He began his career at the U.S. Chamber of Commerce, the world's largest business federation, in the Capital Markets Division in Washington D.C. We process Bisulfite sequencing data using an in-house BisSeq pipeline (Garrett-Bakelman F., Sheridan, C. et al. Location . Email: lcgould@med.cornell.edu. Feature Barcoding assays require additional information for post-processing with cellranger (for collating the feature counts with the gene expression counts). iLab is used by nearly 10,000 researchers in labs and core facilities across more than 50 institutions worldwide. [Application Note]. Streptavidin affinity purification enriches 5hmC-containing DNA sequences and integration with sample preparation steps creates a robust assay that can accept limiting levels of input DNA. *.maxL.bam.bai, *.merged.bam.bai - Index files (.bai files) for each sample which allow for easier viewing of the bam files in genome browsers such as UCSC Genome Browser) or IGV). Determination of concentration of double stranded DNA (dsDNA) using Qubit Fluorometer, Perkin Elmer Labchip GX or agarose gel to determine molecular weight. Please contact us at epigenomicscore@med.cornell.edu to discuss the appropriate number of reads required for your experiments. Hours . The Barbieri lab at Weill Cornell investigates the molecular underpinnings of prostate cancer and other urologic disease. Assay description [SureSelect PDF], Sample Requirement: Ms. Busby is President of Cresco Advisors where she serves as an Entrepreneur in Residence and business advisor to portfolio companies. Load the mixture into a Zymo-Spin Column in a Collection tube. Assay description Note: in most cases R2 is the correct read. Despite its increasing use ChIP-seq libraries are among the most challenging to perform and require significant experience and quality control measures. track type=bedGraph With the addition of Feature Barcoding Technology, you can now also detect and analyze additional cellular readouts such as cell surface markers and antigen specificity to enhance immune cell phenotyping and study dynamic interactions between lymphocytes and target cells. The core offers library preparation for chromatin immunoprecipitated material after successful quality control. Please check user guide (page 10 and page 41 respectively) for details. We can process up to 4 samples at a time. Some studies that have used our ChIPSeq sequencing service: Popovic R. et al. 2014, Qiao Y. et al. PhD student, Weill Cornell Medicine Physiology, Biophysics, and Systems Biology Program. Connor previously co-founded the Miss Kate Foundation, a non-profit focused on fundraising for brain cancer research; the foundation's events have been attended by 800+ people in New York City. For human transcriptome differential gene expression we recommend 4 samples per lane of SR50 sequencing. Phone: (212) 746-3399. Once samples are submitted and pass quality control, they are entered into a sample or library queue. Entrepreneurs in Residence - Our network of industry professionals provide their expertise to help translate your discoveries. Usage Policy. Your Institution’s Accounts Payable Department should mail a check payable to, If you are paying via a wire transfer please send an email to, Libraries made by the core, routinely yield clusters between 750-800 k/mm2, To request a sequencing service, please fill out a request in our. We can process up to 4 samples at a time and can only accept samples from local/internal clients. This pipeline results in the following file types: *.bam - Upon alignment (if requested) the aligned data processed by STAR aligner is in the widely accepted BAM format (a binary version of the SAM format). Weill Cornell Medicine uses your network username and password to login to Box. Please contact us at epigenomicscore@med.cornell.edu for further information and to discuss the details of your project. [Click here for a detailed description of the QC]. [, Given the variety of cells and sample types, general guidelines for sample preparation need to be optimized by each customer. Please download and fill out our form for Feature Barcoding data: FeatureBarcodingInput.xlsx (Replace the examples with representation for your samples). FASTQ files generated as described above are adapter trimmed and aligned to genomes available via Illumina's iGenome using the STAR aligner. It is, however, a very expensive technique due to the sequencing depth required to obtain 20X coverage. Approximate time for library preps and sequencing is 4-8 weeks if all samples pass quality control. Dr. Ali was also a Director of Business Development at International AIDS Vaccine Initiative, where she worked with vaccine and antibody development teams. Formerly, she founded and led Octane Ventures, a venture catalyst firm that works with nonprofits, universities and small biotech/health-tech companies on strategic advice, licensing and operational assistance. She has over two decades of experience in VC and was “one of the 6%,” referring to the exclusive group of female investment professionals. To calculate the sequencing depth required for you panel/species, please use the Illumina coverage calculator. The columns are: Minimizing the presence of cellular aggregates, dead cells, non-cellular nucleic acids and potential inhibitors of reverse transcription is critical to obtaining high quality data. We sequence Chromium single cell samples on a pair end flow cell (28-8-91) with a 2x50 cycles kit. The column headers are as follows: cpg.Sample.10x.txt.gz, The library preparation prices below are for the 5 prime gene expression assay as well as either a T or a B cell V(D)J assay. Jahan Ali, PhD, is the Director of Bioventure eLab at Weill Cornell Medical Center. Weill Cornell Medical College • 1300 York Avenue • New York, NY 10065. iLab is now available at no charge to all WCMC faculty and students who require the equipment and/or services of an iLab core. Quality control statistics for your samples, 2 years data storage on our backed up servers with unlimited password protected access for sequencing projects, Illumina iGenome alignments (if available and when requested for internal customers), Methylation calling for DNA methylation sequencing projects (where genomes are available), Methylation ratios for Epityper mass array projects, Splice junction tables for RNASeq alignments. Submit 150 ng of genomic DNA (300 ng for RRoxBS), of molecular weight >40kb, Nanodrop A260/280 ratio >1.7; A260/230=2.0-2.2; RNA-free and at a concentration of ~20ng/ul, Epigenomics Core Quality Control: Dr. Ali brings a unique perspective to the biotech space, gained from being on multiple sides of early stage technology in technology commercialization at Mount Sinai School of Medicine and Hospital for Special Surgery and led the healthcare investments for the Partnership Fund, an investment fund founded by Henry Kravis. Our RRBS protocol yields about  ~10% of genomic CpG sites (roughly 3M CpGs in the human genome), and provides enrichment in CpG islands and CpG shores, promoters, exons, introns and intergenic regions (Garrett-Bakelman F., Sheridan, C. et al. Do one extra 30 secs spin. Please check the. This may take up to 48 hrs. Sample Requirement: Pipette up and down 3 times. Targeted regions can be interrogated for the purpose of identifying structural rearrangements and SNPs. She has mentored numerous early stage companies, through ELabNYC and Springboard Enterprises; and is adept is building relationships with multiple stakeholders. The bedGraph output is tab delimited with 0-based start coords and 1-based end coords. This method uses cytosine bisulfite conversion followed by single stranded ligation of adapters and PCR amplification. Assay Description It is a sorted bedGraph file that reports the position of a given cytosine and its methylation state. Using Raindance’s single-molecule pico droplet PCR reaction three panels that contain genes specific for heme malignancies have been designed: This is a high-throughput technique, a minimum of 40 samples are required. Please click through our (Epi)Genetic Services menu to find details about Library Preparation and Sequencing. Prior to joining Weill Cornell Medicine, Connor helped start a logistics technology platform in the trucking space. Assay Description Sample Requirement: We have changed our sample drop off protocols and times - click on and read the following PDFs for details: Timeline: In the mid-1990s, Ms. Busby worked at Princeton University’s endowment on its alternative asset portfolio. Submit 300 ng of genomic DNA (400 ng for WGoxBS), of molecular weight >40kb, Nanodrop A260/280 ratio >1.7; A260/230=2.0-2.2; RNA-free and at a concentration of ~20ng/ul. Atrial fibrillation is an abnormal heart rhythm characterized by rapid and irregular activation of the upper chambers of … If your Fund Number is no longer billable for any reason, please contact us at, Once you have posted the transfer, please email us at. We prefer to process up to 4 samples at a time due to workflow constraints and currently only use V3 chemistry. Please contact us at epigenomicscore@med.cornell.edu for further information and to discuss the details of your project. Digitonin - (Promega cat# G9441) Digitonin is supplied at 2% in DMSO. These are tab delimited text files that contain the locations of C's in either CpG, CHG, or CHH, context and their methylation levels Weill Cornell Medical College • 1300 York Avenue • New York, NY 10065. The Chromium Single Cell ATAC (Assay for Transposase Accessible Chromatin) Solution accelerates the understanding of the regulatory landscape of the genome, thereby providing insights into cell variability. The sequencing data from our Single Cell RRBS assays will be demultiplexed and post-processed in the same manner as our RRBS samples. The cgunits file contains the reported sites for CpG context where consecutive CpGs for the forward and reverse strand have been combined into one site, or CpG-unit. The minimum read coverage cutoff for this file is 10 Please contact us at epicore-sc-coord@med.cornell.edu at least three weeks before dropping off your samples to schedule a time. Formerly, she founded and led Octane Ventures, a venture catalyst firm that works with nonprofits, … Sample Requirement: Phone: (212) 746-5454 After iDu Optics took first place in the 2016 Bench to Bedside Initiative (BBI), run by the Dean’s Entrepreneurship Lab at Weill Cornell … If you have less than 24 samples to multiplex, the core will multiplex altogether in one pool, and sequence over the required number of lanes. Only junctions supported by uniquely mapping reads are reported. After your samples are sequenced, we summarize and demultiplex the base calls as required into raw data files with quality information and then use post-processing pipelines optimized to specific sequencing assays (upon request) to generate alignments, methylation calls, summary statistics etc. Leona Cohen-Gould, Core co-Director. B.S. She is also a co-founder of Life Science Vendor Expo, a conference series providing entrepreneurs with educational workshops that address some of their operating challenges. Sequencing data processed at the core is distributed via Pubshare and stored for 2 years. Reduced Representation Bisulfite Sequencing is a modification of the original RRBS protocol (Gu H. et al. Ilab Software Help System Status Request Demo. count methylated The protocol requires a suspension of viable single cells as input. Please contact us at epicore-sc-coord@med.cornell.edu at least three weeks before dropping off your samples to schedule a time. Please Note: Please note that Pubshare and iLab are two separate systems requiring separate accounts and login information. 9am - 5pm, Monday - Friday Whole genome bisulfite sequencing is the gold-standard approach for comprehensive base-pair resolution and quantitative information at most genomic cytosines. [Click here for a detailed description of the QC]. Loren Busby, CFA, MBA is the BioVenture eLab Entrepreneur in Residence. QC1 - Quantity: dsDNA using Qubit Fluorometer. Weill Cornell Medical College. This pipeline results in the following file types: *.maxL.bam - The top/best non-filtered alignment for each read in the widely accepted BAM format (a binary version of the SAM format) for each sample. Specifies which RNA sequencing read contains the Feature Barocde sequence. Assay description The total number of nuclei required in the suspension used as input is determined by the desired cell recovery target (between 500-10,000 cells); required sequencing read depth depends on the desired cell target. The sequencing data from Chromium Single Cell ATAC will be demultiplexed and post-processed using custom pipelines provided by 10x Genomics. Continue to login to Box through your network. Connor graduated with a degree in Business and Management from Skidmore College where he was an All-Conference lacrosse player. Weill Cornell Medical College. Atrial Tissue Modeling. methylcall.CHH.Sample.1x.txt.gz, 2011) and the in-house developed ERRBS method (Akalin A., Garrett-Bakelman F. et al, 2012) for base-pair resolution methylation sequencing analysis based on the use of a restriction enzyme to enrich for CpG fragments. Repeat the wash step. Phone: (212) 746-5454 (Nature Methods, 2017), Sample Requirement: Payment will be processed automatically through WBG/SAP after an Invoice is issued (at the end of the calendar month following the completion of the service). With a legacy of putting patients first, Weill Cornell Medicine is committed to providing exemplary and individualized clinical care, making groundbreaking biomedical discoveries, and educating generations … Please contact us if you wish to use this service. Single Cell RRBS with SMART-Seq Gene Expression. methylcall.CHG.Sample.1x.txt.gz, Garrett-Bakelman, FE. Epigenomics Core Quality Control: Please use a double stranded fluorometric method to determine concentration (Qubit for example); concentrations determined by nanodrop are not reliable for this assay. Degraded DNA, such as that obtained from FFPE is not suitable. Sample Requirement: 100 million (M) read per sample on a single end read flow cell with 100 sequencing cycles (SR100) are recommended for differential methylation analysis, for detailed information please review Garrett-Bakelman F., Sheridan, C. et al. methylation percentage, Sample.bismark.cov.gz - This file contains methylation information for individual cytosines as output by the Bismark methylation extractor. And login information All-Conference lacrosse player combination of these elements: Nucleotide barcode sequence associated with this Feature service Manual! Examples with Representation for your samples to schedule a time choice in on (... 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