Other next-generation sequencing (NGS) data analysis (ATAC-seq, CAGE, ChIA-PET, Hi-C, etc. 10x Genomics Chromium single-cell RNA-seq data for four mouse liver samples.
Variant calling from genotyping/WGS/WES data, and QC, peak calling, differential binding, UCSC Genome Browser visualization, etc.) Single-cell omics analysis (10x Genomics pipeline, clustering, trajectory analysis, spatial transcriptomics, etc.), RNA-seq analysis (from raw sequencing data to QC, to normalized gene expression table, group comparison, pathway analysis, and interactive reporting and visualization of the results), Data management (storage/backup, meta-table management, GEO/dbGap submission), You can use it for Single Cell CNV, Single Cell Gene Expression, Single Cell Immune Profiling, and Single Cell ATAC.Īt this stage, the program will primarily provide NGS data analysis service, including but not limited to:
We also provide a single-cell genomics platform: 10x Genomics CHROMIUM CONTROLLER. It’s an affordable, secured, and customized service that both you and your data deserve. For later, we will take care of your data with seamless service, from data management, data backup, data QC, downstream NGS analysis, till the final uploading to GEO/dbGap before your publication. You can choose either to upload the data to Illumina’s cloud storage or save it to the designated space on Partners’ ERISone high-performance computing cluster. The first method, the 10X Genomics (10XG) Chromium chemistry, incorporates unique molecular indexes (UMI) into single long DNAs and assembles these into gapped. Throughout his career, Robert has authored over 40 publications in several peer-reviewed journals including Science and Nature.As part of the service that our NeuroTech Studio provides, our customers can access the brand new Illumina NextSeq 550 sequencing machine. Robert is also currently a member of the Association of Biomolecular Resource Facilities (ABRF) and has served or is currently serving on the DNA Sequencing Research Group (DSRG), Genomics Research Group (GRG), the Northeast Regional Life Sciences Core Directors annual meeting organizing committee (NERLSCD-OC) and the ABRF Corporate Relations Committee (CRC). The core currently utilizes a number of different Illumina NGS sequencers as well as robotics for Illumina compatible library preparation from DNA and RNA sources. Constant evaluation of the NGS space and related technologies is a critical function of Robert's position. At this time, NGS is the core's largest service, with a growing focus on single cell RNA-Seq using both the Fluidigm C1 and 10X Genomics Chromium technologies. The core provides a number of genomic services such as QPCR, Sanger Sequencing, DNA/RNA sample isolation, NGS library preparation and NGS sequencing. Over the past twelve months the core has provided experimental services to ~2,000 research scientists from 392 labs and 43 institutions and private companies. The core's primary mission is to provide high quality, cutting edge genomics services to the Harvard Medical School faculty but the core is also permitted to provide services to outside researchers. The DF/HCC Single Cell Core seeks to enable breakthrough discoveries by assisting in the design, execution, and interpretation of single cell genomics assays by utilizing cutting-edge, state-of-the-art tools. In his current role as director of the genomics core at Harvard Medical School, Robert is responsible for managing all aspects of the core facility including technology evaluation. In this tutorial, we will show the whole analysis pipeline, starting from the raw FASTQ files to the gorgeous velocity plots (generated by scVelo) that you may like to include in your next analysis or paper.
#HARVARD 10X CHROMIUM HOW TO#
Prior to this position, Robert was a project manager at the Whitehead Institute/MIT Center for Genome Research from September 1991 to July 2000 where he managed groups to develop genetic and physical maps of the mouse and rat as part of the Human Genome Sequencing Project. Here we provide an end-to-end tutorial describing how to perform an RNA-velocity analysis for a 10x Chromium dataset. He has been directing the core facility for 17 years. Our kit does not require optimization, and it's easy to prepare up to eight samples at the same time. Robert Steen is currently Director of the Biopolymers Next-Gen Sequencing (NGS) Genomics Core Facility within the Department of Genetics at Harvard Medical School. Chromium Nuclei Isolation Kit is a universal, standard protocol for suspending cellular nuclei to be used in 3' scRNA-seq, scATAC-seq, and multiome analyses.
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