number: GSE90732; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9073215

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in nasal samples following RSV inoculation. Accession Number: GSE155237; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15523715

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following H1N1 and H3N2 inoculation. Accession Number: GSE52428; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5242816

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE107990; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10799017

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE52005; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5200518

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE29619; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2961919

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE217770; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21777020

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE102012; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10201221

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in nasal samples following influenza vaccination. Accession Number: GSE230494; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23049422

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in nasal samples following influenza vaccination. Accession Number: GSE117580; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11758023

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE61754; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6175411

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE45764; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4576424

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE30101 and GSE48762; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30101 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4876225

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE74817; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7481726

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE48024; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4802426

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE41080; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4108026

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE45735; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4573526

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE59743 and GSE95584; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59743 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9558426

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE29617 and GSE29614; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29617 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2961426

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE59654; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5965426

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE101709; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10170926

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE59635; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5963526

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE101710; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10171026

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE47353; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4735326

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: GSE29615; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2961526

ImmPort: Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: SDY311, SDY312, SDY314, SDY315 and SDY112; https://www.immport.org/shared/study/SDY311, https://www.immport.org/shared/study/SDY312, https://www.immport.org/shared/study/SDY314, https://www.immport.org/shared/study/SDY315 and https://www.immport.org/shared/study/SDY11227

ImmPort: Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: SDY272, SDY648, SDY739, SDY819 and SDY622; https://www.immport.org/shared/study/SDY272, https://www.immport.org/shared/study/SDY648, https://www.immport.org/shared/study/SDY739, https://www.immport.org/shared/study/SDY819 and https://www.immport.org/shared/study/SDY62228

ImmPort: Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: SDY1393; https://www.immport.org/shared/study/SDY139329

ImmPort: Transcriptome datasets to study the transcriptional response in blood samples following influenza vaccination. Accession Number: SDY300; https://www.immport.org/shared/study/SDY300

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following COVID vaccination. Accession Number: GSE247917; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24791730

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following COVID vaccination. Accession Number: GSE190001; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19000131

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following COVID vaccination. Accession Number: GSE220682; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22068232

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following COVID vaccination. Accession Number: GSE171964 and GSE169159; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171964 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16915933

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following COVID vaccination. Accession Number: GSE195673; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19567334

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following COVID vaccination. Accession Number: GSE210229; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21022935

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in blood samples following COVID vaccination. Accession Number: GSE228842; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22884236

NCBI: Gene Expression Omnibus (GEO): Transcriptome datasets to study the transcriptional response in nasal samples following HRV inoculation. Accession Number: GSE11348; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1134813

Acknowledgment

We extend our gratitude to all the researchers who have publicly shared their datasets by depositing them in GEO, ArrayExpress, ImmPort and EGA.

References

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Lan Z, Zhang T, Zhang Y et al. A curated collection of transcriptome datasets to study the transcriptional response in blood and nasal samples following viral respiratory inoculation and vaccination [version 1; peer review: awaiting peer review]. F1000Research 2025, 14:493 (https://doi.org/10.12688/f1000research.162267.1)
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