PalateData: Murine Secondary Palate Development miRNA Expression Data
In MmPalateMiRNA: Murine Palate miRNA Expression Analysis

Description Usage Format Details Source Examples

This data set contains two-color miRNA microarray expression data obtained from mouse embryonic tissue during gestational days (GD) 12, 13, and 14, which represents the critical period of palate development in the mouse.

1	data(PalateData)

The data are in the format of an "RGList", which in this case is a list with the following 9 elements:

R

matrix of dimension 6336 x 9 which contains the red channel foreground measurements

G

matrix of dimension 6336 x 9 which contains the green channel foreground measurements

Rb

matrix of dimension 6336 x 9 which contains the red channel background measurements

Gb

matrix of dimension 6336 x 9 which contains the green channel background measurements

source

source of the images, here "imagene"

Field.Dimensions

numeric vector giving the field dimensions of the array (Metarows, Metacols, Rows and Cols)

weights

matrix of dimension 6336 x 9 which contains the quality weights associated with each spot on the arrays

printer

list containing information on the process used to print the spots on the arrays (number of grid rows / columns and number of spot rows / columns per grid - coincides with Field.Dimensions)

genes

A data.frame containing information on each probe. Has the following columns:

Field: field position for the probe
Meta Row: meta row position for the probe
Meta Column: meta column position for the probe
Row: row position for the probe
Column: column position for the probe
Gene ID: unique gene identifier provided by Miltenyi Biotec
ID: unique probe identifier constructed by concatentating the "Gene ID" with "Meta Row", "Meta Column", "Row", and "Column" information
Name: name of the microRNA
Name.stem: base name of the microRNA
probe.type: type of probe, "MMU miRNAs", "Other miRNAs", "Control", "Empty", and "Other"

RNA samples were isolated from mouse embryonic orofacial tissues (GD-12 - GD-14) and fluorescently labeled with Hy5 (red). Control samples (miRXplore Universal Reference) were labeled with Hy3 (green). The two sets of samples were hybridized to miRXplore Microarrays (Miltenyi Biotec) sing the a-Hyb Hybridization Station (Miltenyi Biotec). Probes for a total of 1336 mature miRNAs (from human, mouse, rat and virus), including positive control and calibration probes, were spotted in quadruplicate on each microarray. Each array included probes for 588 murine miRNAs.

P. Mukhopadhyay, G. Brock, V. Pihur, C. Webb, M.M. Pisano, and R.M. Greene. Developmental microRNA expression profiling of murine embryonic orofacial tissue. Birth Defects Res A Clin Mol Teratol, 88(7):511-34, 2010.