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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.
 
 
 
Research reported in this publication included work performed in the Integrative Genomics Core supported by the National Cancer Institute of the National Institutes of Health under award number P30CA33572. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
 
 
 
 
 
 

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
 
Microarray
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
 
QC
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.
 
 
 

Equipment

 
Platform
No. of reads (flow cell)
Output bases (flow cell)
Run time
Read length
Cost per Run
Cost per MB
Errors
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
 Nanodrop
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
 
 
 
 

 
 
 
 
 
 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                                                                                                                                                        
 
 
 
 
 
 

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
     
Concentrations:
 
  • 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
Chemistry
 
  • 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.
 

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.

Pricing

Current service offering and pricing can be found on our iLab site. Please contact us for further questions.

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
xwu@coh.org
Ext. 65017
Jinhi Wang, Ph.D.
Staff Scientist
jiwang@coh.org
Ext. 61037
Hanjun Qin, Ph.D.
Staff Scientist
qhan@coh.org
Ext. 60638
Lu Yang, Ph.D.
Staff Scientist
luyang@coh.org
Ext. 65793
Basilio Gonzalez
Senior Research Associate
bgonzalez@coh.org
Ext. 62429
Ning Ye Zhou
Senior Research Associate
nye@coh.org
Ext. 65598
Chao Guo
Research Associate II
chguo@coh.org
Ext. 65975
Rosalina Lonergan
Research Associate II
rlonergan@coh.org
Ext. 63349
Charles Warden
Bioinformatics Specialist
cwarden@coh..org
Ext.60233
Bing Mu
Bioinformatics Specialist
bmu@coh.org
Ext. 60553
 

 
 

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.
 
 
 
Research reported in this publication included work performed in the Integrative Genomics Core supported by the National Cancer Institute of the National Institutes of Health under award number P30CA33572. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
 
 
 
 
 
 

Services Provided

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
 
Microarray
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
 
QC
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.
 
 
 

Equipment

Equipment

 
Platform
No. of reads (flow cell)
Output bases (flow cell)
Run time
Read length
Cost per Run
Cost per MB
Errors
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
 Nanodrop
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
 
 
 
 

 
 
 
 
 
 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                                                                                                                                                        
 
 
 
 
 
 

Sample Submission Guidelines

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
     
Concentrations:
 
  • 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
Chemistry
 
  • 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

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.

Pricing

Pricing

Current service offering and pricing can be found on our iLab site. Please contact us for further questions.

Contact Information

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
xwu@coh.org
Ext. 65017
Jinhi Wang, Ph.D.
Staff Scientist
jiwang@coh.org
Ext. 61037
Hanjun Qin, Ph.D.
Staff Scientist
qhan@coh.org
Ext. 60638
Lu Yang, Ph.D.
Staff Scientist
luyang@coh.org
Ext. 65793
Basilio Gonzalez
Senior Research Associate
bgonzalez@coh.org
Ext. 62429
Ning Ye Zhou
Senior Research Associate
nye@coh.org
Ext. 65598
Chao Guo
Research Associate II
chguo@coh.org
Ext. 65975
Rosalina Lonergan
Research Associate II
rlonergan@coh.org
Ext. 63349
Charles Warden
Bioinformatics Specialist
cwarden@coh..org
Ext.60233
Bing Mu
Bioinformatics Specialist
bmu@coh.org
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.
Support Our Research
By giving to City of Hope, you support breakthrough discoveries in laboratory research that translate into lifesaving treatments for patients with cancer and other serious diseases.
 
 
 
 
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NEWS & UPDATES
  • Internship programs are a rite of summer for many high-achieving students. For five Caltech pre-med students, each hoping to make a mark in medicine, that rite led them to the City of Hope campus in Duarte, California, for an exceptional learning experience. The collaboration between the two high-profile resear...
  • Urinary tract stones are hard masses, or calculi, that form in the urinary tract and may cause pain, bleeding or an infection, or even block of the flow of urine. Urinary tract stones begin to form in a kidney and may enlarge in a ureter or the bladder. Depending on where a stone is located, […]
  • Every summer, hospitals nationwide experience a shortage of blood donations. This summer is no exception. Nearly 1.7 million new cancer cases are expected to be diagnosed in the U.S. this year,  and many of those patients will need blood transfusions during their treatment. Patients at City of Hope alone rely o...
  • Non-Hodgkin lymphoma facts: Non-Hodgkin lymphoma is a cancer that starts in cells called lymphocytes, which are part of the body’s immune system. Lymphocytes are in the lymph nodes and other lymphoid tissues (such as the spleen and bone marrow). Non-Hodgkin lymphoma is one of the most common cancers in the U.S....
  • Few clinical cancer trials include older adults – and yet, more than 60 percent of cancer cases in the United States occur in people age 65 and older. The result is a dearth of knowledge on how to treat the very population most likely to be diagnosed with cancer. Now, the American Society of Clinical […]
  • Scientists at City of Hope and UCLA have become the first to inhibit the expression of a protein, called TWIST that promotes tumor invasion and metastasis when activated by cancer cells. As such, they’ve taken the first step in developing a potential new therapy for some of the deadliest cancers, including ovar...
  • Upon completing her final round of chemotherapy for ovarian cancer earlier this month, Maria Velazquez-McIntyre, a 51-year-old Antelope Valley resident, celebrated the milestone by giving other patients a symbol of hope – a Survivor Bell. The bell may look ordinary, but for cancer patients undergoing chemothera...
  • Many Americans understand that obesity is tied to heart disease and diabetes but, according to a new survey, too few – only 7 percent – know that obesity increases the risk of cancer. Specific biological characteristics can increase cancer risk in obese people, and multiple studies have shown correlations betwe...
  • As breast cancer survivors know, the disease’s impact lingers in ways both big and small long after treatment has ended. A new study suggests that weight gain – and a possible corresponding increase in heart disease and diabetes risk – may be part of that impact. In the first study to evaluate weight chan...
  • Becoming what’s known as an independent scientific researcher is no small task, especially when working to translate research into meaningful health outcomes. Yet that independent status is vital, enabling researchers to lead studies and avenues of inquiry that they believe to be promising. Clinicians, especial...
  • 720 days. That’s how long Alex Tung, 38, had to give up surfing after being diagnosed with acute myeloid leukemia. For most people, even some surfers, such a hiatus wouldn’t be a big deal, but for Tung, surfing has been everything. The Southern California resident began surfing when he was in elemen...
  • There are few among us who have not experienced loss of a friend or loved one, often without warning, or like those of us who care for people with cancer, after a lingering illness. It is a time when emotions run high and deep, and as time passes from the moment of loss, we often […]
  • For the past four years, neurosurgeon and scientist Rahul Jandial, M.D., Ph.D., has been studying how breast cancer cells spread, or metastasize, to the brain, where they become life-threatening tumors. Known as secondary brain tumors, these cancers have become increasingly common as treatment advances have ena...
  • Cutaneous T cell lymphomas are types of non-Hodgkin lymphoma that arise when infection-fighting white blood cells in the lymphatic system – called lymphocytes – become malignant and affect the skin. A primary symptom is a rash that arises initially in areas of the skin that are not normally exposed to sunlight....
  • There’s science camp, and then there’s “mystery” science camp. City of Hope’s new science camp for middle school students is of the especially engaging latter variety. From Monday, July 13, to Friday, July 17, rising middle-school students from across the San Gabriel Valley were presented with a “patient” with ...