Single Cell Genomics

Transcription

1 Single Cell Genomics Application Cost Platform/Protocol Note 3 mrna-seq Cell capture/rt/library prep $1,990/Sample 10x Genomics Chromium ,000 cells/sample 5 V(D)J + mrna Cell capture/rt/library prep (B and T cell enrichment) $2,460/Sample 10x Genomics Chromium ,000 cells/sample Sequencing for 10x Genomics 3 single-cell library Sequencing for 10x Genomics 3 single-cell library Sequencing for 10x Genomics 5 V(D)J + 5 mrna single-cell library $1,990 for 350M reads* Illumina NovaSeq Custom 91bp sequencing $3,780 for 400M reads* Illumina NextSeq Custom 98bp sequencing $3,060 for 350M reads* Illumina NovaSeq 2x150bp sequencing Full transcript single cell mrna-seq Cell lysis/rt/qc Library prep and QC Sequencing (2M reads/cell) Sequencing (1M reads/cell) $23/cell $10/cell $10/cell $5.25/cell SMART-Seq A minimum of 2x96-well plates * Price includes bioinformatics QC, alignment, quantification and visualization. For libraries generated by Genomics Core. 1

2 Next-Gen Sequencing-RNA Application Cost* Sample Minimum Sample Requirements Platform Read Type Average Output mrna-seq $349/Sample $298/sample 6 > 40 RIN > ng 1 µg NextSeq 1x75bp 25M reads Ultra low-input mrna-seq $375/Sample 6 RIN > 8 50 ng 400 ng NextSeq 1x75bp 25M reads Total RNA-Seq $599/Sample 6 RNA-Seq for FFPE $349/Sample 6 No mimimum RIN µg DV200 > 30% Total RNA: ng FFPE: ng NextSeq 1x75bp 50M reads NextSeq 1x75bp 10M reads Small RNA-Seq (UMI quantification) $375/Sample 6 RIN > 8 preferable 300 ng 1.5 µg NextSeq 1x75bp 10M reads *Price includes sample QC, library preparation, library QC, sequencing and basic bioinformatics quantification. 2

3 Next-Gen Sequencing-DNA Application Cost* Sample Minimum Sample Requirements Platform Read Type Average Output Human Whole Genome Sequencing (FFPE compatible) $1,200/sample µg non-degraded gdna 1-3 µg FFPE DNA; fragments > 1500 bp NovaSeq 2x150bp 30X coverage Human Whole Exome Sequencing (FFPE compatible) $499/Sample $449/sample 8 > µg non-degraded gdna 1-2 µg FFPE DNA; fragments > 1500 bp NovaSeq 2x150bp 120X coverage ATAC-Seq $489/sample $829/sample 8 5,000 50,000 cells in culture media; > 90% viability NextSeq NovaSeq 2x75bp 2x50bp 2x40M reads 2x120M reads 16S Microbiome Amplicon-Seq $60/Sample** µl/sample in an Eppendorf twin.tec plate in columns MiSeq 2x300bp 10K reads ITS Mycobiome Amplicon-Seq $60/Sample** µl/sample in an Eppendorf twin.tec plate in columns MiSeq 2x300bp 10K reads *Price includes sample QC, library preparation, library QC, sequencing and basic bioinformatics quantification. ** Price includes library preparation, pooled library QC and sequencing. 3

4 Sequencing Only Sequencing Platform Read Output Read type Cost* NextSeq 400M 1x75bp $1,870/Sequencing run NextSeq 2x130M 2x75bp $1,280/Sequencing run NextSeq 2x400M 2x75bp $3,540/Sequencing run NovaSeq 2x1300M 2x50bp $7,290/Sequencing run NovaSeq 2x1300M 2x150bp $11,490/Sequencing run NovaSeq 2x3300M 2x50bp $13,590/Sequencing run NovaSeq 2x3300M 2x150bp $21,290/Sequencing run MiSeq 2x15M 2x25bp $1,080/Sequencing run MiSeq 2x25M 2x300bp $2,180/Sequencing run *Only pooled libraries accepted. Full runs only (no shared runs). Price includes fragment analysis, fluorometric quantification, and sequencing of pooled library. One-time demultiplexing/fastq generation is included. 4

5 High-Throughout qpcr Application Reaction Cost Platform Gene expression 48 (targets*) x 48 (samples) $500/Plate Fluidigm BioMark HD Gene expression 96 (targets*) x 96 (samples) $1,400/Plate Fluidigm BioMark HD Genotyping 48 (targets*) x 48 (samples) $550/Plate Fluidigm BioMark HD Genotyping 96 (targets*) x 96 (samples) $1,100/Plate Fluidigm BioMark HD Human/rodent mirna gene expression panel 745 (genes) x 3 (samples) $980/Plate QuantStudio 12K *Primer pairs must be provided. 5

6 DNA Type Assay Concentration Range dsdna High Sensitivity 50 pg/µl 5 ng/µl bp dsdna High Sensitivity 100 pg/µl 10 ng/µl bp dsdna Standard Sensitivity 5 ng/µl 100 ng/µl DNA Fragment Analysis & RNA Integrity dsdna DNA ng/µl 50 ng/µl bp gdna High Sensitivity 50 pg/µl 5 ng/ml 50 40,000 bp Size Range Cost Platform $20 for row + $5/sample up to 12 samples $60 for chip + $5/sample up to 11 samples bp $20 for row + $5/sample up to 12 samples $20 for chip + $5/sample up to 12 samples $20 for row + $8/sample up to 12 samples Agilent Bioanalyzer Agilent Bioanalyzer gdna Standard Sensitivity 25 ng/µl 250 ng/µl 75 48,500 bp $20 for row + $8/sample up to 12 samples RNA Type Assay Concentration Range Cost Platform Total RNA High Sensitivity 50 pg/µl 5 ng/µl Total RNA RNA Pico 50 pg/µl 5 ng/µl Total RNA RNA Nano ng/µl $20 for row + $5/sample up to 12 samples $60 for chip + $5/sample up to 11 samples $20 for chip + $5/sample up to 12 samples Agilent Bioanalyzer Agilent Bioanalyzer 6

7 Fluorometric Quantification Assay Range Cost Platform dsdna High Sensitivity 10 pg/µl 100 ng/µl; 1-20 µl $6/sample Qubit dsdna Broad Range 100 pg/µl 1 µg/µl; 1-20 µl $6/sample Qubit ssdna* 50 pg/µl 200 ng/µl; 1-20 µl $6/sample Qubit RNA High Sensitivity 250 pg/µl 100 ng/µl; 1-20 µl $6/sample Qubit *Also detects dsdna and RNA. For accurate ssdna concentration, the dsdna and RNA assay kits must be used to detect dsdna and RNA contamination. 7

8 Cell Line Authentication & Mycoplasma Contamination Detection Application Type* Cost Human cell line authentication** Genomic DNA $70/sample Human cell line authentication** Dried cell pellet $90/sample Human cell line authentication Analysis $25/sample Mycoplasma contamination detection Mycoplasma contamination detection Genomic DNA Dried cell pellet $70/sample $90/sample * Inquire about fresh or frozen cells, or if you wish to do both Cell Line Authentication and Mycoplasma Contamination Detection on the same sample. ** Human cell line authentication includes a mouse marker for cross-contamination detection. 8

9 Bioinformatics Analysis & Self-Use Equipment Service RNA-Seq bioinformatics package Custom bioinformatics service Cost $1,000 for first pairwise comparison for internal sequencing ($1,350 for external sequencing); $600 each for additional comparisons $125/hour; 8 hour minimum Extra demultiplexing/fastq generation $60 Custom laboratory service $60/hour Instrument ABI QuantStudio 12K Real-Time PCR System EppendorfVacuum Centrifuge Covaris M220 Focused Ultrasonicator Cost $20/hour $5/hour $4/hour 9