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Integrative Genomics Core

Integrative Genomics Core
The Integrative Genomics Core is committed to providing high quality, efficient, comprehensive, and cost effective genomic services to City of Hope researchers using microarray and high-throughput sequencing technologies. We also provide basic and advanced data analysis services to make complex data biologically interpretable for clinical and basic scientists.

Services Provided

High-throughput Sequencing
We provide a variety of services for deep-sequencing of RNA or DNA samples. We will help you choose the best platform and experimental protocols for your projects:
1) RNA Analysis
    a) RNA-seq (see here for RNA-seq decision tree)
        mRNA expression, transcriptome analysis, alternative splicing, coding SNPs, moonoallelic expression:
(1) Poly(A) enriched mRNA-seq;
(2) Ribo-Zero based transriptome sequencing
(3) Stranded and unstranded RNA-seq;
(4) Low input RNA-Seq
(a) Nugen Ovation® RNA Seq System V2
(b) SMARTer™ Ultra Low RNA Kit
     b) smRNA-seq:
     Profilng miRNA and other small RNAs (piRNA, etc.); siRNA processing;
2) DNA Analysis
    a) ChIP-seq: DNA-protein interactions across the entire genome
    b) Methyl-seq:
i) MDB-seq, MeDIP-seq;
ii) Whole genome bisulfate sequencing
iii) RRBS (Reduced representation bisulfate sequencing)
    c) Targeted resequencing:
i) Exome-seq
 Single point mutation and small indel detection in coding exons (and UTRs), as well as structural variations
ii) Customized panels
(1) Agilent’s SureSelectXT
(2) Life Technology’s AmpliSeq
(3) Agilent’s Haloplex
    d) Whole genome sequencing
i) Single point mutation and indel detection
ii) Structure variant detection: large indels, copy number changes, inversion, translocation and others

    e) De novo sequencing
         Assembly of small genomes or BAC
    f) Metagenomic sequencing
       Baterial 16S rRNA profiling
We provide various RNA and DNA analysis using Microarray technologies from Affymetrix, Agilent and Illumina. Most of the protocols are compatible with FFPE samples:
1)RNA Analysis
    a) Gene Expression
         i) Affymetrix’s GeneChip arrays
         ii) Illumina’s human HT12 v4 array
         iii) Agilent’s genome expression array
2) DNA Analysis
    a) DNA Methylation
         i) Illumina’s Infinium HD 450K array
    b) Copy number analysis
         i) Agilent’s CGH array
        ii) Affymetrix Oncoscan array
    c) Genotyping
        i) Affymetrix SNP array and Oncoscan array
        ii) Illumina’s whole genome and targeted genotyping array
Data Analysis
We provide comprehensive data analysis service for all data generated within our core, including microarray and high-throughput sequencing data. We also support analysis of genomic data downloaded from GEO or other databases:
1) Standard Data Analysis
   a) RNA-seq/miRNA-seq: QC, alignment, counting, differential expression, GO/Pathway
   b) ChIP-seq: QC, alignment, peak calling/annotation, differenti
   c) Exome-seq: QC, alignment, variants calling/annotation
   d) BS-seq: QC, alignment, methylation report, annotation, differential methylatio
   e) Transcriptome: In addition to RNA-seq standard service, identification of novel transcripts/ncRNA, de novo assembly when needed
   f) Microarray (expression): QC, differential expression, GO/pathway
2) Custom Analysis includes any non-standard services, or large projects with more than 20 samples
3) We also actively develop software packages for genomic data analysis
Quality and quantity measurements of nucleotides samples. Both DNA and RNA samples are accepted. Nanodrop Spectrometer or Qubit Fluorometer will be used for quantifying samples. Bioanalyzer will be used for sample quality assurance and library quality.
Sanger Sequencing
We also provide standard Sanger sequencing service for PCR product, BAC, plasmid, bisulfate sequencing etc.


No. of reads (flow cell)
Output bases (flow cell)
Run time
Read length
Cost per Run
Cost per MB
Illumina Hiseq 2500 Regular Mode 1.5 billion SE or PE 300 Gb 2/11 days 2x100bp $12,674 $0.04 Substitution
Illumina Hiseq2500 Rapid Mode 300 million SE or PE 90 Gb 7/40 hr 2x150bp $3,356 $0.04 Substitution
Life Tech Ion Proton 60-80 million SE ~10Gb ~4 hours 100-200bp $1,200 $0.15 Indels at homopolymers
 Illumina's HiSeq 2500 Sequencer
 Illumina's cBot
  Life Technologies' Ion ProtonTM Sequencer
 Life Technologies' Ion One Touch2
  Life Technologies' 3730 DNA Analyzer
 Affymetrix GeneChip System
 Illumina's Hiscan System
 Agilent Microarray System
  Agilent Bioanlyzer
 Qubit Flurometer




Sample Submission Guidelines

You are encouraged to set up a meeting to consult for experimental design with the core director, Dr. Xiwei Wu, to determine the optimal platform, library preparation protocol, and sample size. Please fill out the service request form at the time of sample submission. Typical turnaround time for microarray service is one - two weeks, and three - four weeks for sequencing, one - four weeks for data analysis. Please note that actual turnaround time might vary depending on the work load and complexity of the project.
Sample Requirement for Microarray preparation
Quality check is required for all samples by the core using Agilent Bioanalyzer 2100, NanaDrop1000 or Qubit 2.0. Samples that fail the quality analysis will be returned to researcher and ask for replacement.
RNA Submissions
All RNA must be clean and free from protein and DNA contamination and meet the following minimum requirements:
260/280 ratios must be between 1.9 and 2.1
260/230 ratios must be above 1.8 (if < 1.8, samples has organic contaminants)
We recommend using the QIAGEN RNeasy columns for total RNA purification. When working with Qiagen RNeasy columns for use with the Affymetrix system, please do not use β-mercaptoethanol; it is unnecessary and can cause high background in your GeneChips.
For small RNA: Perform total RNA purification that retains the small RNA such as Qiagen miRNeasy Kit. Total RNA must be submitted, and please do not do the enrichment step. miRNA samples will require two quality control (QC) steps: one for total RNA and one for small RNA.
Usually, 500 ng -1 µg RNA is good enough for QC and sample preparation. But it is varied depending on the technologies of your choice. Please check with our core staff for specific requirement.
DNA Submissions

260/280 ratios must be between 1.8 and 2.0
260/230 ratios must be above 2.0 (if < 2, samples has organic contaminants)
Genomic DNA can be extracted using any method that generated high quality DNA.
Amplified DNA must be purified, and we recommend using the Qiagen QiaQuick PCR purification protocol with samples eluted in nuclease-free water or the elution buffer provided by in the kit.
1-2 µg DNA is required for success analysis. But it is varied depending on the technologies of your choice. Please check with our lab staff for specific requirement.
Sample Requirements for NGS Sample Preparation
Please see appropriate sample requirements below if you would like core staff to prepare sequencing libraries for your samples.
  • DNA Sequencing
100 ng or more for genome DNA, PCR products, BAC, YAC etc suspended in EB buffer or H2O  in a volume not to exceed 50ul. DNA should be as intact as possible, with an OD260/280 ratio of 1.8-2. The DNA amount should be over 250ng for PCR free sequencing library preparation protocol.
  • Targeted Exome Capture (Agilent Sure Select Protocol)
1 – 2 µg of purified DNA suspended in EB buffer in a volume not to exceed 50ul. DNA should be as intact as possible, with an OD260/280 ratio of 1.8-2.
  • Targeted Exome Capture (Life Technologies AmpliSeq Exome Protocol)
100 ng of purified DNA (or 250 ng for FFPE DNA) suspended in EB buffer in a volume not to exceed 20 µl. DNA should be as intact as possible, with an OD260/280 ratio of 1.8-2.
  • Whole Transcriptome (mRNA-Seq) Profiling
0.5-10µg of Purified RNA (DNA free) suspended in nuclease-free H2O in a volume less than, or equal to 50µl. RNA should be as intact as possible, with OD260/280 ratio of 1.8-2 and an OD260/230 ratio over 1.5. Core lab will verify RNA integrity via an Agilent Technologies 2100 Bioanalyzer. RIN ≥8.0 for polyA protocol.
  • Small RNA Sequencing
1 - 10µg of Purified RNA suspended in nuclease-free H2O, concentration >100ng/µl. RNA should be isolated using a method that preserves small RNAs. RNA should be as intact as possible, with OD260/280 ratio of 1.8-2 and an OD260/230 ratio over 1.5.
  • ChIP-Enriched DNA Sequencing
10ng of purified, ChIP-enriched, qPCR-verified, PicoGreen quantified DNA suspended in 30ul EB Buffer should be submitted.

A high-quality library is critical to obtaining high quality data. Protocols used by the Core have been optimized. We also offer library preparation services.
Users interested in making their own libraries to expedite their studies should download and read the current protocols for different kits offered by Illumina. Ordering information for kits is available upon request.
Sample Requirements for Sanger sequencing
      Log on the LIMS system at dnatools.coh.org
  • Template - PCR Product:
Concentration at least 0.5 ng per 100 base pairs for fragments less than 500 bp.
  • Dilute PCR sample to 1 ng/ul if PCR fragment is less than 500 bp.
If your PCR sample is greater than 500bp then dilute PCR to 3ng/ 100 base pairs in 2 ul volume. 

For example: If your PCR size is 600 base pairs, multiply 600 X 0.03 which will give you the total amount of DNA necessary ( 18ng) for sequencing. Then dilute your PCR sample to the correct working concentration of  9ng/ul in 2ul total volume.
  • Template – BAC Clones
1ug/ ul concentration for BAC DNA
Template – Plasmid
  • Concentration at 100 ng/ul
2.0 ul needed per reaction
  • Custom Primers
Concentration at 1pmol/ul
10 pmol/ul for BAC sequencing primers
4ul needed per reaction
Entry Form (After you have clicked Enter DNA Sequencing Requests, and entered the number of reactions)
  • For City of Hope users, leave the PO Number field blank.  This is for outside users only.
  • Under the Grant Code Num. field please enter your grant code.
  • The account number you enter must use the subaccount of 8028. Do not change this.  Enter your entire account number (20/30 – 8028 – 6 digit account number) Ex. 30-8028-xxxxxx
  • Enter the PI name “last name, first name” and in all capitals.  Ex: SMITH, JOHN
  • BigDye_V3.1 – For basic sequencing.  Can read out to approximately 900 base pairs
  • BigDye_V1.1 – Used only for short (less than 500 base pairs) PCR products when high resolution near the priming site is needed
  • • BigDye_3.0-dGTP – Used only for templates that are likely to form strong secondary structures, hairpin loops, or with high GC content (greater than 75%) or bisulfite-treated samples.  When using this chemistry, please include the Tm of your primer in the comments box
Make sure after submitting the entry form, you print 2 copies of the table that appears. One of these copies must be placed in the inbox to inform us that the samples are ready to go.  If we do not receive a copy of this form, your samples will never be sequenced.  The other copy is for your reference.
Please label your samples with less than 8 characters if possible.  Write the labels on the cap of the tubes you are submitting. Make sure that the labels on your tubes matches identically to the labels on the order form.
If you need a Chromatograph viewer, you can download one from Life Technologies.

Sample Submission Forms

Abstract for Grant

The integrative genomics core (IGC) is a shared resource facility within the Beckman Research Institute (BRI) at City of Hope. Partially supported by NCI comprehensive cancer center grant, the goal of the IGC is to provide comprehensive genomic services from pre-experimental consultation, sample processing, data analysis and interpretation to manuscript and grant preparation.
The IGC is committed to providing these services in a cost-effective and timely manner to support basic science, translational, and clinical researchers at City of Hope.
The IGC is equipped with all major state-of-the-art microarray and sequencing platforms for genomic studies, including Illumina’s Hiseq 2500 and Life Technology’s Ion Proton sequencers, Illumina’s Hiscan Beadchip system, Affymetrix’s GeneChip system, and Agilent’s microarray system. 
The core also has a state-of-the-art Hitachi AB model 3730 48-capillary DNA Analyzer with the capacity to analyze 4,000 to 8,000 samples per week. These instruments enable a wide range of genetic, epigenetic and gene expression analysis capabilities, and complement each other for different applications, including transcriptomic and miRNA profiling, protein and DNA/RNA interaction, histone modifications, DNA methylation, SNP/indel, copy number variations and other structural variations, genome-wide and customer genotyping. The core also has an ABI Taqman Real-time PCR system, ViiA 7, an excellent technology for expression validation, as well as Nanodrop, Qubit 2.0 and Agilent Bioanalyzer for sample QC.
With a highly experienced team of bioinformaticians integrated within the core, efficient genomic data analysis services will be provided to convert high throughput data into biologically interpretable results. The team has established analysis pipelines for all major sequencing applications, e.g. RNA-seq, miRNA-seq, ChIP-seq, exome-seq, amplicon-seq, etc., and has extensive expertise in utilizing both commercial and open-source software tools for sequencing data analysis. These include but are not limited to R/Bioconductor, IGV, Bowtie, TopHat, Cufflinks, Novoalign, MACS, MEME, Transfac, BWA, GATK, Samtools, Gene Set Enrichment Analysis (GSEA), Ingenuity Pathway Analysis and DAVID.
The core processes over 1500 samples with microarray and sequencing instruments each year and supports bioinformatics analysis on all the data generated. The bioinformatics team is also experienced in mining public domain data, such as GEO, TCGA, and 1000 genome databases. The core also supports depositing the genomic data into NCBI’s GEO and SRA database for data sharing.


Sanger Sequencing Service      CCSG
Core_Prep      $6.00
Economy      $6.00
User_Prep      $1.00
MS      $3.00
Special_Bac      $9.00
Special Bisulfite      $6.00
Special_EDTA      $3.00
High throughput Sequencing Service      CCSG
Sequencing Regular SR: 40+7       $855
Sequencing Regular PE 100+7+100         $1,578
Sequencing FAST SR: 60+7      $905
Sequencing FAST PE 100+7+100      $1,669
library prep      $175
Ribo-Zero      $240
Qubit QC      $1
QPCR for QC      $10
RNA Nano QC      $48  (1-12 samples)
RNA Pico and DNA QC      $72 (1-11 samples)
Microarray Service      CSSG
Affymetrix Gene Expression 3' Express or Exon      $282.00
Affymetrix Gene Expression WT      $259.00
Agilent Gene Expression mRNA/miRNA      $192.00             
Agilent aCGH      $214.00
Illumina Human HT12 v4 Expression      $209.00
Illumina HD Methylation 450K      $394.00
Data Analysis Service     CCSG
Data Analysis (RNA-seq/smRNA-seq/ChIP-seq)     $40/sample
Data Analysis (Exome-seq/Transcriptome/BS-seq)     $80/sample
Data Analysis (Microarray)     $30/sample
Custom Analysis     $50/hour
The cost for sequencing will depend on the library preparation protocol and sequencing depth. Example cost for commonly used applications are listed below (note the actual cost might slightly vary depending on the sample size)
Application  Cost
smRNA-seq  $283 SR 40+7 15M reads
mRNA-seq  $421 SR 40+7 30M reads
mRNA-seq  $596 PE 100+7+100 30M reads
ChIP-seq  $408 SR 40+7 40M reads
exome-seq  $589 PE 100+7+100 40M reads
exome-seq  $1000 at  50x coverage 

Contact Information

The sequencing facility is located at:
Beckman Research Institute of City of Hope
1500 E. Duarte Road
Lippman Graff Building
First floor, Room 132
The microarray facility is located at:
Beckman Research Institute of City of Hope
Flower Building
1710 Flower Avenue
Duarte, CA 91010-3000
Telephone: 626-256-HOPE (4673), ext. 65071
Fax: 626-256-8727
Xiwei Wu, M.D., Ph.D.
Director DNA
Ext. 65017
Jinhi Wang, Ph.D.
Staff Scientist
Ext. 61037
Hanjun Qin, Ph.D.
Staff Scientist
Ext. 60638
Lu Yang, Ph.D.
Staff Scientist
Ext. 65793
Basilio Gonzalez
Senior Research Associate
Ext. 62429
Ning Ye Zhou
Senior Research Associate
Ext. 65598
Chao Guo
Research Associate II
Ext. 65975
Rosalina Lonergan
Research Associate II
Ext. 63349
Charles Warden
Bioinformatics Specialist
Bing Mu
Bioinformatics Specialist
Ext. 60553

Research Shared Services

City of Hope embodies the spirit of scientific collaboration by sharing services and core facilities with colleagues here and around the world.

Recognized nationwide for its innovative biomedical research, City of Hope's Beckman Research Institute is home to some of the most tenacious and creative minds in science.
City of Hope is one of only 41 Comprehensive Cancer Centers in the country, the highest designation awarded by the National Cancer Institute to institutions that lead the way in cancer research, treatment, prevention and professional education.
Learn more about City of Hope's institutional distinctions, breakthrough innovations and collaborations.
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