This page contains information on the available sequencing platforms and 10X Genomics reagents in order to help you estimate experiment scale and cost. In addition, please follow the instructions for ordering sequencing reagents and submitting samples when taking advantage of the DLMP sequencers.
Method Literature and Product Information
Current best practices for analyzing scRNA-Seq data is reviewed in the following article: Luecken MD and Theis FJ. Current best practices in single-cell RNA-seq analysis: A tutorial. Mol Syst Biol 15(6):e8746, 2019. Further information on specific 10X Genomics assays and software be found in the following links:
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- Chromium Next GEM Single Cell 3’ Reagent Kits v3.1
- Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1
- Chromium Next GEM Single Cell ATAC Reagent Kits v1.1
- Chromium Single Cell Multiome ATAC + Gene Expression
- 10X Genomics Cell Ranger data analysis software
- 10X Genomics Loupe Browser data visualization software.
Further information on Duplex-Seq and related technologies can be found in the following publications:
Original Article: Schmitt et al. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci USA, 109(36):14508-14513, 2012.
Basic Protocol: Kennedy et al. Detecting ultralow-frequency mutations by Duplex Sequencing. Nat Protoc, 9(11):2586-2606, 2014.
Review of NGS error correction: Salk et al. Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations. Nat Rev Genet, 19(5):269-285, 2018.
Supported Analysis Pipeline: Duplex-Seq-Pipeline Github Repository
Ordering/Shipping Instructions
Sequencing reagents must be ordered by each independent lab and shipped directly to the DLMP Virology clinic. When ordering the reagents, please use the following address:
Bob Livingston University of Washington, Lab Medicine Suite 320, Molecular Virology 1616 Eastlake Ave E Seattle, WA 98102 Attn: For (PI Name) Lab Phone: 206.685.7720
When ordering please request tracking and arrival information and provide that information to Dr. Scott Kennedy as soon as possible after ordering.
In addition, all sequencing requires a DNA sequencing request form and Illumina sample sheet information be filled out prior to submitting the samples for sequencing. Send completed forms, provided below, to Scott Kennedy (scottrk@uw.edu).
DNA Sequencing Request Form
For the Illumina Sample Sheet Form, contact Scott Kennedy at scottrk@uw.edu
Libraries ready for sequencing can be dropped off to Scott Kennedy or shipped directly to the Molecular Virology lab at the address indicated above.
Obtaining Your Data
Due to the large size of sequencing data set, we can deliver raw or processed data either through a cloud-backed storage service via Amazon Web Services (AWS) that can be accessed using several user-friendly interfaces (preferred) or by providing an external hard drive to which the data can be transferred (not recommended). A DLMP Research Computing guide for further information on setting up access to this storage infrastructure will be available soon.
Illumina NovaSeq6000 Sequencing Reagent Costs
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Illumina NovaSeq6000 Sequencing Reagent Costs Flow Cell Type
Total Cycles (paired)
Yield (Gb) Cost (v1.5 reagents)
SP (1.3B-1.6B read pairs)
100 (2×50) 65-80 $1,983.00 200 (2×100) 134-137 $2,689.00 300 (2×150) 200-250 $2,983.00 500 (2×250) 325-400 $4,176.00 S1 (2.6B-3.2B read pairs) 100 (2×50) 134-167 $3,613.00 200 (2×100) 266-333 $4,822.00 300 (2×150) 400-500 $5,220.00 S2 (6.6B-8.2B read pairs) 100 (2×50) 333-417 $7,208.00 200 (2×100) 667-833 $8,948.00 300 (2×150) 1000-1250 $9,545.00 S4 (16B-20B read pairs) 35 (1×35) 280-350 $10,440.00 200 (2×100) 1600-2000 $12,851.00 300 (2×150) 2400-3000 $14,317.00
10X Genomics Chromium Reagent Costs
3′ v3.1 Next GEM dual index kits Product Code Product Name Price 1000269
Chromium Next GEM Single Cell 3′ Kit v3.1, dual index, 4 rxns
$6,487 1000268
Chromium Next GEM Single Cell 3′ Kit v3.1, dual index, 16 rxns
$23,588 1000127
Chromium Next GEM Chip G Single Cell Kit, 16 rxns (2 chips)
$557 1000120
Chromium Next GEM Chip G Single Cell Kit, 48 rxns (6 chips)
$1,617 1000215
Dual Index Kit TT Set A, 96 rxns
$863
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Already comes in 3′ kit, this would be for any additional library
1000190
Library construction kit, 16 rxns
$1,125
If doing surface protein detection or CRISPR screens, add:
1000262 3’ Feature Barcode Kit, dual index, 16 rxns $601 1000242
Dual Index Kit NT Set A
$863
If doing Cellplex (sample multiplexing), add
1000262 3’ Feature Barcode Kit, dual index, 16 rxns (Cellplex enabled) $601 1000243 Dual Index Kit NN Set A, 96 rxns $863 1000261 3′ CellPlex Kit Set A, 48 rxns $3,360 3′ LT Next GEM dual index kit Product Code Product Name Price 1000325
Chromium Next GEM Single Cell 3′ LT kit v3.1, 4 rxns + Chip L (2 chips)
$2,310 1000215 Dual Index Kit TT Set A, 96 rxns $863 If doing feature barcoding add (for surface protein only): 1000262 3’ Feature Barcode Kit, dual index, 16 rxns $601 1000242 Dual index kit NT set A, 96 rxns $863 3′ HT Next GEM – dual index Product Code Product Name Price 1000370 3′ HT, 8 rxns w/ one chip $11,800 1000348 3′ HT, 48 rxns w/ five chips $55,000 1000371 3′ chip M, HT (one chip) $1,495 1000215 Dual index kit TT set A, 96 rxn $863 Add only if additional libraries needed, already comes in 3′ kit 1000352 Library construction kit, 48 rxn $3,000 If doing Cellplex (sample multiplexing), add 1000262 3’ Feature Barcode Kit, dual index, 16 rxns (Cellplex enabled) $601 1000243 Dual Index Kit NN Set A, 96 rxns $863 1000261 3′ CellPlex Kit Set A, 48 rxns $3,360 5′ v2.0 Next GEM dual index Product Code Product Name Price 1000265 Chromium Next GEM Single Cell 5′ Kit v2.0, 4 rxns $6,487 1000263 Chromium Next GEM Single Cell 5′ Kit v2.0, 16 rxns $23,588 1000287 Chip K Single Cell Kit for 5′ v2.0, 16 rxns (2 chips) $557 1000286 Chip K Single Cell Kit for 5′ v2.0, 48 rxns (6 chips) $1,617 1000215 Dual Index Kit TT Set A, 96 rxns (same as 3’ kits) $863 If doing V(D)J, add: 1000252 Chromium Single Cell Human TCR Amplification Kit, v2.0, 16 rxns $328 1000253 Chromium Single Cell Human BCR Amplification Kit, v2.0, 16 rxns $328 1000254 Chromium Single Cell Mouse TCR Amplification Kit, v2.0, 16 rxns $328 1000255
Chromium Single Cell Mouse BCR Amplification Kit, v2.0 16 rxns
$328 1000190
5′ v2.0 Library Construction Kit, 16 rxns
$1,125 If doing feature barcoding, add 1000256 5′ Feature Barcode Kit, 16 rxns $601 1000250 Dual Index Kit TN Set A, 96 rxns $863 5′ HT v2.0 Next GEM dual index Product Code Product Name Price 1000374 5′ HT, 8 rxns w/ one chip $11,800 1000356 5′ HT, 48 rxns w/ five chips $55,000 1000375 5′ chip N, HT (one chip) $1,495 1000215 Dual Index Kit TT Set A, 96 rxns (same as 3’ kits) $863 Add only if making extra libraries, otherwise it already comes in 3′ kit 1000352 Library construction kit, 48 rxn $3,000 If doing V(D)J, add: 1000252 Chromium Single Cell Human TCR Amplification Kit, v2.0, 16 rxns $328 1000253 Chromium Single Cell Human BCR Amplification Kit, v2.0, 16 rxns $328 1000254 Chromium Single Cell Mouse TCR Amplification Kit, v2.0, 16 rxns $328 1000255 Chromium Single Cell Mouse BCR Amplification Kit, v2.0, 16 rxns $328 1000352 Library construction kit, 48 rxn $3,000 If doing surface protein/feature barcoding, add 1000256 5′ Feature Barcode Kit, 16 rxns $601 1000250 Dual Index Kit TN Set A, 96 rxns $863 ATAC Next GEM single index, v2 kits Product Code Product Name Price 1000390 Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v2, 4 rxns $6,181 1000406 Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v2, 16 rxns $22,496 1000162 Chromium Next GEM Chip H Single Cell Kit, 16 rxns (2 chips) $557 1000161 Chromium Next GEM Chip H Single Cell Kit, 48 rxns (6 chips) $1,617 1000212 Single Index Kit N Set A, 96 rxns $863 Multiome (ATAC + 3′ Gene Expression) Product Code Product Name Price 1000285 Chromium Next GEM Single Cell Multiome ATAC+Gex Reagent bundle, 4 rxns $11,390 1000283 Chromium Next GEM Single Cell Multiome ATAC+Gex Reagent bundle, 16 rxns $41,475 1000230 Chromium Next GEM Chip J, 16 rxns (2 chips) $557 1000234 Chromium Next GEM Chip J, 48 rxns (6 chips) $1,617 1000215 Dual index plate TT set A $863 1000212 Single index plate N set A $863
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