README
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Dataset title:
Data for: Cellular origin and characterization of autoantibodies against type I IFNs in COVID-19 and APS-1


Recommended Citation:  
Sun, R., Marcotte, H., & Pan-Hammarström, Q. (2026). Data for: Cellular origin and characterization of autoantibodies against type I IFNs in COVID-19 and APS-1 (Version 1) [Dataset]. Karolinska Institutet. https://doi.org/10.48723/hqay-t924
See the Researchdata.se catalogue entry for this dataset - accessible via the DOI link above - for compete metadata, including the dataset description, contact information and information about how to obtain the dataset. 


Responsible organization:
Karolinska Institutet


Description: Autoantibodies (autoAbs) against type I interferons (IFNs) can severely compromise antiviral defense in a broad range of severe viral infections. To investigate the mechanisms underlying autoantibody development, we performed paired scRNA-seq and scBCR-seq on sorted IFN-α2-positive and IFN-α2-negative B cells, together with scRNA-seq of other non-B immune cells. PBMCs were obtained from eight aIFN⁺ patients with severe COVID-19, five aIFN⁻ patients with severe COVID-19, five patients with APS-1, and ten healthy donors.

The total size of the deposited data is approximately 810 GB and it contains approximately 150 files.

License: N/A

Access restrictions: This dataset contains personal data and is subject to legal protections. This dataset can be requested from the Researchdata.se research data catalog using the link above.


Essential information for dataset reuse.
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Autoantibodies (autoAbs) against type I interferons (IFNs) can severely compromise antiviral defense in a broad range of severe viral infections. To investigate the mechanisms underlying autoantibody development, we performed paired scRNA-seq and scBCR-seq on sorted IFN-α2-positive and IFN-α2-negative B cells, together with scRNA-seq of other non-B immune cells. The PBMC samples used for the deposited scRNA-seq dataset were collected in Sweden and Italy. The deposited dataset contains no direct personal identifiers. Populations of the study includes eight patients with aIFN+ severe COVID-19. five aIFN- severe COVID-19 patients, five APS-1 patients, and ten healthy donors controls.

The total size of the deposited data is approximately 1.3 TB. It contains 70 GNU zipped fastq files with raw data and one documentation file summarizing sequencing raw file name and corresponding library name/sample information in xlsx format. All fastq file names are included in the documentation file metadata.xlsx.


Dataset organization
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N/A


Datafile descriptions
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### Raw sequencing data (.fq.gz)

The `.fq.gz` files contain raw paired-end sequencing reads generated using the Illumina NovaSeq 6000 or DNBSEQ-G400 platform. 

The dataset includes 10x Genomics 5′ gene expression (GEX), V(D)J, and hashtag oligonucleotide (HTO) libraries. R1/R2 denote paired-end sequencing reads, while I1/I2 denote index reads. For some sequencing batches, I1/I2 files were also provided by the sequencing facility. Additional files generated by re-sequencing are included where applicable.

The correspondence between raw sequencing files, libraries, samples, and sequencing platforms is provided in `metadata.xlsx`.

### metadata.xlsx

The `metadata.xlsx` file provides sample, library, and raw sequencing file information. Each row represents one sequencing library.

variables:
library name: Unique identifier for each sequencing library.
title: Description of the library, including library type, cell population, and associated samples.
organism: Organism from which the samples were derived (`Homo sapiens`).
tissue: Tissue of origin (`Blood`).
Sort method: Method used for sorting antigen-specific cells (`monomer` or `tetramer`).
molecule: Type of nucleic acid analyzed.
single or paired-end: Sequencing configuration (`paired-end`).
instrument model: Sequencing platform used (`Illumina NovaSeq 6000` or `DNBSEQ-G400`).
description: Name of the .fq.gz file associated with each library, with separate columns for R1/R2, I1/I2, and additional re-sequencing files where applicable.
sizebytes: Size of each raw sequencing file in bytes.


Reference information
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Abbreviations
GEX: Gene expression
VDJ: V(D)J sequencing
HTO: Hashtag oligonucleotide
IFN: Interferon
HD: Healthy donor
COV: COVID-19
AP: APS-1
R1/R2: Read 1/Read 2
I1/I2: Index read 1/Index read 2

Data Quality: The deposited .fq.gz files contain the raw sequencing data without additional processing or modification.