What We Do
Derived from the methods and members of Janelia's completed NeuroSeq team project, Quantitative Genomics provides expert services for cell isolation, transcriptome and epigenetic profiling, and de novo genome assembly using next generation sequencing technologies from Illumina and Ion Torrent. Our goal is to serve as a gateway to the rapidly evolving technologies for high content genomic analysis for both experts and novices. From experimental design to data analysis, we are ready to help Janelians at any phase of a project.
- Illumina HiSeq 2500 and cBot clustering station
- Ion Torrent PGM and OneTouch2 instruments
- Drop-seq workstation
- 3 Leica fluorescent dissecting microscopes
- Agilent Bioanalyzer 2100*
- Covaris S2 and E220 sonicators
- Diagenode Bioruptor*
*generously made available to us by other labs at Janelia
Next Generation Sequencing
Our facility provides next generation sequencing (NGS) using the Illumina HiSeq 2500 and the Ion Torrent PGM platforms. Technical resources are available for all aspects of NGS including cell isolation, nucleic acid purification, library construction, sample barcoding, and limited data analysis.
Our expert staff of Research Specialists provides services, training, and equipment for sample and library preparation, and quality control. The team also provides technical assistance for developing new methods for cell capture/isolation, custom library prep, and barcoding schemes.
Bring us your favorite methods or crazy ideas for new approaches (such as TagMap) and we will work with you to implement a robust pipeline from sample to sequence. We can work with challenging samples and limiting amounts of material that most core sequencing labs won’t touch.
At this time we are providing limited data analysis, with the expectation that most users of this resource have the means to process the raw sequence data we produce.
For all NGS work we provide the raw sequence file (fastq), a fastQC read quality report showing the performance of the sequencing run, and associated run metrics such as the de-multiplexing report.
For transcriptome profiling we have a basic analysis pipeline for adapter trimming, read alignment, and gene expression estimation using RSEM. We have stable genome reference and annotation sets for Drosophila (release 6), mouse (mm10), and zebrafish (danRer10), and can help identify appropriate reference annotations for other species as needed. We provide the aligned reads (bam), gene expression tables (counts, FPKM, and TPM), and additional information such as the ERCC spike-in performance.
We can also perform basic de novo genome assembly for sequences as small as a plasmid and as large as human-sized genomes such as Parhyale hawaiensis. We can help with transcriptome assembly, gene prediction, and feature annotation to create a reference assembly and annotation set where none exists.
We can transfer terabytes of data to the cloud (Amazon, Dropbox) or to your collaborators. When the time comes to publish your results, we can help prepare the data for submission to online databases such as the NCBI sequence read archive (SRA) and gene expression omnibus (GEO).
Careful dissection of fly brains prior to tissue digestion and manual isolation of specifically labeled neurons is critical to the health of the cells and the quality of transcriptomic data we produce.
Preparing to manually isolate mouse neurons requires extensive experience with mouse neuroanatomy and precise microdissection of specific brain regions.
Our HiSeq 2500 is the workhorse of the Quantitative Genomics facility, generating up to 3 billion reads per week at maximum capacity.
A simple Drop-seq workstation for single cell transcriptome analysis utilizes an inverted light microscope to visualize reagent flow in the microfluidic chambers, three syringe pumps to control reagent flow, and a magnetic stir platform for gentle mixing of cells and oligo beads.