BioMicroCenter:Illumina Library Preparation

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Sample Preparation available in BioMicro

Generating high-quality data on the Illumina sequencing platform requires high-quality libraries. The BMC currently offers library preparation services for a variety of starting materials. Prior to sequencing, all samples must pass the BioMicro Center’s Sequencing Quality Control process, which verifies selection of inserts of a desired size and correct ligation of Illumina adapters.
Sample Prep questions can be directed to Stuart Levine.

Sample Prep Services

Please follow the links in the table below for more information about our library preparation offerings.

Standard DNA Methods include Standard RNA Methods include
High Throughput DNA Methods include
  • Amplicon / 16S
  • NexteraXT
  • low input NexteraXT (coming soon)
High Throughput RNA Methods include
  • High Throughput 3' Digital Gene Expression (HT3DGE)



ChIP-Seq: Sonicated chromatin will undergo IP on the IPstar. RNase A, Proteinase K, Phenol:Chloroform extraction and purification will be performed off of the instrument and submitted for QC on the BioAnalyzer. These ChIP samples may be picked up for qPCR or sent directly to SPRI for library construction and sequencing (options are listed on submission forms). Users will be contacted if ChIP samples fail QC. These samples will not be submitted to SPRI-works but will be charged for the IP.

Sonicated chromatin should be submitted at 5-7 million cells per 200uL volume. Antibodies must be submitted at the same time(at least 3ug of antibody per IP). Chromatin should be prepared on the SAME DAY as the ChIP whenever possible. Full details about isolation methods can be found on the chromatin IP page.


The BMC offers PippinPrep Size Selection post library construction if custom insert sizes are needed.


All library preparation service include indexing. Molecular barcoding - identifying individual molecules from library preparation is available on SPRIworks and as part of HT3DGE.


Unless otherwise instructed, the BMC reserves 50% of submitted DNA in case of failures during sample prep. If you would like us to utilize the full sample, please indicate it in the notes section.

DNA– DNA samples must be submitted in either water or TE. Although the SPRIworks robot is not highly sensitive to the amount of DNA input, care must be taken to submit an appropriate amount of adapter to ensure efficient ligation. If you select the Nextera kit instead of the SPRIworks, we will require 50ng of DNA input. If PCR products are submitted for Nextera prep, we recommend purifying the material prior to submission for best results.

RNA – Total RNA samples must be submitted in water or TE. The quantity of total RNA needs to be between 0.1-4ug for Illumina TruSeq, 1ug-4ug for strand specific RNAseq, >100pg for Low Input RNAseq.

Sample Submission Forms


Good quality control is crucial for optimizing the number of reads and quality of data produced by the sequencers. For more information on QC methods and protocols please visit the Sequencing Quality Control page.


  • Fragmentation - All samples must be fragmented to the point where the majority of the fragment distribution is between 100 to 300 base pairs. RNA-seq samples are usually fragmented after poly-A selection and before first strand synthesis.
  • End Repair and 3’ dA Addition – Any end damage that may have occurred during fragmentation is repaired and then an extra A is added to all 3’ ends to increase efficiency during ligation.
  • Adapter ligation – Partial Illumina adapter sequences are ligated to the sample fragments, a total addition of 66bp between the two ends. Each adapter sequence has a T-overhang to increase efficiency. It is very important to maintain a good ratio of sample material to adapter. Illumina recommends a 1:10 ratio, to avoid the presence of primer-dimer after enrichment.
  • Size Selection – This step is designed so that only the fragments within the desired size range (generally ~200–400bp) are included in the final library. Size selection is very important: fragments that are too large will create oversized, overlapping clusters on the Illumina flowcell and can result in a loss of read count in the final data. Fragments much smaller than the optimal size range may include residual primers and primer-dimers. Size selection is usually performed using an agarose gel.
  • Enrichment – The DNA is PCR-amplified using the complete primer constructs required for binding and clustering on the flowcell. This adds 53bp of adapter sequence total between the two ends, for a final adapter length of 119bp. It is very important to optimize the number of PCR cycles so that there is sufficient material for clustering while limiting PCR biases.

Traditional Illumina protocols can be found on our protocols page.

Pricing and Priority

Full pricing information is available on our price list.

Priority for Illumina sample prep is currently given to labs associated with the BioMicro Center Core departments. We are able offer our services to other MIT and non-MIT users as space allows.