Internal customers (Weill Cornell Medicine) require Fund Numbers for work to begin. Please follow the instructions in the WCMC iLab Instructions PDF to add fund numbers to your Agilent Crosslab/iLab account.
External academic customers - please ensure that you include details for your PI and financial administrator and that your financial manager enters a correct billing address in their Agilent Crosslab/iLab account. Please use this W-9 Tax form if required, towards setting up payment.
Click the Initiate Request button to the right of the service and follow the instructions for the service to submit an online request. Notes:
Make sure to fill in the appropriate sample/library submission table in Crosslab depending on the service that you are requesting. (NOTE: Please de-identify any patient samples before submitting them to us.)
Quality Control is included in the sequencing requests.
Please wait for the Epigenomics Core to Approve the request and provide your lab with a Price Quote. This may take up to 48 hrs. Once approved, your quote can be downloaded as a PDF from within your Agilent Crosslab/iLab request.
Requests without financial approval will not be honored:
Internal customers must have a valid Fund Code and Approve the Price Quote.
External Academic Customers must update the payment information in Agilent Crosslab/iLab once they have obtained a Purchase Order Number for the quoted price.
After financial approval in Agilent Crosslab/iLab, print out the sample submission form, make sure you enter the Agilent Crosslab/iLab service ID in the appropriate field. Samples will not be processed without an accompanying Agilent Crosslab/iLab request.
Label the individual tubes clearly with the sample number you have indicate in the sample submission form AND Agilent Crosslab/iLab service IDs
Samples requiring dry ice (RNA, ChIPd) or ice temperatures (DNA) must be in an appropriate insulated container with the samples protected inside the shipping container. [Please reference the service you would like to use for specific details of sample submission.]
Ship samples with sample submission form to: Epigenomics Core Facility
Weill Cornell Medicine
413 East 69th Street, Room A-427
New York, NY 10065
OR
Bring samples with sample submission form to: Epigenomics Core Facility at Weill Cornell Medical College,
1300 York Avenue, A-427, New York, NY 10065
If you are dropping off your samples please do so between 9:30am and 4:30pm on business days
Invoice will be generated after completion of the project; internal customers will be billed through SAP, External Academic customers please refer to payment instructions on our website.
CORE OPERATING PROCEDURES:
Quality control is performed on all samples before sequencing using Qubit Fluorometer, Agarose Gels and/or Bioanalyzer Chip depending on the type of assay. Please click through our (Epi)Genetic Services menu for more information on the sample requirements and quality control for the assay you are interested in.
Samples that pass our quality checks are processed for library preparation and/or sequencing as requested. Please click through our (Epi)Genetic Services menu to find details about Library Preparation and Sequencing.
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. Please review the Data Processing section in the assay of your choice in on our (Epi)Genetic Services menu for more information.
Sequencing data processed at the core is distributed via Pubshare and stored for 2 years. Please note that Pubshare and iLab are two separate systems requiring separate accounts and login information. For more information on data retrieval, please visit the Data Analysis and Retrieval section of our FAQ.
FINISHING UP:
For customers paying from the Weill Cornell Medical College:
A Fund Number valid for the entire length of the service in Agilent Crosslab/iLab is required.
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).
Please pay by Fund Transfer from CU to WCMC using your central institutional account, and include a copy of the invoice. Reach out to your accounting personnel for directions and clarification on how to process internal transfers between our campuses.
Once you have posted the transfer, please email us at all2041@med.cornell.edu in order to ensure credit to your iLab account.
For External Academic customers:
External Academic customers must pay via check or wire transfer ONLY, we do not accept credit cards.
After completion of the service an invoice referencing the provided PO number will be generated.
The Invoice will be emailed through iLab to the Financial Manager and/or PI - who is responsible for delivering it to the Institution's Accounts Payable Department.
Your Institution’s Accounts Payable Department should mail a check payable to Weill Cornell Medical College along with a copy of your invoice to: Epigenomics Core Facility
Weill Cornell Medical College, Box 288
1300 York Avenue
New York, NY 10065
If you are paying via a wire transfer please send an email to all2041@med.cornell.edu to arrange the proper transfer.
TIP: click on the orange buttons to expand (or close) each section in the workflow.
Frequently Asked Questions:
Click on the question of interest below to access answers.
Epigenomics is the study of heritable genome wide changes in phenotype (appearance) or gene expression caused by mechanisms other than changes in the underlying DNA sequence. The proper control and ordering of gene expression is associated and partially controlled through DNA sequence-independent biochemical events collectively known as epigenetic gene regulation. These include but are not limited to DNA methylation and histone modification through acetylation, methylation, ubiquitylation, phosphorylation, or sumoylation. Similar to the genetic information found within the sequence of DNA, epigenetic information can be inherited across generations, transmitted by mother to daughter cells, and is required for life. Epigenetic regulation is known to affect gene expression, and recent research shows that aberrant DNA methylation patterning may play a role in the manifestation, progression and therapy of several diseases. A deeper understanding of the epigenetic changes associated with disease can lead to improved diganostics and can ultimately be applied towards development of therapy.
Sequencing
Our Services page contains detailed information about the starting material and QC requirements for each service. Click on the assay of your choosing from the left hand vertical menu on the services page to access these details.
The number of samples you can sequence in a lane and/or the number of lanes you need to sequence depends on you specific project. Specifically, it depends on some of the following parameters:
The size of the genome, piece of the genome (ERRBS, Exome Capture etc.) or transcriptome (RNASeq) that you expect to sequence.
Your pooling/multiplexing design (if you are submitting pooled libraries).
We also have a multiplexing calculator to help you calculate the cost for multiplexing your samples across lanes.
It is recommended that you discuss your sequencing design with the bioinformatician who will be analyzing your data before sequencing your samples.
Data Analysis and Retrieval
The Epigenomics Core processes and aligns sequencing data at no additional cost if requested at the time of sequencing (see below for details of the data processing provided by the core). We can also provide additional or customized data processing and analysis support on a per project basis (see the Bioinformatics Support section of our services page for additional information). Please email us at epigenomicscore@med.cornell.edu to discuss your data analysis project.
Sequence data (base call files or bcl files) generated from the sequencer are demultiplexed and converted to FASTQ files using the Illumina bcl2fastq software.
Your raw data will be available for download as a tar compressed archive (Sample_*.tar) of gzipped FASTQ files for each sample. Raw data can be post-processed upon request.
If requested at the time of sequencing, the sequence data is aligned to default standard assembled genomes available for the assay. If custom genomes are required, please discuss with us before submitting your request.
Genomic Alignment Pipeline Results
FASTQ files generated as described above are aligned to genomes available via Illumina's iGenome using the BWA-MEM aligner. 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.
*.merged.bam - all alignments (including best and multiple alignments) for each read in the widely accepted BAM format (a binary version of the SAM format) for each sample.
*.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).
*-metrics.log - Summary metrics such as adapter trimming and alignment rates.
ERRBS Pipeline Results
We process Bisulfite sequencing data using an in-house BWA meth pipeline to generate methylation calls, related statistics and bam files for the samples.
The Sample_*.methylKit.gz files are tab delimited text files that contain all the reported locations of C's in either CpG, CHG, or CHH, context and their methylation levels.
The minimum read coverage cutoff for this file is 1
The *.10x.txt.gz files are tab delimited text files that contain the locations of C's in either CpG, CHG, or CHH, context and their methylation levels with a coverage greater than or equal to 10 (>=10x)
Sample_sorted.bam
Sample_sorted.bam.bai
This file contains the complete alignments in binary (BAM) format and a index (.bai) for this BAM file.
Sample_summary.txt
This file summarizes adapter trimming, alignment information, and mapping efficiency of the sample against the genome.
The column headers for the *.methylkit.gz and *.10x.gz are as follows:
chrBase = This is the name (chromosome.base location)
chr = chromosome on which the methylated base is located
base = location of methylated base on the chromosome
For your convinience we have also provided a perl script that allows you to filter, line-by-line, a given methylcall file for a given coverage.
[filterMethylcall.pl] - Please rightclick and save the link as file.
For example, the following command will filter the methylcall.CHH.Sample.mincov0.txt for sites >= 10x coverage:
filterMethylcall.pl methylcall.CHH.Sample.mincov0.txt 10
The pre-processed (and post-processed if requested) data files will be provided for download through our PubShare data protal: https://abc.med.cornell.edu/pubshare/ [Currently data from July 2013 onwards is available in PubShare. However, we cannot guarantee continued access to your data after 2 years of it's release.]
Note: Large .bam files may not download successfully when user older versions of web browsers on 32-bit operating systems, such as Windows XP.
To copy data from this webpage via UNIX shell (example: to your server home or data directory) you can use the provided wget commands.
Instructions for wget:
Just as when you use a web browser to download the tracks, you need to provide a username and password for the download with wget. You can generate a one-line wget command using the "Links" button in the cart.
[Please note that any .wgetrc files that you may have previously created may interfere with this wget command so you may need to rename these files.]
Alternatively, you can create a text file listing the links for the samples you wish to download (for example: links.txt) and use: wget --no-check-certificate --content-disposition --ask-password --user=youremail@your.institution.edu -i links.txt
(you can get the download link for the sample you wish to download on by right clicking the sample link in a browser and selecting the option for copying the link)
You can view your bigBed (s_N.nh.bb) and bigWig (s_N.nh.overlap.bw) files in the UCSC genome browser using the following steps:
In the input box where it says "Paste URLs or data:" edit and paste the following:
track type=bigWig name="some_meaningful_name_here" description="sample_description_here" bigDataUrl=http://epicore.med.cornell.edu/pubshare/more_url_here/s_N.nh.overlap.bw visibility=full color=128,0,255
You can get the URL for your file by right-clicking it and copying the link address. Copy and paste the whole URL in the bigDataUrl part of the custom track description. If you have several tracks, it may be useful to assign meaningful names and descriptions in the appropriate places as well.
Click the submit button next to the input box.
A link should be generated with the name you indicated in the input box in the custom tracks table.
Click on the "go to genome browser" button next to this link. This should bring you to your wiggles in the UCSC genome browser.
To view your .bam alignment file in the Integrative Genomics Viewer (IGV) you must have the corresponding .bai index file in the same folder as the .bam file. Please review the related IGV help page for more information.
