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IS3.1: Immune Signatures Data Resource 2.0 (ISDR 2.0)

A sub-project of Immune Signatures 3 (IS3)

Project Overview

Principal Investigator

Title

HIPC Immune Signatures Data Resource 2.0 (ISDR 2.0): a standardized, computable compendium of vaccine-response transcriptomics and antibody data

Condition studied

Response to vaccination — 36 vaccines spanning 51 studies and 109 cohorts

Scale

2,554 participants · 17,824 samples (9,638 expression + 8,186 antibody-response)

Data types

Bulk RNA-seq, microarray & scRNA-seq transcriptomics; antibody response (HAI, ELISA, neutralization, MBAA)

Objective

Assemble unified computable datasets from ImmPort/GEO, delivered as Bioconductor SummarizedExperiment / MultiAssayExperiment objects with reproducible pipeline code.

Sponsoring organization

NIAID · HIPC Coordinating Center

Manuscript

In preparation — DOI pending

Dataset summary metrics

Studies51

Cohorts109

Participants2,554

Vaccines36

Expression samples9,638

Response samples8,186

Curated dataset composition

These tables declare which ImmuneSpace/ImmPort studies make up ISDR 2.0. Study IDs link into the live query interface; transcriptomics rows carry the GEO accession used for ingestion.

Study ID	Pathogen · vaccine type	Participants	Transcriptomics samples	Antibody response samples
{{ r.id }}	{{ r.pathogen }}	{{ r.participants }}	{{ r.txSamples }}	{{ r.samples }}

{{ studiesCount }} studies with antibody-response data. Study IDs open the query interface filtered to that study (/query/results); assay badges add the matching assay-ontology filter (MBAA is unmapped, so those aren't linked).

Study ID	Sample type	Platform	Technique	Timepoints (days)	GEO
{{ r.id }}	{{ r.sample }}	{{ r.platform }}	{{ r.tech }} {{ r.tech }}	{{ r.times }}	{{ r.geo }}

Microarray and RNA-seq (and scRNA-seq) sourced from GEO. Because each row carries a GEO accession, the microarray half is linkable — the outstanding portal work is mapping those into the query schema.

Study ID	Pathogen · vaccine type	Assay	Participants	Samples
{{ r.id }}	{{ r.pathogen }}	{{ r.assay }} {{ r.assay }}	{{ r.participants }}	{{ r.samples }}

Antibody assays: HAI, ELISA, neutralization (NEUT) and multiplex bead array (MBAA).

Data Resource & Downloads

All Data

↗ View on Zenodo (DOI of record)

DOI: 10.5281/zenodo.XXXXXXX (pending) · Format: Bioconductor SummarizedExperiment / MultiAssayExperiment objects saved as .rds, read into R via readRDS(). Derived from data on ImmPort/GEO; reuse under the ImmPort data use agreement.

Data Record

File	Dataset	R object class
{{ r.file }}	{{ r.desc }}	{{ r.klass }}

Code & pipeline

Reproducible processing pipeline (rendered reports). Preprocessing depends on standard nf-core workflows plus the ImmuneSpace integration tooling (Zenodo DOI: 10.5281/zenodo.XXXXXXX, pending).

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