Project description:Methylation-based liquid biopsies show promise in detecting cancer from circulating cell-free DNA, but current limitations impede clinical application. Most assays necessitate substantial DNA inputs, posing challenges. Underrepresented tumor DNA fragments may go undetected during exponential amplification steps of traditional sequencing methods. Here we report LABS (Linear Amplification based Bisulfite Sequencing), enabling linear amplification of bisulfite-treated DNA fragments in a genome-wide, unbiased fashion, detecting cancer abnormalities with sub-nanogram inputs. Applying LABS to 100 patient samples revealed cancer-specific patterns, copy number alterations, and enhanced cancer detection accuracy by identifying tissue-of-origin and immune cell composition.
Project description:We report RNA sequencing data from the infraspinatus muscles of 3-month old male C57BL/6J (Jackson Labs stock 000664) or MRL/MpJ mice (Jackson Labs stock 000486). Mice underwent a full-thickness infraspinatus tenectomy and denervation, and four weeks later muscles were collected for analysis. Comparisons are made to control male mice of the same strains who did not undergo infraspinatus tenectomy and denervation.
Project description:Compendium of high-throughput sequencing datasets derived from murine CD8+ T cells responding to infection, profiled by RNA-seq, ChIP-seq, and ATAC-seq at Naïve, Effector, and Memory timepoints across the Kaech, Goldrath, and Pereira labs, and ChIP-seq of various transcription factors across several labs Submission contains both original data from the Kaech lab and reanalysis of data from the Pereira and Goldrath labs, as well as various other labs corresponding to individual transcription factor ChIP-seq datasets, totaling to 96 reanalyzed GSM samples across several GSE series Included GSE series are: GSE95237 (Genome-wide maps of chromatin state and chromatin accessibility in CD8 T cell subsets), GSE95238 (Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation), GSE88987 (Dynamic changes in chromatin accessibility in CD8+ T cells responding to viral infection), GSE58075 (Genome-wide mapping of Myc, AP4, and phosphorylated RNA polymerase II binding in activated CD8 T cells by ChIP sequencing), GSE54191 (ChIP-Seq analysis of BATF, IRF4, the Jun proteins, and histone modifications in effector CD8+ T cells), GSE20898 (Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types), GSE46943 (Transcription Factor Foxo1 Controls Memory CD8+ T Cell Responses To Infection [ChIP-Seq]), GSE72997 (ChIP-Seq analysis of Helios and histone modifications in CD4+ and CD8+ Tregs), GSE50128 (Genome-wide maps of Runx3 bound regions in splenic IL-2-activated CD8+ T cells), GSE72565 (Binding of STAT5 upon IL-2 treatment to genomic sites in mouse CD8 T cells costimulated in vivo through CD134 plus CD137), GSE49930 (The transcription factor IRF4 is essential for T cell receptor affinity mediated metabolic programming and clonal expansion of T cells [ChIP-seq]), and GSE52070 (Genome-wide maps of Tcf1 binding locations in splenic CD8 T cells)