Project description:We recently showed that the Slamf6 protein isoform Slamf6-H1 markedly diminishes T cell–dependent disease upon introduction of a Slamf6-H1–expressing transgene into the lupus-prone Sle1b mouse, which lacks this isoform. In this study we purified CD4+ T cells from Sle1b, Sle1b.Slamf6-H1, or B6 mice and a global gene expression profile was analyzed.
Project description:HDMYZ cells were treated with 2ug/ml ActD for 0, 4 and 12 hours. Small RNAs of 15-40 bases were gel-purified from 10 ug total RNA, and subjected to multiplex Illumina small RNA library preparation. Small RNA libraries were sequenced on a HiSeq2000 (Illumina) with 3 samples per lane. To quantify miRNA and isoform abundance, sequence reads were processed by the miRDeep2 package, with the following modifications. First, to remove adaptor sequence, we removed both the main adaptor sequence present in the sequencing reads, as well as the second most abundant adaptor variant. In addition, we did not restrict the size of small RNAs during adaptor removal. Second, we used miRBase v18 for mapping the reads. Third, for quantifying miRNA and isoform frequency, we limited reads to more or equal to 15 bases in length with zero mis-match during mapping. The number of reads that were mapped to known miRNAs was used to normalize read frequencies for each miRNA or each miRNA isoform. For quantification purposes, we only considered miRNAs or isoforms that had frequency >= 1x10e-6 in samples without ActD treatment, which correspond to ~21-30 reads in raw count. These miRNAs or isoforms were referred to as reliably quantifiable.To analyze mapping to the genome, we removed reads that mapped to miRNA precursors. The rest of the reads were then mapped to the genome with Bowtie.
Project description:Comparison of gene expression in pancreatic islets of BTBR-ob/ob mouse model of obesity-induced type 2 diabetes, and in non-diabetic control mice, B6-ob/ob identified Asf1b as an important gene candidate predictive of diabetic outcome. Asf1B expression was suppressed in response to age in both B6 and BTBR islets, induced by obesity only in B6 islets. This is consistent with other studies reporting a decline in -cell proliferation with age. Asf1b also strongly correlated (R ~ 0.98) with cellular proliferation marker Mki67. Overexpression of Asf1B induced β-cell proliferation in human islets. We show that many genes involved in regulation of cell cycle or programmed cell death are differentially regulated by Asf1B overexpression.
Project description:We recently showed that the Slamf6 protein isoform Slamf6-H1 markedly diminishes T cell–dependent disease upon introduction of a Slamf6-H1–expressing transgene into the lupus-prone Sle1b mouse, which lacks this isoform. In this study we purified CD4+ T cells from Sle1b, Sle1b.Slamf6-H1, or B6 mice and a global gene expression profile was analyzed. Comparison of isolated cells from three strains of mice (12wk old females) at three time points of anti-CD3 activation with three biological replicates for each group (unless indicated otherwise).