Welcome!
The mission of the Integrated CITI Platforms consisting of the Immunomonitoring Laboratory (IML), Discovery lab (DL) and Computational Immunology Platform (CIP) at the Cleveland Clinic is to provide cutting edge technologies and assays for the comprehensive immunophenotyping and specialized sequencing of blood and tissue. It allows investigators to monitor the impact of therapeutic interventions on immunologic profiles, interrogate mechanisms and pathways related to treatment protocols, and advance the conceptual basis for targeted treatment strategies. We work with scientists, clinicians, industry collaborators, and a broad array of investigators on both clinical trials and discovery based immunologic research within and outside Cleveland, Ohio.
C. Marcela Diaz, Ph.D | IML Scientific Director
Jennifer Ko, M.D, Ph.D | IML Medical Director
Raghvendra Srivastava, Ph.D | Discovery Lab Scientific Director
Vladimir Makarov, M.D, M.S | Computational Immunology Platform (CIP) Scientific Director
Patricia Rayman, M.S. | IML Manager
| Hours | |
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Monday - Friday 8am - 7pm |
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| Name | Role | Phone | Location | |
|---|---|---|---|---|
| Marcela Diaz |
Director IML
|
diazc2@ccf.org
|
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| Vladimir Makarov |
Director CIP
|
MAKAROV@ccf.org
|
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| Raghvendra Srivastava |
Director Discovery Lab
|
SRIVASR@ccf.org
|
| Service list |
| ► Computational Immunology Platform (CIP) (14) | |||
| Name | Description | Price | |
|---|---|---|---|
| CIP - Bulk RNA-Seq alignment |
STAR alignment to reference genome, Pre/Post alignment QC collection, raw and normalized read counts over genes. |
Inquire | |
| CIP - Two condition RNA-Seq differential expression analysis |
Differential gene expression as specified by users. Users are expected to provide metadata files according to provided templates. |
Inquire | |
| CIP - GSEA Pathway Analysis and xCell Immune Deconvolution |
Gene set enrichment analysis (GSEA) and pathway analysis and xCell Deconvolution (tumor samples only) for 64 Immune cell types. |
Inquire | |
| CIP - Targeted/Whole Exome/Whole Genome Sequencing alignment |
Alignment to reference and Pre/Post alignment QC collection. |
Inquire | |
| CIP - DNA profiling (genetic fingerprinting) |
Add DNA fingerprinting to post-alignment QC report to ensure matching Tumor and Normal samples. Can be applied to WES/WGS. |
Inquire | |
| CIP - Post-alignment Targeted/WES/WGS data processing |
Somatic or germline variant calling and annotation (SNV/INDELS), Allele Specific Copy Number calling, Microsatellite instability (MSI). |
Inquire | |
| CIP - Single Cell RNA-Seq |
Standard Cell Ranger pipeline, Loupe objects per sample and per project, Pre/Post alignment QC metrics collection. |
Inquire | |
| CIP - Post-alignment Single Cell RNA-Seq analysis |
Includes standard Seurat pipeline, generating Integrated Seurat Object and automated cell typing. |
Inquire | |
| CIP - T-cell/Antibody Immune Repertoires Analysis |
T-cell/Antibody Immune Repertoires Analysis. Data normalization, CDR3 identification, clonal dynamics, and repertoire features such as diversity and Shannon metrics. We will need to discuss metadata, comparison, and other parameters prior to analysis. For TCR Sequencing, please consult with Discovery Lab. |
Inquire | |
| CIP - ChIP-Seq alignment |
Alignment to reference genome and Pre/Post alignment QC collection. |
Inquire | |
| CIP - Peak calling with MACS2 |
Apply MACS2 peak calling algorithm to identify areas in the genome that have been enriched with aligned reads |
Inquire | |
| CIP - Peak annotation with Homer software | Inquire | ||
| CIP - Upload genomics data to repositories |
Uploading genomics data we have processed/analyzed to SRA or GEO data repositories for publication. Clients will be asked to fill in the forms required by repositories. |
Inquire | |
| CIP - Custom work |
Any additional work to our pipeline output (needs to be discussed). Can be accepted or rejected on bioinformatics group discretion. Only applies to the data processed/analyzed by our group. Hourly rate ($175/Hr) will be applied. |
Inquire | |
| ► Discovery Lab (3) | |||
| Name | Description | Price | |
| DL - HLA Sequencing (CareDx AlloSeq) |
The HLA sequencing service permits investigators to characterize and identify HLA genotypes for research use only. Data output uses CareDx's AlloSeq Assign software. |
Inquire | |
| DL - TCR-beta Sequencing; sendout to Adaptive Biotechnologies | Inquire | ||
| DL - Single Cell RNA Sequencing library preparation (3' or 5') + Bioanalyzer QCs | Inquire | ||
| ► IML - Sample Procurement, Processing and Banking - Blood (2) | |||
| Name | Description | Price | |
| IML - Processing of whole blood for PBMC, Plasma (or Serum) and freezing | Inquire | ||
| IML - PBMC retrieval, thawing and counting | Inquire | ||
| ► IML - Sample Procurement, Processing and Banking - Fresh Tissue (2) | |||
| Name | Description | Price | |
| IML -Procure specimen | Inquire | ||
| IML - Dissociate to single cell suspension and freeze | Inquire | ||
| ► IML - Sample Procurement, Processing and Banking - Frozen Tissue (8) | |||
| Name | Description | Price | |
| IML - Frozen tissue, retrieve, transfer, re-file, initial specimen | Inquire | ||
| IML - Frozen tissue, retrieve, transfer, re-file, additional specimen | Inquire | ||
| IML - Retrieve, OCT embed, transfer, re-file, each specimen | Inquire | ||
| IML - Retrieve, OCT embed, transfer, re-file, additional specimen | Inquire | ||
| IML - Frozen section, unstained (2 sections/slide), additional slide | Inquire | ||
| IML - Frozen section, unstained (2 sections/slide), each slide | Inquire | ||
| IML - Frozen section + HE/Dif Quick stain, each side | Inquire | ||
| IML - Frozen Shaving in Tube wl Pre & Post HE stains, each tube | Inquire | ||
| ► IML - Sample Procurement, Processing and Banking - Formalin-fixed, paraffin embedded tissue (6) | |||
| Name | Description | Price | |
| IML - Pull and re-file slides, per case | Inquire | ||
| IML - Block selection per case | Inquire | ||
| IML - Cut piece of tissue from block, re-embed case (Daughter block) | Inquire | ||
| IML - Cassette, process, and embed tissue block | Inquire | ||
| IML - Unstained paraffin recut, Initial Slide | Inquire | ||
| IML - Unstained paraffin section in Eppendorf tube | Inquire | ||
| ► IML - Fresh Tissue (1) | |||
| Name | Description | Price | |
| IML - Mouse Tumor Digest |
Use Miltenyi Mouse Tissue Dissociation Kit |
Inquire | |
| ► IML - Immune Analysis - Nucleic acid isolation and analysis (9) | |||
| Name | Description | Price | |
| IML - RNA Isolation |
RNA isolation from fresh tissue/PBMC |
Inquire | |
| IML - Single cell CITE-Seq (capture, expression, CITE-seq, TCR and BCR library prep and sequencing) |
Single cell CITE-Seq (capture, library prep and sequencing) |
Inquire | |
| IML - RNA isolation from fresh tissue/PBMC | Inquire | ||
| IML - DNA isolation from fresh tissue/PBMC | Inquire | ||
| IML - RNA isolation from frozen tissue | Inquire | ||
| IML - DNA isolation from frozen tissue | Inquire | ||
| IML - RNA isolation from FFPE tissue | Inquire | ||
| IML - DNA isolation from FFPE tissue | Inquire | ||
| IML - Nanostring nCounter gene expression analysis | Inquire | ||
| ► IML - Immune Analysis - Flow Cytometry (8) | |||
| Name | Description | Price | |
| IML - Multicolor flow cytometry standard panels whole blood |
|
Inquire | |
| IML - Multicolor flow cytometry standard panels PBMCs |
|
Inquire | |
| IML - High parameter flow cytometry myeloid panel |
|
Inquire | |
| IML - High parameter flow cytometry T cell panel |
|
Inquire | |
| IML - High parameter flow cytometry T cell exhaustion panel |
|
Inquire | |
| IML - Custom panel design and optimization | Inquire | ||
| IML - Staining and FACS cell sorting | Inquire | ||
| IML - Mouse HP Flow Cytometry |
CD45 PDL1 CD11c Anti-Mouse I-A/I-E CD25 Ly6G CCR2 CD8 CD11b CXCR2 CD4 PD1 F4/80 CD127 |
Inquire | |
| ► IML - Immune Analysis - Cytokine/Serology Assays (5) | |||
| Name | Description | Price | |
| IML - Multiple cytokine analysis (56 analytes); Send-Out | Inquire | ||
| IML - Multiple cytokine analysis (56 analytes); Shipping | Inquire | ||
| IML - Proteomics Olink platform (Price per sample per panel 92 analytes); Send-Out | Inquire | ||
| IML - Proteomics Olink platform (Price per sample per panel 92 analytes); Shipping | Inquire | ||
| IML - Tumor Antigen ELISA | Inquire | ||
| ► IML - Immune Analysis - Functional Assays (4) | |||
| Name | Description | Price | |
| IML - Luminex SARS-CoV-2 Serology Assay | Inquire | ||
| IML - T cell proliferation assay ELISPOT | Inquire | ||
| IML - T cell proliferation assay intracellular cytokine | Inquire | ||
| IML - T cell suppression assay | Inquire | ||
| ► IML - Immune Phenoptics (5) | |||
| Name | Description | Price | |
| IML - H&E paraffin recut, per slide | Inquire | ||
| IML - Enzyme histochemistry, per slide | Inquire | ||
| IML - Conventional special stain | Inquire | ||
| IML - Tumor circling and purity quantification |
Pricing will vary depending on number of cases |
Inquire | |
| IML - Multispectral Imaging- UC | Inquire | ||
