Project description:Methyl-seq data was obtained from total peripheral blood mononuclear cells of two patients with systemic lupus erythematosus who were characterized as having>2 standard deviations more ARID3a-expressing B lymphocytes than healthy controls. Similarly, methyl-seq data was also obtained from two SLE patient samples with normal (low) numbers of ARID3-expressing B lymphocytes. Our previous studies showed that increased ARID3a expression in B lymphocytes was associated increased disease activity. Data were generated on an Illumina Hiseq 2000 with paired-end 100bp reads and quality control metrics were assessed with Picard tools. Methylation profiles of genomic DNA from four SLE patient PBMC samples, two with high numbers of ARID3a expressing B cells (ARID3aH) versus two with normal numbers of ARID3a+ B cells (ARID3aN), were generated on an Illumina Hiseq 2000 with paired-end 100bp reads.
Project description:Mammary glands of 8 adult (10 week-old) female mice were collected. Freshly sorted basal and luminal epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100bp paired-end reads.
Project description:This SuperSeries is composed of the SubSeries listed below. Mammary glands were collected from female mice of various ages: pre puberty (2 weeks), pubescent (5 weeks), adult (10 weeks) and pregnant (12.5 days mid-pregnancy). Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. In some cases, cells were further sorted into basal and luminal subsets. Cells were visualized under a microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were sequencing on an Illumina HiSeq 2000 to achieve 100bp paired-end reads or on an Illumina NextSeq to achieve 75bp paired-end reads.
Project description:To understand the genetic regulation of gene expression and patterns of gene co-expression, we sequenced the transcriptome of the hippocampus of founder mice of both sexes. Mice were sacrificed between 6-8 weeks of age and hippocampus dissected. Total hippocampal RNA was isolated using a TRIzol Plus RNA purification kit (Life Technologies) and mRNA sequencing library was prepared using a TruSeq kit (Illumina), both according to manufacturer's protocols. Paired-end 100bp reads were obtained using the Illumina HiSeq 2000.
Project description:The study used two Drosophila melanogaster fly lines, Alstonville and Dahomey, which have mitochondrial DNA variants but otherwise similar genomes. Female third instar larvae from both lines were fed on two diets, one with a 1:2 protein:carbohydrate ratio and the other with a 1:16 ratio. RNA was extracted and profiled by RNA-seq. Samples were sequenced on an Illumina Hiseq 2000 sequencer at the Ramaciotti Centre for Genomics, Sydney, Australia to produce 100bp paired end reads. At least 80 million read pairs were generated per sample.
Project description:Methyl-seq data was obtained from total peripheral blood mononuclear cells of two patients with systemic lupus erythematosus who were characterized as having>2 standard deviations more ARID3a-expressing B lymphocytes than healthy controls. Similarly, methyl-seq data was also obtained from two SLE patient samples with normal (low) numbers of ARID3-expressing B lymphocytes. Our previous studies showed that increased ARID3a expression in B lymphocytes was associated increased disease activity. Data were generated on an Illumina Hiseq 2000 with paired-end 100bp reads and quality control metrics were assessed with Picard tools.