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 |