Bulk Tissue and Cell-Free Sequencing

Whole Exome Sequencing:

Description:	A capture-based assay to assess the entire exome.
Starting Material:	DNA or DMP Library
Library Chemistry:	KAPA Hyper
Capture Chemistry:	xGen v2.0 from IDT (human); SinglePlex Mouse Exome from Twist (mouse)
Sequencing Read Length:	PE100
Sequencing Coverage:	Varies (see below)
Deliverable:	FASTQ; 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 Hyper
Capture Chemistry:	Custom probes
Sequencing Read Length:	PE100
Sequencing Coverage:	500X T/250X N (IMPACT/HemePACT); 60M reads (ACCESS); 30M reads (CMO-CH)
Deliverable:	cBioPortal instance (IMPACT & HemePACT), pipeline analysis (ACCESS, M-IMPACT); in development (CMO-CH)

Transcriptome Sequencing:

Description:	Techniques to enrich RNA and assess expressed transcripts
Starting Material:	RNA or cells (SMARTer only)
Library Chemistry:	TruSeq stranded mRNA (polyA), TruSeq stranded total (Ribodepletion), SMART-Seq v4 + KAPA Hyper (SMARTer)
Sequencing Read Length:	PE100
Sequencing Coverage:	10-100M+
Deliverable:	FASTQ; analysis options from BIC at an additonal cost; pipeline analysis (Archer only)

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 Hyper
Sequencing Read Length:	PE150 (deep WGS); PE100 (shallow/bacterial WGS)
Sequencing Coverage:	Varies; see below
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), DNA – 4 sample minimum (EPIC)
Library Chemistry:	Nextera XT (ATAC), KAPA HTP (ChIP), TruSeq Methyl Capture (EPIC)
Sequencing Read Length:	PE100
Sequencing Coverage:	40-50M (ATAC), 10M (ChIP; more reads can be requested), 40M (EPIC)
Deliverable:	FASTQ

TCR Sequencing:

Description:	Methods to enrich T-cell receptor sequences
Starting Material:	RNA - 7 sample minimum (Archer), Cells (10X Genomics), RNA - IGO-TCR
Deliverable:	FASTQ + Pipeline output

 

Please email us if your sequencing needs do not fit in one of these categories.

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:	PE28/91
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 28/90 (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 or FFPE tissue
Library Chemistry:	Visium Spatial Gene Expression
Sequencing Read Length:	PE28/90
Sequencing Coverage:	25-50K reads/1-10 cells
Deliverable:	FASTQ, Space Ranger output

Mission Bio Tapestri:

Description:	A targeted single-cell platform to detect SNVs and CNVs in off-the-shelf or custom panels.
Starting Material:	Single cell or nuclei suspension
Sequencing Read Length:	PE150
Sequencing Coverage:	Panel dependent
Deliverable:	FASTQ + Tapestri Platform output

PlateSeq:

Description:	A single- or low-cell Smart-seq 2 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:	PE50
Sequencing Coverage:	5M 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

Nanostring GeoMx:

Description:	A spatial transcriptomics platform allowing for targeted RNA-seq of manually selected regions of interest.
Starting Material:	FFPE slides
Sequencing Coverage:	variable
Deliverable:	FASTQ; GeoMx pipeline output

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

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; Qubit/Quant-it; %Human for PDX; Cell Line Authentication
Pathology Services:	Sectioning (curls); Sectioning (slides); H&E Staining; Slide scraping; Macrodissection