Research Sequencing Service: Forms and Resources
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:
- 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).
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
| Flow Cell Type |
Total Cycles |
Yield (Gb) | Cost (v1.5 reagents) |
|---|---|---|---|
|
SP |
100 (2x50) | 65-80 | $1,983.00 |
| 200 (2x100) | 134-137 | $2,689.00 | |
| 300 (2x150) | 200-250 | $2,983.00 | |
| 500 (2x250) | 325-400 | $4,176.00 | |
| S1 (2.6B-3.2B read pairs) |
100 (2x50) | 134-167 | $3,613.00 |
| 200 (2x100) | 266-333 | $4,822.00 | |
| 300 (2x150) | 400-500 | $5,220.00 | |
| S2 (6.6B-8.2B read pairs) |
100 (2x50) | 333-417 | $7,208.00 |
| 200 (2x100) | 667-833 | $8,948.00 | |
| 300 (2x150) | 1000-1250 | $9,545.00 | |
| S4 (16B-20B read pairs) |
35 (1x35) | 280-350 | $10,440.00 |
| 200 (2x100) | 1600-2000 | $12,851.00 | |
| 300 (2x150) | 2400-3000 | $14,317.00 |
10X Genomics Chromium Reagent Costs
| 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 |
|
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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |