• Illumina NextSeq 2000
• Illumina MiniSeq
• PacBio Sequel IIe
• Diagenode Megaruptor 3
• Agilent Femto Pulse Systems
• Agilent Bioanalyzer 2100
• Formulatrix MANTIS Automated Liquid Dispenser
• 10X Genomics Chromium single-cell controller
• 3 Leica fluorescent dissecting microscopes
• SONY SH800S Cell Sorter
• Agilent 4200 TapeStation System

Next Generation Sequencing

Our facility provides two different sequencing platforms to meet various research objectives. Illumina NextSeq 2000 and MiniSeq platforms specialize in high throughput short-read sequencing; and PacBio Sequel IIe focus on high accuracy long-read sequencing in identify rare variants, challenging repeating sequences and transcript isoforms.

Technical resources are available for all aspects of genome analysis including tissue dissection, cell or nuclei 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 collection, library preparation, and quality control.  The team also provides technical assistance for developing new methods for cell isolation, custom library prep, and barcoding schemes (Smart-SCRB, link to protocols.io). We can work with challenging samples and limiting amounts of material that most core sequencing labs won’t accept (For example, hand-sorting cells from extremely sparse or fragile samples).

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. 

Data Processing

At this moment we are providing limited data analysis. For transcriptome profiling we have a basic analysis pipeline (STARSolo) for adapter trimming, read alignment, and gene expression estimation.  We have stable genome reference and annotation sets for Drosophila, mouse, green monkey, and zebrafish. We 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.

For 10x Chromium single cell data, we use the Cell Ranger analysis pipeline which can be found in Chromium support webpage, to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis.

In addition, for all Illumina sequencing we provide the raw sequence file (fastq), de-multiplexing report, fastQC read quality report showing the performance of the sequencing run, and associated run metrics. For all PacBio sequencing we provide the raw HiFi reads (bam or fastq), run QC and post-run analysis report by SMRT Link, such as HiFi read yield metrics, HiFi read length and quality distribution. We are open to help with some customized analysis by the SMRT Tools or other open resources for genome assembly, 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).