Public datasets

Here we provide a list of publicly-available datasets that we have generated and uploaded to repositories. Some of the data is yet to be released, and will be available following publication.

• Public datasets
  • NCBI Sequencing Read Archive
    • Summary
    • Datasets
  • European Nucleotide Archive
    • Summary
    • Datasets

NCBI Sequencing Read Archive

The following datasets have been uploaded to the NCBI Sequencing Read Archive (SRA) database in their original FASTQ data format.

Summary

Sequencing type	Sequencing runs (uploaded)
Bulk transcriptomics	425
Single-cell transcriptomics	2
Shotgun metagenomics	310
16S amplicon	1,069
ITS amplicon	373

Datasets

Host organism	Context	BioProject	Availability	Bulk transcriptomics	Single-cell transcriptomics	Shotgun metagenomics	16S amplicon	ITS amplicon
Human	Infant cystic fibrosis	PRJNA978345 – 2024	✅ Released			96 stool samples	75 BAL samples
Rat	Early life stress + mild traumatic brain injury	PRJNA940177 – 2024	✅ Released				76 stool samples
Mouse	SHIP-deficient model of Crohn's-like ileitis and chronic lung inflammation	PRJNA1086166 – 2024	✅ Released				24 stool samples
Human	Paediatric healthy + infant wheeze	PRJNA1076275 – 2024	✅ Released	188 nasal swabs + 73 blood samples			320 nasal swabs	135 nasal swabs
Human	Early life + airways	PRJNA694493 – 2021	✅ Released	85 nasal swabs			118 nasal swabs + 119 oropharyngeal swabs	119 nasal swabs + 119 oropharyngeal swabs
Mouse OTII cells	Germinal centre expansion + IL-21 role	PRJNA776662 – 2021	✅ Released	8 culture samples
Mouse	Allergic airway inflammation	PRJNA641984 – 2020	✅ Released			20 stool samples	127 stool samples
Human	Male-associated infertility	PRJNA509076 – 2018	✅ Released				94 seminal fluid samples
Human	Early life + immune development	PRJNA475630 – 2018	✅ Released	16 tracheal aspirates			45 tracheal aspirates
Human	Paediatric severe wheeze + asthma	PRJNA1080233	⏳ To be released	55 bronchial brushes		28 bronchial brushes
Mouse	High fat diet	PRJNA1131116	⏳ To be released			24 ileum luminal samples + 24 ileum mucosal samples + 22 colon luminal samples
Mouse	Early life antibiotic treatment	PRJNA1112091	⏳ To be released		2 lung structural cell digests	96 stool samples	41 lung tissue samples + 30 BAL samples

European Nucleotide Archive

The following datasets have been uploaded to the European Nucleotide Archive (ENA) database in their original FASTQ data format.

Summary

Sequencing type	Sequencing runs (uploaded)
16S amplicon	1,179

Datasets

Host organism	Context	Project ID	16S amplicon	Availability
Human	Early life + atopic dermatitis	PRJEB42268 – 2022	✅ Released	1,179 lateral upper arm swabs