Comparative RNA sequencing of the jejuna of two lines of chickens divergently selected for antibody response to sheep red blood cells, with and without antigen exposure
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ABSTRACT:
PROVIDER: PRJNA852232 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19805418.fastq.gz | Fastqsanger.gz | |||
| SRR19805419.fastq.gz | Fastqsanger.gz | |||
| SRR19805420.fastq.gz | Fastqsanger.gz | |||
| SRR19805421.fastq.gz | Fastqsanger.gz | |||
| SRR19805422.fastq.gz | Fastqsanger.gz |
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Project description:Two lines of White Leghorn chickens have been continuously divergently selected for high (HAS) or low (LAS) 5 day post injection antibody titer to injection with sheep red blood cells (SRBC) for over 40 generations. Much remains to be understood about their antibody response phenotypes, therfore we chose to sequence the transcriptomes of the jejunum from individuals of the two lines which had (HASI/LASI) and had not (HASN/LASN) been injected with SRBC to examine differences in gene expression related to divergent selection and antibody response.
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Project description:Divergently selected chickens for either high growth (HG genotype) or low growth (LG genotype) developed 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 HG and LG chickens are different in various phenotypic and metabolic measurements, including growth rate, abdominal fat, plasma glycemia, insulinemia, T4, T3, triglyceride and NEFA. The HG and LG chickens are valuable as a model for 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 number of 531 differentially expressed genes were identified. The greatest number of genes was detected at 7 weeks of age where 178 genes were up-regulated in the HG and 162 genes up-regulated in the LG. The differentially expressed genes include metabolic enzymes, acute phase proteins, immune factors and transcription factors involved in various pathways (i.e., fatty acid and amino acid metabolism, glycolysis, oxidative phosphorylation, growth factor signaling and immune defense). Several of these functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the HG and LG lines. Keywords: divergently selected chickens, growth, transcriptional profiling, differentially expressed genes
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2013-04-16 | GSE42980 | GEO
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 abdominal adipose 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 abdominal adipose during juvenile development using a balanced block hybridization design. Fluorescence intensities were normalized within array (without background subtraction), and between array (aquantile method) in LIMMA package R [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3] producing M-values (log-2 expression ratios) and A-values (average log-2 expression values). Normalized values were analyzed using a two factor ANOVA model. A total of 3,669 unique differentially expressed functional genes were identified (FDR<0.05). Genes were determined to have a significant effect of age (3,222), genotype (344), or an age by genotype interaction (254). The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation 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. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes
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Project description:Chickens divergently selected for either high growth (HG genotype) or low growth (LG genotype) by F.H. Ricard at SRA-INRA, Nouzilly France were used for time-course transcriptional profiling of abdominal fat during juvenile development (1 to 11 weeks of age) to identify differentially expressed genes. The HG and LG chickens are different in various phenotypic and metabolic measurements, including growth rate, abdominal fat, plasma glycemia, insulinemia, T4, T3, triglyceride and NEFA. Thus, the HG and LG chickens are valuable as a model for biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in abdominal adipose during juvenile development using a balanced block hybridization design. Log2-transformed fluorescence intensities were analyzed with the linear mixed model (MIXED) procedure in SAS (SAS Institute Inc., Cary, NC, USA). A total of 3,957 differentially expressed functional genes were identified (FDR<0.05) as having a significant effect of age (2,918), genotype (312), or an age by genotype interaction (727). The differentially expressed genes include adipokines, metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors and transcription factors involved in various pathways. Keywords: abdominal fat, divergently selected chickens, growth, transcriptional profiling, differentially expressed genes, lipogenesis A balanced 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 (HG or LG) at six different ages (1, 3, 5, 7, 9 and 11 wk).
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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 abdominal adipose 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 abdominal adipose during juvenile development using a balanced block hybridization design. Fluorescence intensities were normalized within array (without background subtraction), and between array (aquantile method) in LIMMA package R [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3] producing M-values (log-2 expression ratios) and A-values (average log-2 expression values). Normalized values were analyzed using a two factor ANOVA model. A total of 1,020 differentially expressed functional genes were identified (FDR<0.05). Genes were determined to have a significant effect of age (422), genotype (344), or an age by genotype interaction (254). The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation 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. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes A balanced 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).
2012-04-26 | E-GEOD-37585 | biostudies-arrayexpress
Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at Station Recherches Avicoles, Institut National de la Recherche Agronomique Nouzilly, France were used to profile abdominal fat gene expression at 7 weeks of age. The fat line (FL) and lean line (LL) chickens differ in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and triiodothyronine (T3). The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. Massively parallel RNA sequencing (RNA-Seq) was completed on an Illumina HiSeq 2000 System for transcription analysis of FL and LL abdominal fat. Statistical analysis was completed using CLC Genomics Workbench software. A total of 1,703 genes were differentially expressed in the FL versus LL adipose tissue [FDR<0.05 and fold change (FL/LL) > 1.2]. The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors, vasoregulators and transcription factors involved in various pathways. Several of the functional genes identified are also positional candidate genes within quantitative trait loci (QTL) in an F2 population created from an intercross of the FL and LL lines. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes Abdominal fat mRNA profiles of fat line (FL) and lean line (LL) chickens at 7 weeks of age were generated by deep sequencing (on an Illumina HiSeq 2000 system) employing several sequencing schemes to determine depth of coverage from 1, 4, and 8 multiplexed libraries per sequencing lane. Transcriptional analysis was completed by averaging short paired-end sequence reads (101 bp) for each bird across three sequencing depths.
2013-04-16 | E-GEOD-42980 | biostudies-arrayexpress