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 platforms from Illumina. 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.

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Equipment

Illumina NextSeq 2000
Illumina MiniSeq
10X Genomics Chromium single-cell controller
3 Leica fluorescent dissecting microscopes
Agilent Bioanalyzer 2100
Sage HLS HMW Library System
BioRad CHEF MAPPER PFGE system

Resources

Next Generation Sequencing

Our facility provides next generation sequencing (NGS) using the Illumina NextSeq 550 and MiniSeq 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 accept.

Data Processing

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 (STAR), and gene expression estimation (RSEM). We have stable genome reference and annotation sets for Drosophila (release 6), mouse (mm10), and zebrafish (danRer11), 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 gene expression omnibus (GEO).

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Select Publications

Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.

Spatial Gene-Expression Gradients Underlie Prominent Heterogeneity of CA1 Pyramidal Neurons.

The genome of the crustacean Parhyale hawaiensis—a model for animal development, regeneration, immunity and lignocellulose digestion

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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.