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Bioinformatics

Analysis Service

In this stage, the program will primarily provide NGS data analysis service, including but not limited to:

  • Data management (storage/backup, meta-table management, GEO/dbGap submission),
  • RNA-seq analysis (from raw sequencing data to QC, to normalized gene expression table, group comparison, pathway analysis, and interactive reporting and visualization of the results),
  • Small RNA-seq analysis (g. miRNAs, circRNAs, piRNAs, eRNAs, etc.),
  • Single-cell omics analysis (10x Genomics pipeline, clustering, trajectory analysis, spatial transcriptomics, etc.),
  • ChIP-seq analysis (e.g. QC, peak calling, differential binding, UCSC Genome Browser visualization, etc.)
  • Variant calling from genotyping/WGS/WES data, and
  • Other next-generation sequencing (NGS) data analysis (ATAC-seq, CAGE, ChIA-PET, Hi-C etc.)

Data Service

Data is an asset. As a unique feature, we will also provide high-quality, curated, standardized data service to the faculty of the departments. Nowadays, more and more big biomedical datasets become publicly available, including UK Biobank, AMP-PD, AMP-AD, GTEx, PPMI, ROSMAP, CommonMind, ENCODE, PsychENCODE, etc. We will maintain the Data User Agreement application, renewal, and data access for the faculty members. We will also provide tutorial of what is included in the dataset, how to use the dataset etc. The users will only need to pay salary of the staff and the cost of data storage. We will also aim to improve the data sharing environment in the community by the FAIR principle.

Q&A

1. How does it work?

Like many other bioinformatics cores, we will set up a in-person or zoom meeting first to understand your project, your need, your timeline, your budget etc. From there we will let you know if we can take the job, and how many hours we estimate to finish the job, and how we will deliver the results. If we both agree to go ahead, we will sign a contract and follow what we agreed. Just keep in mind, we try to run this in a business model, but we are still doing research. Not every scientific question can be answered as expected. We might need more frequent discussion and may need to revise our contract.

2. Is it free?

Yes and No.

The first meeting is free. Most of the trainings are free. But we are expected to becomes self-sustaining after the two-year angel fund fron NTS. Service can be charged in three modes:

(1) Regular: $125/hour after a free initial meeting and an agreement on the estimated amount of work. If a PI wish to purchase more hours upfront, we offer a lower hourly rate for a bulk sale (see the Table for details).

Tier Hours of services pre-paid Rate
1 100 (about 2 weeks) $125/hr
2 350 (about 2 months) $100/hr
3 1000 (about 6 months) $80/hr

(2) Collaborative grant: The PIs can put a % of effort for Dr. Dong and/or his staff member in their grant. We are open to discuss this option in person.

(3) Institutional commitment: Since the Neurotech Studio provide the seed fund, the program will primarily serve the labs in the neuro community in Brigham for now, including Neurology, Neuroscience, Neurosurgery, Neuro-oncology, etc. Down the road, we will also provide bioinformatics service to other departments or institutes in BWH or Harvard community, if the partner institute or department could commit to a specified amount of funds that will be used to subsidize consults for their researchers.

3. Who should I contact?

Dr. Xianjun Dong, Director of the Genomics and Bioinformatics Hub (xdong@rics.bwh.harvard.edu).

Note that Dr. Dong works on the hub with only 40% of his efforts, literally on every Monday and Thursday. So, please expect some delay for any email response.

Genomics

High-throughput DNA and RNA sequencing

As part of the service that our NeuroTech Studio provides, our customers can access the brand new Illumina NextSeq 550 sequencing machine. You can choose either to upload the data to Illumina’s cloud storage or save to the designated space on Partners’s ERISone high-performance computing cluster. For later, we will take care of your data with seamless service, from data management, data backup, data QC, downstream NGS analysis, till the final uploading to GEO/dbGap before your publication. It’s affordable, secured, and customized serviece that both you and your data deserve. Check here fore more info >> 

Single-cell Genomics

We also provide single-cell genomics platform: 10x Genomics CHROMIUM CONTROLLER. You can use it for Single Cell CNV, Single Cell Gene Expression, Single Cell Immune Profiling, and Single Cell ATAC. Check here fore more info >> 

Q&A

1. How can I use the instruments?

You have to create an acount and reserve the instruments on the Partners’s Research Core website: https://researchcores.partners.org/nts/about. First reserved, first use.

2. Is it free?

Nearly free. Donations from our generous philanthropists have covered most of the cost for the instrument. For our users, you just need to pay a very small fee for using the machine (e.g. used for the maintenance). Of course, you have to provide your own reagent and kits for the experiment.

3. Who should I contact?

For more information about equipment, training and usage, please contact: Dr. Lai Ding, Senior Imaging Scientist—NeuroTechnology Studio (lding@bwh.harvard.edu) or Teri Zgoda (zgoda@bwh.harvard.edu).
For data storage and data analysis questions, please contact: Dr. Xianjun Dong, Director of the Genomics and Bioinformatics Hub (xdong@rics.bwh.harvard.edu).

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