A place to keep track of public or confidential datasets available to the Cobey Lab.
Contact Katie G (kgostic@uchicago.edu) if you need help adding a new dataset or want to propose a new category.
DO NOT post confidential data to this repo. Instead, upload a description of where the data can be found (e.g. on Midway).
- Influenza titer panel data - humans - cross-sectional individual titers to a panel of flu strains. Some studies include two or more timepoints.
- Influenza titer panel data - ferrets - panel data from naive ferrets used to construct antigenic maps.
- Influenza cohort data - data from studies that follow a cohort of individuals over time. Usually includes a combination of PCR-confirmed infections, and serological data.
- [Influenza epidemiological/surveillance data] -
- [Influenza sequence data] -
- [B cell data] -
- [SARS-CoV-2 epi data] -
- [Other SARS-CoV-2 data] -
- [Other pathogens] -
| Article | Project name | Public | Sample collection years | Strain years | Subtype(s) | Assay | Primary source | File locations |
|---|---|---|---|---|---|---|---|---|
| Fonville et al. 2014 | Ha Nam | Y | 2007-2012 | 1968-2011 | H3N2 | HAI | Table S3 | link to all data sets |
| Lessler et al. 2012 | Fluscape (Guangzhou) | Y | 2009 | 1968-2008 | H3N2 | NT | Dataset S1 | |
| Yang et al. 2020 | Fluscape (Guangzhou) | Y | Baseline: 2009-2010 Follow-up:2014-2015 | 1968-2014 | H3N2 | HAI | See Github link | |
| Vinh et al. 2020 | NA - Analyzed Vietnam blood bank samples | Y | 2009-2015 | 1918-2009 | H3N2, H1N1, B/Vic, B/Yam | Protein Microarray | See data/code link | |
| Fonville et al. 2016 | NA - Analyzed blood bank samples from children ages 9-24mo in the Netherlands. | Y | 1995-2011 | 1989-2011 | H3N2 | HAI | Dataset S2 |
| Article | Public | Notes | Strain panel years | Subtypes | Primary source | File location |
|---|---|---|---|---|---|---|
| Fonville et al. 2014 | Yes | Study-specific. | 1992-2011 | H3N2 | Table S1 | link to all data sets |
| Bedford et al. 2014 | Yes | Compiled panel data from many studies, including Smith et al. 2004. Strains from the late 1990s and 2000s are dramatically overrepresented. | 1968-2007 | H1N1, H3N2, B/Vic, B/Yam | Dryad archive | |
| Fonville et al. 2016 | Yes | Tested 24 ferrets (each with serum to a unique strain) against 23 strains. | 1989-2011 | H3N2 | Dataset S3 |
- NPICS - [description pending]
- HIVE - [description pending]