BioMicroCenter:Illumina Sequencing

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The MIT BioMicro Center has a MiSeq i100 and supports NovaSeqXplus sequencing from Illumina. We support a wide variety of applications, such as ChIP-Seq, miRNA sequencing and RNA-seq.

Illumina Massively Parallel Sequencing

Service Illumina Sequencing INPUT Illumina libraries MIN VOLUME 40uL Miseq i100 12 uL NextSeq/MiSeq 22 uL NovaSeq6k per flow cell 110 uL NovaSeqXplus per lane MIN CONCENTRATION 2nM* (~0.4ng/uL for a 300bp library) INCLUDED SERVICES Quality Control:Fragment Analyzer and qPCR Illumina Sequencing Demultiplexing ADDITIONAL SERVICES Quality Control Illumina library preparation DATA FORMATS FASTQ BCL (stored 30d) QUALITY CONTROL FASTQC Basic run metrics (alignment rate, complexity) Basic RNAseq metrics (where applicable) Basic paired end metrics (where applicable) Contamination checks PRICING LINK SUBMISSION MIT - ilabs External Users - form

Illumina sequencing-by-synthesis is the primary workhorse of the BioMicro Center. These instruments produce millions to billions of reads simultaneously and are used in a very broad spectrum of applications. The Center currently supports a MiSeqi100 walkup sequencer and NovaSeqXplus through collaboration with other local academic core facilities. Typical Workflow Illumina sequencing at the core begins with library quality control, during which the Center verifies the anchor elements and insert size using qPCR and the Fragment Analyzer. Users may elect to bypass this step if they provide the sample concentration and the concentration they would like to load at. Samples are then entered into the sequencing queue. Typical queues in the BioMicro Center are short, rarely exceeding 1-2 weeks, and samples are frequently run within a couple days. We do guarantee a minimum number of reads per lane provided if: a) BMC performed the QC, b) the samples are high-complexity, especially in the first few nucleotides, and c) the samples are at least 2nM. Illumina sequencing through the BioMicro Center is only available in full lanes and not on a per read basis. You are welcome to collaborate with other laboratories in order to pool samples. However, please be sure to minimize any possibility of cross-contamination of indexes as well as index crosstalk. When ordering lanes, please be aware that only full flowcells will be sequenced ASAP. More lanes may be purchased to facilitate sequencing. The wait time for individual lanes can vary widely. Full flowcells have priority for sequencing. Data Handling Following sequencing, data is handled using a custom analytical pipeline. If libraries were made in the Center or an index was provided, samples are split by index and identified by DNA-ID. FASTQ files and other desired formats will be placed in a delivery folder based on the project name, along with several quality control checks done for the sequencing data. We will provide an initial review of your project where we do try to identify any issues including incorrect indexes, sample contaminants, etc. Please note that our pipelines are built to find problems and are NOT designed to provide an initial analysis of your data. These analyses are built for speed, simplicity, and are not tuned in any way to your samples. We are always happy to discuss these results with you. Data will be available in your lab folder for 90 days post delivery, after which most of the data is deleted. FASTQ file will still be downloadable for two years but is delivered on a case by case basis. Custom Sequencing Users may elect to prep their samples with custom oligos. If this is the case, custom sequencing oligos must be provided along with the samples at the time of submission. At least 15uL of each kind custom sequencing primer at 100 uM should be submitted per lane of most Illumina sequencers. At least 30uL of each kind of custom sequencing primer at 100uM should be provided per NovaSeqXplus flowcell. It is strongly recommended to contact biomicro@mit.edu before planning a custom library preparation.

Additional services available: Illumina library preparation Bioinformatics Support Data storage and Computation

Illumina Platforms

SPEC	MiSeq i100+	NovaSeqX+
SEQUENCER
READS/LANE Low number is minimum per lane for standard Illumina libraries.	5M 25M (50m and 100m lanes due in late 2025)	10B (8 lanes) 25B (8 lanes or full flowcell)
LENGTHS AVAILABLE	100nt, 300nt, 600nt	100nt(25B full FC only),300nt
KEY NOTES	Patterned flowcell / X-amp chemistry: UDIs recommended. 2 color chemistry - G=dark. Walkup available.	Patterned flowcell Struggles with low complexity libraries Lane by Lane
DONATED BY	MIT VPR, Drs. Gene Li, Michael Birnbaum, Dept. of Biololgy, Scott Ritterbush '89, SM '92	Collaborations with local academic cores.