Project description:Next-generation sequencing measuring ribosome mRNA occupancy and translation efficiency in CD4+ T cells isolated from Mettl3 KO and WT mice
Project description:CD4+ T cells were isolated by StemCell CD4+ T cell isolation kit of spleen and lymph nodes WT mice. Total RNAs were isolated from the pure CD4+ T cells, subjected to standard m6A RIP protocol. The libraries were generated with IPed and Input RNAs and subjected to sequencing. Raw sequencing reads were aligned to the mouse genome (mm10) with Tophat, and gene expression levels were measured by Cufflinks.
Project description:Methylated RNA immunoprecipitation(MeRIP) with specific m6A antibody and used for library construction and the next generation sequencing, to identify m6A modified transcripts in WT or Ythdf1 deficiency colon epithelial cells after DSS treatment
Project description:RPE cells from WT and Total RNA was isolated from WT and LC3b-/- mice were isolated by enzymatic treatment and gentle dissociation, followed by RNA extraction. RNA-sequencing by the Next-Generation Sequencing Core of the University of Pennsylvania.
Project description:Naïve T cells of Mettl3 KO and WT were pulse labeled by s4U for 15 min before and after IL-7 stimulation for 15min/30min/45min/60min/75min/90min. The total input RNAs or s4U nascent RNAs were isolated and prepared for next-generation sequencing. The RNA response to IL-7 and RNA decay rates were then modeled and calculated, to infer the m6A/Mettl3 effects.
Project description:Epigenetic profile of tissues is reprogrammed under diseased conditions. H3K4Me3 and H3K27Me3 represent active and repressive epigenetic marks, respectively. ChIP-seq is an effective tool to study global protein-DNA interactions. To study global epigenetic differences, we used H3K4Me3 antibody to evaluate its enrichment in pancreatic acinar cells of WT and Mist1-/- mice followed by next generation sequencing. We found specific hotspots that showed differential enrichment for H3K4Me3 both in WT and Mist1-/- mice. The data show that pancreatic acinar cells are epigenetically reprogrammed under stressed cellular conditions. Global H3K4Me3 profiling of WT and Mist1-/- pancreatic acinar cells using ChIP-seq.
Project description:We analyzed the total proteome of CD4+ T cells isolated from WT mice, either non stimulated or at 5 different time points of stimulation with anti-CD3 and anti-CD4 antibodies (30s; 120s; 300s; 600s)
Project description:To investigate the role of DREAM (a transcriptional repressor) in regulating gene transcription in neutrophils under inflammatory conditions, we conducted the next generation sequencing using unstimulated and TNF-alpha-stimulated neutrophils isolated from WT and DREAM KO mice.
