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.
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 |
1,099 |
| ITS amplicon |
373 |
Datasets
| Host organism |
Context |
BioProject |
Availability |
Bulk transcriptomics |
Single-cell transcriptomics |
Shotgun metagenomics |
16S amplicon |
ITS amplicon |
| Mouse |
High fat diet |
PRJNA1131116 – 2024 |
 Released |
|
|
24 ileum luminal samples + 24 ileum mucosal samples + 22 colon luminal samples |
30 stool samples |
|
| Mouse |
Early life antibiotic treatment |
PRJNA1112091 – 2024 |
Released |
|
2 lung structural cell digests |
96 stool samples |
41 lung tissue samples + 30 BAL samples |
|
| Mouse |
SHIP-deficient model of Crohn's-like ileitis and chronic lung inflammation |
PRJNA1086166 – 2024 |
Released |
|
|
|
24 stool samples |
|
| Human |
Paediatric severe wheeze + asthma |
PRJNA1080233 – 2024 |
Released |
55 bronchial brushes |
|
28 bronchial brushes |
|
|
| Human |
Paediatric healthy + infant wheeze |
PRJNA1076275 – 2024 |
Released |
188 nasal swabs + 73 blood samples |
|
|
320 nasal swabs |
135 nasal swabs |
| 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 OTII cells |
Germinal centre expansion + IL-21 role |
PRJNA776662 – 2021 |
Released |
8 culture samples |
|
|
|
|
| Human |
Early life + airways |
PRJNA694493 – 2021 |
Released |
85 nasal swabs |
|
|
118 nasal swabs + 119 oropharyngeal swabs |
119 nasal swabs + 119 oropharyngeal swabs |
| 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 |
|
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 |