Gene expression profile analysis of F2 cross between Fat and Lean chickens
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ABSTRACT:
ORGANISM(S): Gallus gallus
SUBMITTER: Cécile Berri
PROVIDER: E-GEOD-17428 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:cDNA microarrays were used to identify the expression of the genes in uterus by comparison with two others regions of the oviduct not involved in the shell deposition. A total of 605 sequences specifically over-expressed were revealed. The expression of 15 of them was also confirmed using qRT-PCR, and confirmed the microarray expression. The 605 uterine transcripts corresponded to 469 and 437 different genes and proteins respectively. A global interpretation of their functions was assessed using the Gene Ontology terms and the most over-represented terms are relative to the mineral transport and transfer necessary to the calcification process. The study has revealed 53 proteins which could be secreted to be deposited in the shell to be biologically actives. The study of their functions reveals proteins known for their involvement in the biomineralization or with calcium binding properties to interact with the mineral phase during the eggshell fabric. A large group of proteins could be involved in the folding of the matrix, and a notable group of uterine secreted proteins was also identified as antibacterial to contribute to the antimicrobial protection of the egg. Finally the study revealed proteases and protease inhibitors which could play an active role in the regulation of the protein activities in the acellular uterine fluid where the eggshell is formed. Keywords: Laying hen, eggshell, oviduct, uterine expression, cDNA microarray, indirect cDNA labelling, Alexa Fluor dyes A balanced block hybridization design (Dye switch) was used where half of the samples were labelled with Alexa® 555 fluorescent dye and the other half with Alexa® 647. A total of 16 microarray slides were used for hybridization to 32 samples that correspond to four tissue contrast (uterus versus magnum and uterus versus white isthmus).
2010-05-06 | E-GEOD-17267 | biostudies-arrayexpress
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Project description:Head and neck squamous cell carcinomas (HNSCCs) is the seventh most common solid malignancy in the United States, accounting for more than 47,000 new cancer cases. HNSCC shows significant diversity in its clinical behavior after treatment, which cannot be predicted using the current clinical or pathological markers. Despite tumor complexity, many studies have tried unsuccessfully to test single genes to be used as prognostic markers in HNSCC. A group of tumor samples can be characterized in terms of the behavior of modules. These modules include clusters of coexpressed genes, such as genes that belong to the same pathway or functional category. Cancer is a multifaceted phenomenon that involves activation and/or disruption of various cellular processes. Thus, the identification of pathways or group of genes such as those involved in the development of lymph node metastasis and recurrent disease may help understanding the complex biology of cancer. Samples were obtained during surgery and neck dissection of 47 patients with primary untreated HNSCC at the Head and Neck Surgery Department from the Hospital AC Camargo (São Paulo, Brazil) between 1998 and 2003. Diagnosis of HNSCC was determined by biopsy. All patients signed a pre-informed consent and the study was approved by our institutional review board. After surgery, all patients were treated with adjuvant radiotherapy. Recurrence were diagnosed by imaging or biopsy. Tumor samples were snap-frozen in liquid nitrogen. Before RNA extraction, diagnosis was confirmed by hematoxylin-eosin staining. Frozen samples were hand dissected for removal of normal cells, necrosis, and infiltrating inflammatory cells. Total RNA was extracted using TRIzol. RNA quality was accessed by spectrophotometry and gel electrophoresis. To be considered as high-quality, the RNA had to have a 260/280 ratio higher than 1.7 and a 18S/28S rRNA ratio ~2. Amplifictaion of the mRNA was done using a T7-based protocol and cDNA was indirectly labeled with Alexa Dye 555 or 647. Samples and a common RNA reference were hybridized overnight at 42oC in dye-swap to a 4,800-element in-house printed microarray, enriched with cancer-related ESTs derived from the Human Cancer Genome Project. After washing, slides were scanned on a confocal laser scanner and data were extracted.
2010-06-10 | E-GEOD-22055 | biostudies-arrayexpress
Project description:Mice were intranasally instilled at 6 weeks of age with silica, titanium dioxide, or saline control and macrophages were harvested by broncho-alveolar lavage at 14 weeks of age. RNA was isolated using RNeasy Mini kits (Qiagen). Due to low yield of RNA, mRNA was amplifed by RiboAmp kits (Arcturus) and resulting aRNA was indirectly labeled with Alexa-Fluor 647 dye (Molecular Probes). This was hybridized against Universal Mouse Reference RNA (Stratagene) which was indirectly labeled with Alexa-Fluor 555 dye (Molecular Probes). Slides were printed in house using PCR product cDNA targets on GAPS slides (Corning). Slides were scanned with an Axon GenePix 4000B scanner and data was analyzed using GenePix Pro 4.0 software and Iobion GeneTraffic Duo software. Data was normalized to a total 1:1 ratio of read to green dye.
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Project description:Even though feather pecking (FP) in laying hens has been extensively studied, a good solution to prevent chickens from this behavior under commercial circumstances has not been found. Selection against FP behavior is possible, but for a more effective selection across different populations, it is necessary to characterize the genetic mechanism associated with this behavior. In this study, we use a high FP selection line, which has been selected for 8 generations. We present evidence of the presence of a major dominant allele affecting the FP behavior by using an argument based on the presence of mixture in the distribution of the observed FP and by studying the evolution of the proportion of very high FP along the sequence of 8 generations. This hypothesis is further supported by the fact that the gene transcription profile of the birds performing high FP differs from the profile of the other birds performing FP (456 genes differentially expressed from a total of 14,077 investigated genes). Keywords: severe feather pecking , selection , modeling , inheritance pattern From each selection line (high feather pecking line, low feather pecking line and control line) 60 animals were randomly selected. Within each line the birds were randomly assigned to a cage of 20. The cages were kept in a randomized block design. Number of samples analyzed in total: 179 (60 high feather pecking line, 60 low feather pecking line, 59 control line samples. Common reference design using total-RNA purified from brain from a single F1 cross between the high and low feather pecking line as reference.
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Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile hepatic gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in liver during juvenile development using a balanced block hybridization design. Log2-transformed fluorescence intensities were analyzed with a two-stage mixed model. A total of 905 differentially expressed "functional" genes were identified (FDR<0.10). The greatest number of differentially expressed genes (400) was detected at 7 weeks of age. The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, immune factors and transcription factors involved in various pathways. Several of the functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the FL and LL lines. A balance block design was used for microarray hybridizations, where half of the birds of each genotype and age were labeled with Alexa Flour 647 (red) and the other half with Alexa Flour 555 (green). Four biological replicates were used for each genotype (FL or LL) at six different ages (1, 3, 5, 7, 9 and 11 wk).
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