#10X CHROMIUM COST FULL#
#10X CHROMIUM COST SOFTWARE#

The analysis requires a great deal of knowledge about statistics, wet-lab protocols, and some machine learning due to variability and sparseness of the data. The cellular resolution and genome wide scope make it possible to draw new conclusions that are not otherwise possible with bulk RNA-seq. P3 is 1.1 billion reads.Single-cell RNA-seq analysis is a rapidly evolving field at the forefront of transcriptomic research, used in high-throughput developmental studies and rare transcript studies to examine cell heterogeneity within a populations of cells. Kits available from Illumina ( Quotes in DropBox): Visium Spatial Gene Expression Slide & Reagent Kit Kits available from 10X ( Quotes in DropBox):ģ’ Chromium NextGEM Library & Gel Bead Kitĥ’ Chromium NextGEM Library & Gel Bead KitĪTAC Chromium NextGEM Library & Gel Bead Kit Slack channel (user-driven knowledge base) Single cell, spatial, and bulk assay analysis in R or Partek Flow (first come, first serve basis with limited bandwidth).Guidance/advising for analysis and troubleshootingĬollaborative analysis (comprehensive assistance).

#10X CHROMIUM COST SOFTWARE#

Partek Flow web-based software for bulk and single cell NGS analysis.

Template scripts and SOPs for Hyak node use.

Hyak supercomputer node with RStudio and packages for sequence alignment, annotation, data QC, etc.

Independent analysis (minimal to moderate assistance)

New assays can be added when resources/capabilities allow.

Guidance for experiment execution and troubleshooting.

Lab space and equipment for sequencing library preparation.

Analysis findings validation via RNAscope ISH assays.

Sequencing of Illumina compatible libraries (on Illumina NextSeq2000).

Library QC and quantification via qPCR, Agilent TapeStation, Qubit fluorometer.

Most bulk RNAseq, ATACseq, ChIPseq and similar assay kits (check with Mary before ordering).

All 10x single cell assays (scRNAseq, scATACseq, scMultiome, etc).

Assistance with protocol/kit selection and preparations.

Instrument training (Illumina NextSeq2000, Agilent TapeStation, 10x Chromium X).

Arrangement for analysis should be made as a part of experimental planning – Mary can help with or lead analysis, but due to limited bandwidth this is often not the fastest option. Users must supply reagents and consumables and are responsible for conducting experiments with guidance from Mary as needed. *The ISCRM Genomics Core does not currently offer services for fee.

It takes 20-40 hours to generate 300GB-1TB of data, which is then transfered to the ISCRM Hyak node where the end-user can analyze the data according to the specifications desired, resulting in an unbiased, high quality data output. Once that is determined you pool your samples, place the pool into the cartridge, and the run starts. Once the library generation is complete and cells are barcoded for the sequencer, use of the Illumina NextSeq 2000 is relatively straightforward – simply do the math for the number of cells per sample, how many samples, and the desired saturation (gene coverage). The Visium system pairs nicely with the ISCRM Histology center, and allows for high quality sectioning. The TapeStation also provides checks during several parts of the pipeline, catching user mistakes before expensive parts are used. The instrumentation is complex, but Genomics Core staff will guide you through the process. The end-user only needs to provide consumables such as plastics, reagents, and the kits and cartridges from 10x, Agilent, and Illumina. The ISCRM Genomics Core provides all the equipment needed to perform all of the pipeline steps.

#10X CHROMIUM COST FULL#

The final data output is analyzed by a full featured range of applications hosted on a ISCRM reserved node of the UW Hyak supercomputer. The pipeline includes a 10x Chromium with Visium capabilities for library generation and cell encapsulation and an Agilent TapeStation 4200 for quality control, sequenced by an Illumina NextSeq 2000 capable of reads in the 400 million to 1.1 billion range. The ISCRM Genomics Core provides a full sequencing pipeline, from tissue or single cells to analysis.

10x chromium cost