Massachusetts Institute of Technology
Stuart Levine
31 Ames St. 68-322
Cambridge, MA 02139
http://biomicro.mit.edu
RRID: RRID:SCR_026413
10X Genomics Chromium Plus Genetic Analyzer
Genetic analyzer, referred to as Chromium Controller for combining large partition numbers with a diverse barcode library to generate >100,000 barcode-containing partitions. [Product Link]
RRID:SCR_019326
Agilent 2100 Bioanalyzer Instrument
This Bioanalyzer Instrument is used for sample quality control of biomolecules. [Product Link]
RRID:SCR_019389
Agilent 5300 Fragment Analyzer System
Fragment Analyzer System can separate up to 48 or 96 samples in parallel. [Product Link]
RRID:SCR_019411
Agilent Femto Pulse System
Femto Pulse System separates large molecular weight DNA fragments and detects nucleic acids into femtogram range. [Product Link]
RRID:SCR_019498
BioTek Synergy H1 Hybrid Multi-Mode Microplate Reader
Configurable multi mode microplate reader. [Product Link]
RRID:SCR_019748
Covaris E220evolution Focused-Ultrasonicator
Focused ultrasonicator that enables multi sample, batch preparation, capable of processing wide range of sample types and volumes. [Product Link]
RRID:SCR_019817
Covaris R230 Focused-Ultrasonicator
Focused ultrasonicator that can be fully integrated on many liquid handler platforms with high throughput sample processing with AFA energetics and AFA TUBE TPX plates. [Product Link]
RRID:SCR_019821
Illumina iSeq 100 Sequencing System
Makes next generation sequencing easier. Designed for simplicity, it allows labs of all sizes to sequence DNA and RNA at push of button. [Product Link]
RRID:SCR_020125
Illumina NovaSeq 6000 Sequencing System
Unleashes groundbreaking innovations that leverage our technology Now you can get scalable throughput and flexibility for virtually any sequencing method, genome, and scale of project. [Product Link]
RRID:SCR_020150
Perkin Elmer Chemagic 360 Genetic isolation Workstation
Nucleic Acid Extractor for Medium to High Throughput. Based on our patented chemagen magnetic bead technology the chemagic 360 instrument represents the best solution for nucleic acid isolation in a huge variety of research market segments including but not limited to Biobanking/Human Genetics, HLA Typing, Virus and Bacteria Detection. Experience the revolutionary compact benchtop design of our newly developed chemagic 360 Nucleic Acid Extractor. Based on the well-established chemagen Technology, the system offers a flexible solution for different sample processing and throughput needs. Configurable with three kinds of chemagic Rod Heads (see table below) the system can process sample volumes from 10 ?l 10 ml. [Product Link]
RRID:SCR_020394
Roche Light Cycler 480 qPCR Real Time PCR System
Real time PCR device that allows use of additional thermal block cycler units 96 well and 384 well format. [Product Link]
RRID:SCR_018626
Sage Science BluePippin system
Used for DNA Size Selection for Next-Gen Sequencing, with Pulsed-Field (100bp ? 50kb).BluePippin has the DNA capabilities of the Pippin Prep, plus the extra benefit of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA. For long-range genomic applications, high-pass filtering allows users to collect all fragments above a size threshold set by the user. Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples/gel cassette may be run, with no possibility of cross contamination. [Product Link]
RRID:SCR_020505
TTP Labtech Mosquito HV Automated Liquid Handler
TTP Labtech introduced the mosquito HV liquid handler to bridge the gap between nanolitre and microlitre pipetting. It provides accurate liquid handling for low volume serial dilutions and assay plate preparation across the intermediate volume range of 500 nL 5 ?L. TTP Labtech's mosquito HV can be employed for a wide range of chemical and biological-based applications; including compound and small molecule screening, cell- or bead-based assays, enzyme kinetic assays, ELISAs, and molecular biology applications including rtPCR/qPCR set-up, RNAi screening and SNP genotyping. [Product Link]
RRID:SCR_020866
10X Genomics Cytassist
Spatial Transcriptomics Support
Biolytic Dr.Oligo
Oligo Synthesizer
DNAscript Syntax
Oligo Synthesizer
Element Biosceinces AVITI24
Seqeuncing and Multiomics
n6tec iconPCR
qPCR system
Oxford Nanopore PromethION P2
Sequencing System
Singular G4
Sequencing System
Tecan EVO150
Liquid Handler
ThermoFisher Varioskan
Plate Reader
10x Genomics
16S Amplicon Sequencing
Automated Liquid Handling
AVITI Sequencing
Bioinformatics
Computational - Bioinformatics
Copy Number Variation (CNV)
Data Analysis
Data Processing And Interpretation
DNA Analysis
Genomics
Library Services
Microbiome
oligo synthesis
Real-time qPCR
RNA analysis
RNA Integrity
Sequencing - DNA Sequencing
Sequencing - Next Generation Sequencing (NGS)
Single-cell Sequencing
1.) Jiang Z, Li P, Wang Y, Liu H, Wei D, Yuan C, Wang H (2019 Sep 10). Arsenic mobilization in a high arsenic groundwater revealed by metagenomic and Geochip analyses. Scientific reports, 9(1), 12972. . PMID: 31506464.
2.) Bai R, Wang JT, Deng Y, He JZ, Feng K, Zhang LM (2017). Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers. Frontiers in microbiology, 8(), 945. . PMID: 28611747.
3.) Qi Q, Zhao M, Wang S, Ma X, Wang Y, Gao Y, Lin Q, Li X, Gu B, Li G, Zhou J, Yang Y (2017). The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture. Frontiers in microbiology, 8(), 976. . PMID: 28659870.
4.) Xia Y, Hu M, Wen X, Wang X, Yang Y, Zhou J (2016 Jan 8). Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch. Scientific reports, 6(), 18509. . PMID: 26743465.
5.) Bouskill NJ, Wood TE, Baran R, Ye Z, Bowen BP, Lim H, Zhou J, Nostrand JD, Nico P, Northen TR, Silver WL, Brodie EL (2016). Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism. Frontiers in microbiology, 7(), 525. . PMID: 27148214.
6.) Zhang B, Xia Y, Wen X, Wang X, Yang Y, Zhou J, Zhang Y (2016). The Composition and Spatial Patterns of Bacterial Virulence Factors and Antibiotic Resistance Genes in 19 Wastewater Treatment Plants. PloS one, 11(12), e0167422. . PMID: 27907117.
7.) Cai M, Nie Y, Chi CQ, Tang YQ, Li Y, Wang XB, Liu ZS, Yang Y, Zhou J, Wu XL (2015 Nov 3). Crude oil as a microbial seed bank with unexpected functional potentials. Scientific reports, 5(), 16057. . PMID: 26525361.
8.) Yue H, Wang M, Wang S, Gilbert JA, Sun X, Wu L, Lin Q, Hu Y, Li X, He Z, Zhou J, Yang Y (2015 Sep). The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands. The ISME journal, 9(9), 2012-20. . PMID: 25689025.
9.) Wood SA, Almaraz M, Bradford MA, McGuire KL, Naeem S, Neill C, Palm CA, Tully KL, Zhou J (2015). Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture. Frontiers in microbiology, 6(), 90. . PMID: 25926815.
10.) Tsvetanova NG, von Zastrow M (2014 Dec). Spatial encoding of cyclic AMP signaling specificity by GPCR endocytosis. Nature chemical biology, 10(12), 1061-5. . PMID: 25362359.
11.) Chu H, Wang S, Yue H, Lin Q, Hu Y, Li X, Zhou J, Yang Y (2014 Oct). Contrasting soil microbial community functional structures in two major landscapes of the Tibetan alpine meadow. MicrobiologyOpen, 3(5), 585-94. . PMID: 25044404.
12.) Wohlbach DJ, Rovinskiy N, Lewis JA, Sardi M, Schackwitz WS, Martin JA, Deshpande S, Daum CG, Lipzen A, Sato TK, Gasch AP (2014 Sep). Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production. Genome biology and evolution, 6(9), 2557-66. . PMID: 25364804.
13.) Nam M, Kim JS, Lim S, Park CY, Kim JG, Choi HS, Lim HS, Moon JS, Lee SH (2014 Mar). Development of the large-scale oligonucleotide chip for the diagnosis of plant viruses and its practical use. The plant pathology journal, 30(1), 51-7. . PMID: 25288985.
14.) Vimolmangkang S, Zheng D, Han Y, Khan MA, Soria-Guerra RE, Korban SS (2014 Jan 15). Transcriptome analysis of the exocarp of apple fruit identifies light-induced genes involved in red color pigmentation. Gene, 534(1), 78-87. doi: 10.1016/j.gene.2013.10.007. PMID: 24140126.
15.) Wang X, Xia Y, Wen X, Yang Y, Zhou J (2014). Microbial community functional structures in wastewater treatment plants as characterized by GeoChip. PloS one, 9(3), e93422. . PMID: 24671164.
16.) Jung SH, Yim SH, Oh HJ, Park JE, Kim MJ, Kim GA, Kim TM, Kim JS, Lee BC, Chung YJ (2013 Dec 9). De novo copy number variations in cloned dogs from the same nuclear donor. BMC genomics, 14(), 863. . PMID: 24313905.
17.) Willmund F, del Alamo M, Pechmann S, Chen T, Albanèse V, Dammer EB, Peng J, Frydman J (2013 Jan 17). The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis. Cell, 152(1), 196-209. . PMID: 23332755.
18.) Yang Y, Xu M, He Z, Guo J, Sun G, Zhou J (2013). Microbial electricity generation enhances decabromodiphenyl ether (BDE-209) degradation. PloS one, 8(8), e70686. . PMID: 23940625.
19.) Holmes KJ, Klass DM, Guiney EL, Cyert MS (2013). Whi3, an S. cerevisiae RNA-binding protein, is a component of stress granules that regulates levels of its target mRNAs. PloS one, 8(12), e84060. . PMID: 24386330.
20.) Jung SH, Lee A, Yim SH, Hu HJ, Choe C, Chung YJ (2012 Aug 31). Simultaneous copy number gains of NUPR1 and ERBB2 predicting poor prognosis in early-stage breast cancer. BMC cancer, 12(), 382. . PMID: 22938721.
21.) Eskra L, Covert J, Glasner J, Splitter G (2012). Differential expression of iron acquisition genes by Brucella melitensis and Brucella canis during macrophage infection. PloS one, 7(3), e31747. . PMID: 22403618.
22.) Bates JG, Salzman J, May D, Garcia PB, Hogan GJ, McIntosh M, Schlissel MS, Brown PO (2012). Extensive gene-specific translational reprogramming in a model of B cell differentiation and Abl-dependent transformation. PloS one, 7(5), e37108. . PMID: 22693568.
23.) Martowicz ML, Meyer MB, Pike JW (2011 Aug). The mouse RANKL gene locus is defined by a broad pattern of histone H4 acetylation and regulated through distinct distal enhancers. Journal of cellular biochemistry, 112(8), 2030-45. . PMID: 21465526.
24.) del Alamo M, Hogan DJ, Pechmann S, Albanese V, Brown PO, Frydman J (2011 Jul). Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes. PLoS biology, 9(7), e1001100. . PMID: 21765803.
25.) Seo SM, Koh YS, Jung HO, Choi JS, Kim PJ, Baek SH, Youn HJ, Lee KH, Seung KB (2011 Jul). Deoxyribonucleic Acid copy number aberrations in vasospastic angina patients using an array comparative genomic hybridization. Korean circulation journal, 41(7), 385-93. . PMID: 21860640.
26.) Tsvetanova NG, Klass DM, Salzman J, Brown PO (2010 Sep 10). Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PloS one, 5(9), . . PMID: 20844764.
27.) Kwon HJ, Hong YK, Park C, Choi YH, Yun HJ, Lee EW, Kim BW (2010 Apr 1). Widdrol induces cell cycle arrest, associated with MCM down-regulation, in human colon adenocarcinoma cells. Cancer letters, 290(1), 96-103. doi: 10.1016/j.canlet.2009.09.003. PMID: 19828235.
28.) Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, Brown PO (2009 Nov). Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS biology, 7(11), e1000238. . PMID: 19901979.
29.) Fink J, Gu F, Ling L, Tolfvenstam T, Olfat F, Chin KC, Aw P, George J, Kuznetsov VA, Schreiber M, Vasudevan SG, Hibberd ML (2007 Nov 21). Host gene expression profiling of dengue virus infection in cell lines and patients. PLoS neglected tropical diseases, 1(2), e86. . PMID: 18060089.
The BioMicro Center is an integrated genomics/bioinformatics facility located at MIT. The core supports sample isolation, library preparation, short and long read sequencing, single cell and spatial analysis, bioinformatics, and data management.
