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HTG Sequencing

HTG Molecular

HTG Molecular’s EdgeSeq is a fully automated sample and library preparation platform for targeted RNA sequencing that pairs HTG’s extraction-free, high-specificity Edge Chemistry with the high sensitivity and dynamic range of next-gen sequencing. EdgeSeq enables digital quantitation of miRNA and mRNA expression from difficult sample types such as formalin-fixed, paraffin-embedded (FFPE) tissues, plasma and exosomes.

Assays that are available with HTG include:

  • HTG EdgeSeq Oncology Biomarker Panel (OBP)
  • HTG EdgeSeq Precision Immuno-Oncology Assay (IO)
  • HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA)
  • HTG EdgeSeq PATH Panel (PATH)
  • HTG EdgeSeq Lymphoma Panel (DLBCL)
  • HTG EdgeSeq Mouse mRNA Tumor Response Panel (TRP)

Sequencing and pooling recommendations can be found in the chart below:

Service Samples per Pool* Platform Cycles
HTG (2 million reads per sample) 8 MiSeq Single End/50x
HTG (5 million reads per sample) 48 HiSeq 2500
HTG (2.5 million reads per sample) 96 HS4000
*Note: Dependent on the total number of samples that is provided, more efficient pooling plans may be available

 

For more information on HTG, please visit https://www.htgmolecular.com/

10X Genomics

Please note that 10X whole genome has been discontinued.

Single Cell Gene Expression (sc 10X)

The Chromium Single Cell Gene Expression Solution provides a comprehensive, scalable solution for cell characterization and gene expression profiling of hundreds to tens of thousands of cells. It can help to uncover gene expression variability and identify rare cell types in heterogeneous samples to better characterize cellular contributions during development and disease.

Optionally with Feature Barcoding Technology
10X Genomics’s latest improvements allow researchers to:

  1. CRISPR Screening – identify cell-specific CRISPR-mediated perturbations on gene expression via direct capture of gRNAs and polyadenylated mRNAs from the same single cell
  2. Cell Surface Protein – measure both gene and cell surface protein expression in the same cell to identify protein isoforms, detect protein for low abundance transcripts, and further increase phenotypic specificity

Single Cell ATAC

Single Cell ATAC accelerates the understanding of the regulatory landscape of the genome, thereby providing insights into cell variability. The chromatin profiling of tens of thousands of single cells in parallel allows researchers to see how chromatin compaction and DNA-binding proteins regulate gene expression at high resolution.

Sequencing and pooling recommendations can be found in the table below, A more complete lost of cycles and platforms can be found on 10x Genomics Library Indexes and Sequencing Requirements in Forms and Guides, Alternative Technologies.

Sequencing and pooling recommendations can be found in the table below:

Service Samples per pool Platform Cycles (Single Cell 3’ V2) Cycles (Single Cell 3’ V3) Cycles (ATAC seq)

  • 10x 3′ trans
  • ATACseq 5000 cells

 

1 HiSeq 4000 26x8x98 28x8x91 50x8x16x50
3 NovaSeq SP
6 NovaSeq S1
15 NovaSeq S2
40 NovaSeq S4
*Note: 5000 living cells are required for successful library preparation. Please provide more cells to compensate for any cell death that may occur during transportation to HTSF. For 5000 cells, the HTSF recommends providing 8000 cell input.
** Note: For each set of 5000 living cells, sequencing should yield approximately 250 million clusters

 

Please contact the HTSF before submitting for 10X Genomics.
For more information on 10X genomics, please visit https://www.10xgenomics.com/

Relevant Alternative Services Forms and Guides

HTSF Sample Preparation Requirement Guide
Illumina Platform Comparison and Specification Table
NovaSeq Requirements
Approved Containers Information
10x Genomics Submission Manifest for HTSF Made Libraries
10x Genomics Library Indexes and Sequencing Requirements
10x Genomics Manifest for Study Made Libraries with Indexes and Sequencing Requirements
NovaSeq White Paper
HTG White Paper
10x Genomics White Paper