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data-emporium's Introduction

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).

Contents:

  • 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

Influenza cohort data

  • NPICS - [description pending]
  • HIVE - [description pending]

data-emporium's People

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