Project description:To investigate the effect of TMIGD2 on transcriptional functions in human AML cell line, we performed gene expression profiling analysis using data obtained from RNA-seq of HEL cells upon TMIGD2 knockdown.
Project description:We used bs-ATLAS-seq to comprehensively map the genomic location and assess the DNA methylation status of human full-length LINE-1 elements (L1) in the genome of 2102Ep cells (E-MTAB-10895). We also achieved targeted nanopore sequencing to assay DNA methylation over a subset of loci (E-MTAB-12247). To further study the link between L1 DNA methylation and expression, we performed, in the same cell line, RNA-seq (E-MTAB-12246), as well as YY1 and H3K4me3 ChIP-seq (this dataset).
Project description:Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling, however the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read non-destructive approach that directly analyzes DNA and RNA fragments in real time. Recently, computational tools have been developed that enable base-resolution detection of 5mC from Oxford Nanopore sequencing data. In this chapter we provide a detailed protocol for preparation, sequencing, read assembly and analysis of genome-wide 5mC using Nanopore sequencing technologies.
Project description:A variety of newly developed next-generation sequencing technologies are making their way rapidly into the research and clinical applications, for which accuracy and cross-lab reproducibility are critical, and reference standards are much needed. However, there is still a lack of well-characterized reference materials which include epigenomic and proteomic data. Our previous multicenter studies under the SEQC-2 umbrella using a breast cancer cell line with paired B-cell line have produced large amount different genomic data including whole genome sequencing (Illumina, PacBio, Nanopore), HiC, and scRNA-seq with detailed analyses on somatic mutations, single-nucleotide variations (SNVs), and structure variations (SVs). Here we further performed ATAC-seq, Methyl-seq, RNA-seq, and proteomic analyses and provided a comprehensive catalog of epigenomic landscape, which overlapped with the transcriptomes and proteomes for the two cell lines. We identified >7,700 peptide isoforms, where the majority (95%) of the genes had a single peptide isoform and found that the protein expression levels of the transcripts overlapping CGIs were much higher than the protein expression levels of the non-CGI transcripts in both cell lines. We observed that open chromatin regions had low methylation while closed chromatin regions had high methylation, which were largely regulated by CG density, where CG-rich regions had more accessible chromatin, low methylation, and higher gene and protein expressions. The CG-poor regions had higher repressive epigenetic regulations (less open chromatin and higher DNA methylation), resulting in a cell line specific methylation and gene expression patterns. Our studies provide well-defined reference materials consisting of two cell lines with genomic, epigenomic, transcriptomic, scRNA-seq and proteomic characterizations which can serve as standards for validating and benchmarking not only on various omics assays, but also on bioinformatics methods. It will be a valuable resource for both research and clinical communities.
Project description:In order to confirm the functional dependency on KDM4C under treatment conditions with the JAK-inhibitor ruxolitinib (RUX), we applied a genome-wide CRISPR-Cas9 screen in the human JAK2-mutated cell line HEL by CRISPR/Cas9.
