Gene expression profiling between chicken tissues
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
SUBMITTER: Huaijun Zhou
PROVIDER: E-GEOD-21817 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Chicken 60-mer oligonucleotide microarray, including 39854 cDNA and ESTs, entire Marek’s disease virus and avian influenza virus genomes, and 150 chicken microRNAs, was developed. Cecal tonsil, ileum, liver and spleen from 6 chickens were selected for hybridization to validate the microarray performance. There are 2886, 2886, 2660, 358, 3208 3355, and 3710 genes significantly expressed between liver and spleen, spleen and cecal tonsil, cecal tonsil and ileum, liver and cecal tonsil, liver and ileum, spleen and ileum at the P<10-7. Number of tissue specific genes for cecal tonsil, ileum, liver and spleen was 95, 71, 535, and 108, respectively with p < 10-7. More than 95% of spots had high SNR (>10). Keywords: characteristics of newly developed microarray using different normal tissue Loop design was carried on for all of tissue samples from the six chickens. Samples of four tissues from a chicken were used in each loop. The order of the tissues in each loop was changed so that all pairs of tissues were combined on an array with an equal number of times. Dye swap was used so that each tissue was measured an equal number of times with each dye. Data from 12 measurements for each tissue were collected, in total, 48 measurements from 24 arrays.
2008-02-28 | E-GEOD-7452 | biostudies-arrayexpress
Project description:Campylobacter jejuni (C. jejuni) is a zoonotic pathogen that causes human diarrhea worldwide. Chickens are a natural reservoir of C. jejuni. Understanding the host response to C. jejuni infection at the molecular level will lay the foundation to control human campylobacterosis by reducing food contamination. Two distinct genetic lines, resistant (line A) and susceptible (line B) to C. jejuni colonization, were utilized to profile the host response to C. jejuni infection using an Agilent chicken 44K microarray. Day-old chickens were challenged orally with C. jejuni and spleens collected for total RNA 7 days post-challenge. Twenty infected samples with highest (a) or lowest bacterial number (b) in cecal content and twenty non-infected (c) in each line were randomly pooled into four biological replicates. The pair comparisons among these three groups within each line were analyzed. The signal intensity of each gene was normalized using LOWESS method. A mixed model was used to identify differentially expressed genes by SAS (P < 0.001). This was opposite to previous cecal tonsil microarray result. There were 468, 743, and 939 genes differentially expressed between groups a and c, groups a and b, and groups b and c in line A, respectively, and 201, 37, 126 genes in line B, respectively. More differentially expressed genes in spleen in line A than in line B were found. The results indicated that significantly different response to C. jejuni infection occurred between resistant and susceptible chicken lines, and the effects of interaction between genetics and tissue should be considered. Chickens in two broiler lines were inoculated with 10^5 cfu C. jejuni on one day after hatch. The cecal content and cecal tonsil was collected and bacterial number in cecal content was counted on day 7 after inoculation. Twenty samples were separated into 3 groups (high burden, low burden, and control) based on bacterial burden of cecal content in each line, 5 samples were mixed randomly into one pool. A dual color, balanced design was carried on for all samples. Three comparisons were used in each line, non-infected/susceptible, susceptible/resistant, resistant/non-infected, totally, four biological replicates in each line. A Dye swap was used in each pair of comparisons including AN/AS, AS/AR, AR/AN; BN/BS, BS/BR, and BR/BN. Background subtracted signal intensity were collected from 24 arrays and normalized for data analysis.
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Project description:To determine the host response to Salmonella Typhimurium (ST) in heterophils, a whole chicken genome array was used to analyze RNA isolated from heterophils stimulated in vitro with ST (30 min, 1 h, 2 h, and 3 h) or medium control (NS). Dual-color, direct comparisons were carried between ST-stimulated and non-stimulated controls (30 min vs. NS (30M/NS), 1 h vs. NS (1HR/NS), 2 h vs. NS (2HR/NS) and 3 h vs. NS (3HR/NS)). Each comparison includes four biological replicates. There were 2791, 3744, 12947 and 12482 genes differentially expressed in the comparisons of 30M/NS, 1HR/NS, 2HR/NS and 3HR/NS, respectively (P < 0.001) , while 50, 82, 153, and 146 genes were related to immune function, respectively. More than 80% of immune-related genes overlapped between the comparisons (30M/NS vs. 1HR/NS, 1HR/NS vs. 2HR/NS, and 2HR/NS vs. 3HR/NS). These candidate genes include cytokines (e.g. Interleukin (IL) 1β, -6, -10B and -12B), chemokines (e.g. IL-8, CCL4, K60 and K203) and cluster of differentiation (CD) markers (e.g. CD44, -47 and -83). A relatively large increase in the number of differentially expressed immune-related genes was observed between 1 h and 2 h post-stimulation. The results of continuous transcriptional change provide important information to elucidate both the cellular and molecular mechanisms of ST stimulation in chickens. Dual-color, common reference comparisons were carried between ST-stimulated (30M, 1HR, 2HR and 3HR) and non-stimulated controls (NS). Four biological replicates, with dye swap labeling, were included in the comparisons of each post-stimulation time point (30M/NS, 1HR/NS, 2HR/NS and 3HR/NS). Background subtracted signal intensity were collected from 16 arrays and normalized before data analysis.
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