BioMicroCenter:Illumina Sequencing

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The MIT BioMicro Center has six high-throughput Illumina sequencers including one NovaSeq 6000, one HiSeq 2000, two NextSeq 500s and two MiSeqs. We support a wide variety of applications, such as ChIP-Seq, miRNA sequencing and RNA-seq. Each lane can potentially accommodate dozens of barcoded samples (depending on sequence complexity and desired coverage). Read lengths vary, depending on users, between 20nt and 325nt per end.

Illumina Massively Parallel Sequencing

Service Illumina Sequencing
INPUT Illumina libraries
MIN VOLUME 12uL (100uL for NovaSeq 6000)
MIN CONCENTRATION 2nM* (~0.4ng/uL for a 300bp library)
Can handle samples to 0.2nM, but read count not guaranteed
  • Quality Control:Frag.Analyzer and qPCR for 1 sample
  • Illumina Sequencing
  • Demultiplexing
  • Quality Control
  • Illumina library preparation
  • FASTQ (stored 90d)
  • SAM (stored 90d)
  • ARCHIVAL BAM (stored 2y)
  • BCL available upon request
  • Basic run metrics (alignment rate, complexity)
  • Basic RNAseq metrics (where applicable)
  • Basic paired end metrics (where applicable)
  • Contamination checks

Illumina sequencing-by-synthesis is the primary workhorse of the BioMicro Center. These instruments produce millions of reads simultaneously and are used in a very broad spectrum of applications. The Center supports 1 NovaSeq 6000, 1 HiSeq2000, 2 NextSeq500s, and 2 MiSeqs. In addition, we have access to additional instrumentation through a long standing collaboration with the Whitehead Genome Technologies Core.

Illumina sequencing 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. For custom sequencing, primer(s) should be provided with ~15 uL at 100 uM per read per lane of HiSeq or flowcell of MiSeq, NextSeq. At least 30uL should be provided per NovaSeq flowcell.

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 and we are happy to split lanes if you like, but we feel it is critical that you are aware of the other samples on your lane to minimize any possibility of cross-contamination of indexes as well as index crosstalk.

Following sequencing, data is handled using a custom analytical pipeline. Samples are split by index if one was provided and identified by DNA-ID. FASTQ, SAM and BAM files will be placed in a delivery folder based on the project name, along with several quality control checks done on the lane. We 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 analyses are built to find problems and NOT to provide an initial analysis of your data. These analyses are built for speed, simplicity, and are not tuned in any way for your samples. We are always happy to discuss these with you. Data will be available in your lab folder for 90 days post delivery, after which most of the data is deleted. Archival BAM files (non-sorted and including all reads) are retained for 2 years and can be used to recreate the FASTQ file using SAMtools.

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Additional services available:

Illumina Platforms

SPEC HiSeq2000 MiSeq NextSeq500 NovaSeq6000
Hiseq 2000.jpg
BMC miseq.png
BMC Next500.png
BMC Nova6000.jpg
Low number is minimum per lane for standard Illumina libraries.
  • 1 Lane: 150-220M
  • v2: 8-15M
  • v3: 12-25M
  • Nano: 1M
  • High output: 250-500M
  • SP, S1, S2 (2 lanes): 650M, 1.3B, 3.3B
  • 18 nt/day
  • 3 days/run
  • 288 nt/day
  • 1-3 days/run
  • 150 nt/day
  • 1-2 days/run
  • 150 nt/day
  • 1-2 days/run
  • 40SE
  • v2: 75nt, 300nt, 500nt
  • v3: 150nt,600nt
  • 75nt,150nt,300nt
  • 100nt,200nt,300nt,500nt(SP only)
  • ChIPseq
  • Bisulfite sequencing
  • Copy Number Variation
  • smRNA
  • SgRNA Screens
  • siRNA screens
  • Small genome resequencing
  • Targeted resequencing
  • 16S Metagenomes
  • smRNA
  • de novo sequencing
  • SNP detection
  • Exome sequencing
  • Splicing analysis in RNAseq
  • High coverage
  • DeNovo Seq
  • Metagenomics
  • scRNA sequencing for many cells
  • Exome sequencing
  • High coverage
  • Useful for counting applications
  • Best for low complexity libraries.
  • 2 color chemistry - G=dark.
  • Struggles with low complexity libraries
  • Struggles with large libraries
  • Patterned flowcell
  • Struggles with low complexity libraries
  • Platform still evolving
DONATED BY Drs. Penny Chisholm and Chris Burge and HHMI Drs. Chris Love, Michael Birnbaum and the Dept. of Biological Engineering. Drs. Penny Chisholm, Doug Lauffenburger, Myriam Heiman, Li-Huei Tsai and the Dept. of Biology and the Koch Institute. Drs. Manolis Kellis, Li-Huei Tsai and MIT, The MIT Stem Cell Initiative and the Dept. of Biology and the Koch Institute.