shoemaker2015: Time course transcriptomic from mouse lung tissues infected...

In NelleV/timecoursedata: A data package for timecourse RNA-seq and microarray gene expression data sets

Description

Time-course microarray data from "An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation".

Usage

data(shoemaker2015)

Format

A list with two related datasets: a gene expression data set (element data) and corresponding meta data (element meta). The column names of data correspond to the rownames of meta, linking the samples together in the two datasets. See examples for accessing these two data.frames.

Details

This is data from a micro-array time-course experiment, exposing mice to three different strains of influenza, and collecting lung tissue during 14 time-points after infection (0, 3, 6, 9, 12, 18, 24, 30, 36, 48, 60 hours, then 3, 5, and 7 days later) [8]. The three strains of influenza used in the study are (1) a low pathogenicity seasonal H1N1 influenza virus (A/Kawasaki/UTK4/2009 [H1N1]), a mildly pathogenic virus from the 2009 pandemic season (A/California/04/2009 [H1N1]), and a highly pathogenic H5N1 avian influenza virus (A/Vietnam/1203/2004 [H5N1]. Mice were injected with 105 PFU of each virus. An additional 42 mice were injected with a lower dose of the Vietnam avian influenza virus (103 PFU).

data is a data frame with 39544 rows corresponding to genes and 209 corresponding to samples. The rownames give the RefSeq name of the gene.

meta is a data frame with 209 rows corresponding to samples and 3 named columns (the first column is just an index from 0-208):

Group

The treatment group of the sample. "C"=Control, "K"=Kawasaki strain, "M"=California strain, "VH"=Vietnam strain, "VL"=Vietnam at lower dosage (103 PFU).

Replicate

Identifies the replicate – each combination of treatment and timepoint was replicated three times (except for VH at timepoint 3, which has only 2 replicates).

Timepoint

Identifies the time passed (in days) since infection of the sample

References

Shoemaker et al. (2015) PLOS Pathog. (PubMed)

Examples

data(shoemaker2015)
data = attr(shoemaker2015, "data")
meta = attr(shoemaker2015, "meta")

NelleV/timecoursedata documentation built on June 30, 2021, 11:07 p.m.