“one-color microarray-based gene expression analysis—low input quick amp labeling” version 6.9.1  (Agilent technologies)

Journal: PLoS ONE

Article Title: Subclinical endometritis in dairy cattle is associated with distinct mRNA expression patterns in blood and endometrium

doi: 10.1371/journal.pone.0220244

Figure Lengend Snippet: ( A ) Principal component analysis (PCA) plots using all genes (probes) from microarray-based data obtained from endometrium and circulating white blood cells (WBC) collected from the same individuals (dairy Holstein cows) at 45–55 days postpartum (DPP). Plots and cluster distributions on 19,479 gene patterns are presented for endometrial biopsies and circulating white blood cells collected from 4 cows with subclinical endometritis (SCE; follicular phase, n = 1; luteal phase, n = 3) and from 4 healthy cows either in follicular phase (FP; n = 2) or in luteal phase (LP; n = 2). All SCE females were gathered in a unique group. The PCA score plots showed segregation between endometrium and WBC. Endometrial samples from SCE cows, healthy LP cows and healthy FP cows are indicated in green, dark blue and light blue color respectively. Circulating white blood cells (WBC) from SCE cows, healthy LP cows and healthy FP cows are indicated in orange, red and pink color respectively. ( B, C) Volcano plot analyses were used to show the differentially expressed genes in endometrium and in circulating white blood cells from cows with subclinical endometritis (SCE, n = 4) compared with healthy (n = 4) Holstein dairy cows at 45–55 days postpartum (DPP) respectively. The x-axis represents the log2 of the fold change (FC), which was plotted against the −log10 of the p-value. The p-value is equal to the f.value for down regulated genes or 1-f.value for up-regulated genes. The f.value thresholds 0,005 and 0,995 were used for down- or up-regulated genes (in green and red respectively). These threshold values lead to a selection error equal to 1%. ( D, E ) Principal component analysis (PCA) plot using differentially expressed genes (DEGs) identified in endometrium and circulating white blood cells from 4 Holstein dairy cows with subclinical endometritis (SCE) compared with 4 healthy Holstein dairy cows in luteal phase (LP; n = 2) or in follicular phase (FP; n = 2) at 45–55 days postpartum (DPP). ( D ) Endometrial biopsies from SCE cows (n = 4), healthy LP cows (n = 2) and healthy FP cows (n = 2) are indicated in green, dark blue and light blue color respectively. ( E ) Circulating white blood cells (WBC) from SCE cows (n = 4), healthy LP cows (n = 2) and healthy FP cows (n = 2) are indicated in orange, red and pink color respectively.

Article Snippet: The Agilent protocol “One-Color Microarray-Based Gene Expression Analysis–Low Input Quick Amp Labelling” version 6.5, May 2010 (Cat # G4140-90050) was used for RNA labeling.

Techniques: Microarray, Selection