Project description:The contrasting dose of sex chromosomes in males and females potentially introduces a large-scale imbalance in levels of gene expression between sexes. In many organisms dosage compensation has thus evolved to equalize sex-linked gene expression in males and females1,2, in mammals achieved by X chromosome inactivation and in flies and worms by up- or down-regulation of X-linked expression, respectively. Another form of dosage compensation ensures that expression levels on the X chromosome and on autosomes are balanced3,4. While otherwise widespread in systems with heteromorphic sex chromosomes, the case of dosage compensation in birds (males ZZ, females ZW) remains an unsolved enigma5,6. Here we use a microarray approach to show that male day 18 chicken embryos generally express higher levels of Z-linked genes than female birds, both in soma and in gonads. The distribution of male-to-female fold-change values for Z chromosome genes is wide and has a mean of 1.4-1.6, which is consistent with absence of dosage compensation and sex-specific feedback regulation of gene expression at individual loci2. Intriguingly, without global dosage compensation, female chicken has significantly lower expression levels of Z-linked compared to autosomal genes, which is not the case in male birds. The pronounced sex difference in gene expression is likely to contribute to sexual dimorphism among birds, and potentially has implication to avian sex determination. Experiment Overall Design: Sample collection Experiment Overall Design: Fertilized eggs from White Leghorn fowl were purchased from OVA Production (MorgongM-CM-%va, Sweden). The eggs were incubated at 37.5C and 60% relative humidity, and were turned every 3 hours. After 18 days of incubation (ed18), the embryos were euthanized by decapitation. A piece from the apical part of the heart was collected and the left gonad and the brain were excised. The cerebellum, the optic lobes and the cerebral hemispheres were removed from the brain and, consequently, the brain sample included the intact diencephalon and remaining parts from other regions. The samples were immediately frozen in liquid nitrogen and then stored at -70 M-BM-0C. The embryos were sexed by ocular inspection of the gonads and MM-CM-<llerian ducts. Experiment Overall Design: RNA preparation and microarray hybridization Experiment Overall Design: Heart, left gonads and diencephalon from each of four male and four female embryos were homogenized by syringe and needle followed by use of the Homogenizer system (Invitrogen, Carlsbad, CA, USA). RNA was extracted from heart and brain homogenates with the PureLink Micro-to-Midi Total RNA Purification System (Invitrogen), and RNA was then DNase treated with a DNA-free kit (Ambion, Austin, TX, USA). Due to limited amounts of available tissue, gonad RNA extraction was performed with an RNeasy Micro Kit (Qiagen, Hilden, Germany) with integrated DNase treatment. RNA concentration was measured with ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA quality was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc, Palo Alto, CA). Two micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChipM-BM-. Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA). Affymetrix GeneChipM-BM-. expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45M-BM-0C incubator, rotated at 60 rpm. According to the GeneChipM-BM-. Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA), the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChipM-BM-. Scanner 3000 7G. In total, 24 hybridizations were made (4 individuals x 3 tissues x 2 sexes), however, three samples failed to meet Affymetrix quality control criteria and were removed from further analysis (heart and brain from one male, and gonads from one female). Experiment Overall Design: Microarray data analysis. All pre-processing and statistical analysis of microarray data was performed in R version 2.4.1 using Bioconductor packages release 1.9 (ref. 29). The CEL files were processed using GCRMA30, a background adjustment method taking into account the GC content of probes when assessing non-specific binding, followed by quantile normalization and median-polish summarization of probe intensities into probe set intensities. A linear model was fitted to the log2 of the expression levels based on all probe sets and considering sex and tissue as a combined factor using the Limma package. After pre-processing and linear model fitting the probe sets were filtered on expression; an expression threshold was set on both average expression level and absent/present calls from the R implementation of the Affymetrix MAS 5.0 algorithm. Only probe sets with average expression over a defined threshold and present in more than half of the samples within at least one tissue-sex combination were considered as significantly expressed. This resulted in 15,398 probe sets for heart, 16,846 for brain and 17,438 for gonads, and these probe sets composed the reference for analysis of differently expressed genes between the sexes. Experiment Overall Design: Annotation of probe sets Experiment Overall Design: Annotations for the probe sets were extracted from Ensembl (www.ensembl.org) via biomRt in R. The Ensembl mapping of probe sets is based on alignments of individual probes to the chicken genome version 2.1 (WASHUC2 May 2006) and covers 21,885 of the 37,693 chicken-specific probe sets, which is close to the total number of protein-coding genes in the chicken genome identified by Ensembl. Several transcripts are represented by more than one probe set; the 21,885 probe sets with annotation corresponds to 14,414 unique transcripts. The genomic location for probe sets was taken from Ensembl. Experiment Overall Design: Statistical analysis Experiment Overall Design: Fold-change was calculated as the average male expression over ave Experiment Overall Design: rage female expression, and a Bayesian moderated t-statistic for differential expression between males and females was then generated for each tissue. To take multiple testing into account p-values (corrected p-values) were adjusted using the Benjamini and Hochberg false discovery rate (FDR) method32. Probe sets with an absolute fold-change value larger than various threshold levels were considered sex-biased. Statistical testing of differences in levels of hybridization intensities between sex and/or chromosome categories was done by bootstrapping. The FisherM-bM-^@M-^Ys exact test was used to test the distribution of gene ontology terms and the distribution of sex-biased genes across chromosomes. Spearman rank correlation coefficients were calculated for the continuous fold-change values and several genomic parameters including gene density, microsatellite and CR1 retrotransposons repeat density, and GC content, all taken from Ensembl. These parameters were estimated based on averaging over a 100 kb window surrounding each gene.

Project description:DNA from Epstein-Barr virus (EBV)-transformed lymphocyte cell lines (LCLs) has proven very useful for studies of genetic sequence polymorphisms. Whether EBV-LCL DNA is suitable for methylation studies is less clear. We conduct a genome-wide methylation investigation using an array set with 45 million probes to investigate the methylome of EBV-LCL DNA and technical duplicates of whole blood (WB) DNA from the same 10 individuals. Methylation sites that show variation between individuals are potentially useful as biomarkers in disease studies. Our comparison is, therefore, focused specifically on these methylation variable sites. The sample correlations (i.e., a measure of whether the rank of the signals remains consistent between two samples from the same individual) for the methylation variable probes ranged from 0.69-0.78 for the WB duplicates and from 0.27-0.72 for WB versus EBV-LCL. To compare the pattern of the methylation signals, we grouped adjacent probes based on their inter-correlations. These analyses showed ~29,000 blocks in WB and ~14,000 blocks in EBV-LCL. Furthermore, merely 31% of the methylated regions detected in WB were detectable in EBV-LCLs. Our study shows that there are substantial differences in the DNA methylation patterns between EBV-LCL and WB. Thus, EBV-LCL DNA cannot be used as a proxy for WB DNA in methylation studies. The methylation of technical duplicates of DNA extracted from whole blood from 10 individuals, as well as DNA extracted from EBV-transformed lymphocyte cell lines (EBV-LCL) from the same samples of whole blood, are investigated using the Affymetrix GeneChip Human Tiling 2.0R array set. In total, 30 samples from 10 individuals were investigated on 7 arrays. The supplementary "GSE35204_ChrXX_bgc_qt.txt" files contain the background-corrected and quantile-normalized data for all 30 samples per chromosome. The files include 32 columns: 'Seq' refers to the chromosome, 'Pos' indicates the position in the genome on that chromosome, and columns 3-32 indicate the sample numbers.

Project description:Macrophages play a critical role in innate immunity, and the expression of early response genes orchestrate much of the initial response of the immune system. Macrophages undergo extensive transcriptional reprogramming in response to inflammatory stimuli such as Lipopolysaccharide (LPS). To identify gene transcription regulation patterns involved in early innate immune responses, we used two genome-wide approaches - gene expression profiling and chromatin immunoprecipitation-sequencing (ChIP-seq) analysis. We examined the effect of 2 hrs LPS stimulation on early gene expression and its relation to chromatin remodeling (H3 acetylation; H3Ac) and promoter binding of Sp1 and RNA polymerase II phosphorylated at serine 5 (S5P RNAPII), which is a marker for transcriptional initiation. Our results indicate novel and alternative gene regulatory mechanisms for certain proinflammatory genes. We identified two groups of up-regulated inflammatory genes with respect to chromatin modification and promoter features. One group, including highly up-regulated genes such as tumor necrosis factor (TNF), was characterized by H3Ac, high CpG content and lack of TATA boxes. The second group, containing inflammatory mediators (interleukins and CCL chemokines), was up-regulated upon LPS stimulation despite lacking H3Ac in their annotated promoters, which were low in CpG content but did contain TATA boxes. Genome-wide analysis showed that few H3Ac peaks were unique to either +/-LPS condition. However, within these, an unpacking/expansion of already existing H3Ac peaks was observed upon LPS stimulation. In contrast, a significant proportion of S5P RNAPII peaks (approx 40%) was unique to either condition. Furthermore, data indicated a large portion of previously unannotated TSSs, particularly in LPS-stimulated macrophages, where only 28% of unique S5P RNAPII peaks overlap annotated promoters. The regulation of the inflammatory response appears to occur in a very specific manner at the chromatin level for specific genes and this study highlights the level of fine-tuning that occurs in the immune response. 4 pairs of THP-1 cells either stimulated with LPS or not This submission represents transcriptome component of study.

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Hepatosplenic T cell lymphoma

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