Platforms & Deliverables

Platforms & Deliverables

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Bulk Tissue and Cell Free services

Bulk Tissue and Cell-Free Sequencing

Whole Exome Sequencing & MSK-NeoQual:

Description:A capture-based assay to assess the entire exome.
Starting Material:DNA or DMP Library
Library Chemistry:KAPA EvoPrep
Capture Chemistry:xGen v2.0 from IDT (human); SinglePlex Mouse Exome from Twist (mouse)
Sequencing Read Length:PE100
Sequencing Coverage:30-250X+
Deliverable:FASTQ; NeoQual pipeline analysis (human); Pipeline analysis options available from CMO or BIC with additional charges

Targeted Sequencing:

Description:Capture-based assays to assess specific genes within the exome.
Starting Material:DNA or DMP Library
Library Chemistry:KAPA EvoPrep
Capture Chemistry:Custom probes
Sequencing Read Length:PE100
Sequencing Coverage:500X T/250X N (IMPACT); 60M reads (ACCESS); 30M reads (CMO-CH)
Deliverable:FASTQ (IMPACT; pipeline analysis options available from BIC with additional charges), pipeline analysis (ACCESS); in development (CMO-CH)

Transcriptome Sequencing:

Description:Techniques to enrich RNA and assess expressed transcripts
Starting Material:RNA or cells (SMARTer only)
Library Chemistry:Watchmaker mRNA (polyA), Watchmaker w/ Polaris Depletion (Ribodepletion), SMART-Seq v4 + KAPA EvoPrep (SMARTer)
Sequencing Read Length:PE100
Sequencing Coverage:10-100M+
Deliverable:FASTQ + BAM; analysis options from BIC at an additional cost

Whole Genome Sequencing:

Description:Assess the entire genome using PCR-free methods, minimal PCR cycles, or a shallow sequencing for CNV.
Starting Material:DNA
Library Chemistry:KAPA EvoPrep
Sequencing Read Length:PE150 (deep WGS); PE100 (shallow/bacterial WGS)
Sequencing Coverage:1-120X+
Deliverable:FASTQ

Epigenome Sequencing:

Description:Various methods to assess the epigenetic structure of the genome
Starting Material:Cells - no more than 24 samples/batch (ATAC), Transposed DNA (ChIP), gDNA (Methyl)
Library Chemistry:Nextera XT (ATAC), KAPA EvoPrep (ChIP), NEBNext + Twist probes (Methyl)
Sequencing Read Length:PE100
Sequencing Coverage:40-50M (ATAC), 10M (ChIP; more reads can be requested), 30-40X (Methyl)
Deliverable:FASTQ + methylation report (Methyl)

TCR Sequencing:

Description:Methods to enrich T-cell receptor sequences
Starting Material:Cells (10X Genomics), RNA - IGO-TCR
Deliverable:FASTQ + Pipeline output

Other Bulk Sequencing:

Description

Sequencing

Read Length

Sequencing CoverageDeliverable

Amplicon

Sequencing

variesvariesFASTQ
CRISPR Cut Site SequencingPE15075K readsFASTQ + CRISPRESSO analysis


Single Cell services

Single Cell Sequencing

10x Genomics Single Cell:

Description:Single-cell platforms to interrogate gene expression, immune repertoire, and/or protein expression.
Starting Material:Single cell or nuclei suspension
Library Chemistry:Chromium Single Cell
Sequencing Read Length:PE28/88
Sequencing Coverage:20K reads/cell (GEX), 5K reads/cell (V(D)J & cell hashing)
Deliverable:FASTQ, Cell Ranger output

10x Genomics Multiome:

Description:Single-cell ATAC-Seq + RNA-Seq from the same nucleus.
Starting Material:Single nuclei suspension
Library Chemistry:Chromium Single Cell
Sequencing Read Length:PE 28/88 (GEX), PE50 (ATAC)
Sequencing Coverage:20K reads/cell (GEX), 25K reads/cell (ATAC)
Deliverable:FASTQ, Cell Ranger output

10x Genomics Visium:

Description:Transcriptome sequencing of 1-10 cells along with spatial information.
Starting Material:Fresh Frozen, Fixed Frozen or FFPE tissue
Library Chemistry:Visium Spatial Gene Expression v1 (frozen only) or CytAssis
Sequencing Read Length:PE28/88
Sequencing Coverage:25-50K reads/1-10 cells
Deliverable:FASTQ, Space Ranger output

10x Genomics Visium HD:

Description:Single cell resolution on the Visium platform
Starting Material:FFPE, Fresh Frozen, or Fixed Frozen tissue
Library Chemistry:Visium probe set v2
Sequencing Read Length:custom
Sequencing Coverage:>50% sequencing saturation
Deliverable:FASTQ, Space Ranger output

10x Genomics Xenium:

Description:A single molecule imaging program for targeted single-cell spatial transcriptomics
Starting Material:FFPE or Fresh Frozen
Sequencing Coverage:N/A
Deliverable:Analysis with Xenium Ranger

Bruker CosMx:

Description:

A single molecule imaging program for targeted single-cell spatial transcriptomics

Starting Material:

FFPE or Fresh Frozen

Sequencing Coverage:

N/A

Deliverable:

Analysis in the AtoMx

SmartSeq:

Description:A single- or low-cell Smart-seq v3 method to accommodate projects without enough cells for 10X Genomics, or users interested in capturing the entire body of the gene.
Starting Material:Sorted cells
Library Chemistry:SMART-Seq + Nextera XT
Sequencing Read Length:PE100
Sequencing Coverage:~20K reads/cell
Deliverable:FASTQ

DLP:

Description:A method to detect CNV in single cells.
Starting Material:Single cell suspension
Library Chemistry:Custom protocol
Sequencing Read Length:PE150
Sequencing Coverage:2M reads/cell
Deliverable:FASTQ


Other services

Other Platforms

Digital PCR:

Description:PCR-based services for mutation detection, fusion detection, viral detection, or CNV. Hundreds of assays have been validated commercially or in house, but if your gene of interest is not on the list, IGO offers design & optimization services.
Starting Material:DNA, RNA, Library
Deliverable:Report

Optical Genome Mapping:

Description:Structural variant detection on the Bionano platform
Starting Material:Tissue or Cells
Sequencing Coverage:Report in collaboration with MCCF
Deliverable: 

Tissue and Bulk Extraction:

Description:Manual and automated methods for purifying RNA, DNA, or both from a variety of starting materials and sample types.
Starting Material:

Plasma; Frozen tissue/cells (OCT, RLT, TRIzol, pellet); Viably frozen cells; Blood; FFPE; Fingernails

Other? Contact us.

Deliverable:Nucleic acid + QC report

QC & Pathology:

Description:Other services offered by IGO.
QC Services:BioAnalyzer or TapeStation QC; Quant-it; %Human for PDX
Pathology Services:Sectioning (curls); Sectioning (slides); H&E Staining; Slide scraping; Macrodissection

Please email [email protected] if your sequencing needs do not fit in one of these categories.