data-emporium

A place to keep track of public or confidential datasets available to the Cobey Lab.

Contact Katie G ([email protected]) 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] -

Influenza titer panel data - humans

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

Influenza titer panel data - ferrets

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