S.No. | Company | Reagent | Cat. No. | |
1 | 10X genomics | Dynabeads MyOne TM SILANE | 2000048 (store at 4°C) | |
2 | 10X genomics | Chromium Next GEM Single Cell 3ʹ Gel Bead Kit v3.1, 16 rxns | 1000122 (store at -20°C and -80°C according to manufacturer’s instructions) | |
3 | 10X genomics | Chromium Next Gem Chip G Single Cell Kit, 48 rxns | 1000120 (store at RT) | |
4 | 10X genomics | Dual Index Plate TT Set A | 3000431 (store at −20°C) | |
5 | Ambion | Nuclease free Water | AM9937 | |
6 | Thermo Fisher Scientific | Low TE Buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA) | 12090-015 | |
7 | Millipore Sigma | Ethanol, Pure (200 Proof, anhydrous) | E7023-500ML | |
8 | Beckman Coulter | SPRIselect Reagent Kit | B23318 | |
9 | Bio-Rad | 10% Tween 20 | 1662404 | |
10 | Ricca Chemical Company | Glycerin (glycerol), 50% (v/v) Aqueous Solution | 3290-32 | |
11 | Qiagen | Qiagen Buffer EB | 19086 |
Action | Item | 10x PN | Preparation & Handling | Storage | |
Equilibrate to Room Temperature | Chromium Single Cell 3’ v3 Gel Beads | 2000164 | Equilibrate to RT 30 min before loading the chip. | −80°C | |
RT Reagent B | 2000165 | Vortex, verify no precipitate, centrifuge briefly. | −20°C | ||
Template Switch Oligo | 3000228 | Centrifuge briefly, resuspend in 80 μl Low TE Buffer. Vortex 15 sec at maximum speed, centrifuge briefly, leave at room temperature for ≥ 30 min. After resuspension, store at −80°C. | −80°C | ||
Reducing Agent B | 2000087 | Vortex, verify no precipitate, centrifuge briefly. | −20°C | ||
Place on Ice | RT Enzyme C | 2000085/ 2000102 | Centrifuge briefly before adding to the mix. | −20°C | |
Cell Suspension | |||||
Obtain | Partitioning Oil | 2000190 | - | Ambient | |
Chromium Next GEM chip G | 2000177 | - | Ambient | ||
10x Gasket | 370017/ 3000072 | Ambient | |||
10x Chip Holder | 330019 | Ambient | |||
10x Vortex Adapter | 330002 | Ambient | |||
50% glycerol solution If using <8 reactions | - | -Ambient |
Action | Item | 10x PN | Preparation & Handling | Storage | |
Equilibrate to Room Temperature | Reducing Agent B | 2000087 | Thaw, vortex, verify no precipitate, centrifuge. | −20°C | |
cDNA primers | 2000089 | Vortex, centrifuge briefly. | −20°C | ||
Beckman Coulter SPRIselect Reagent | - | Manufacturer’s recommendations. | - | ||
Agilent Bioanalyzer High Sensitivity Kit If used for QC and quantification | - | Manufacturer’s recommendations. | - | ||
Agilent TapeStation ScreenTape and Reagents If used for QC and quantification | - | Manufacturer’s recommendations. | - | ||
Qubit dsDNA HS Assay Kit If used for QC and quantification | - | Manufacturer’s recommendations. | - | ||
Dynabeads MyOne SILANE | 2000048 | Vortex thoroughly (≥30 sec) immediately before adding to the mix. | 4°C | ||
Place on ice | Amp Mix | 2000047/ 2000103 | Vortex, centrifuge briefly. | −20°C | |
Thaw at 65°C | Cleanup Buffer | 2000088 | Thaw for 10 min at 65°C at max speed on a thermomixer. Verify no visible crystals. Cool to room temperature. | −20°C | |
Obtain | Recovery Agent | 220016 | - | Ambient | |
Qiagen Buffer EB | - | Manufacturer’s recommendations. | - | ||
Bio-Rad 10% Tween 20 | - | Manufacturer’s recommendations. | - | ||
10x Magnetic Separator | 230003 | - | Ambient | ||
Prepare 80% Ethanol - Prepare 15 ml for 8 reactions. | - | - |
Obtain the following 10X kit and other components | |||||
Action | Item | 10x PN | Preparation & Handling | Storage | |
Equilibrate to Room Temperature | Fragmentation Buffer | 2000091 | Vortex, verify no precipitate, centrifuge briefly. | −20°C | |
Adaptor Oligos | 2000094 | Vortex, centrifuge briefly. | −20°C | ||
Ligation Buffer | 2000092 | Vortex, verify no precipitate, centrifuge briefly. | −20°C | ||
Dual Index Plate TT Set A | 3000431 | - | −20°C | ||
Beckman Coulter SPRIselect Reagent | B23318 | Ambient | |||
Agilent Bioanalyzer High Sensitivity kit If used for QC | - | ||||
Place on Ice | Fragmentation Enzyme DNA Ligase | 2000090/ 2000104 | Centrifuge briefly. | −20°C | |
DNA Ligase | 220110 | Centrifuge briefly. | −20°C | ||
Amp Mix | 220131 | Centrifuge briefly. | −20°C |
# | Sample ID | Cells per ul | Cells to capture | Vol of suspension | Vol. of Water | ||
1 | |||||||
2 | |||||||
3 | |||||||
4 | |||||||
5 | |||||||
6 |
Master Mix | PN | 1X (μl) | 4X + 10% (μl) | 8X + 10% (μl) | |
RT Reagent B | 2000165 | 18.8 | 82.2 | 165.0 | |
Template Switch Oligo | 3000228 | 2.4 | 10.4 | 20.8 | |
Reducing Agent B | 2000087 | 2.0 | 8.6 | 17.3 | |
RT Enzyme C | 2000085/ 2000102 | 8.7 | 38.4 | 76.8 | |
Total | - | 31.8 | 139.9 | 279.8 |
Sample ID | Total counts | Live counts | Viability | Dilution | Total counts | Live counts | Viability | ||
1 | |||||||||
2 | |||||||||
3 | |||||||||
4 | |||||||||
Step | Temperature | Time | |
1 | 53°C | 00:45:00 | |
2 | 85°C | 00:05:00 | |
3 | 4°C | Hold |
Dynabeads Cleanup Mix (Add reagents in the order listed) | PN | PN 1X (µl) | 4X + 10% (µl) | 8X + 10% (µl) | |
Cleanup Buffer | 2000088 | 182 | 801 | 1602 | |
Dynabeads MyOne SILANE Vortex thoroughly (≥30 sec) immediately before adding to the mix. If still clumpy, pipette mix to resuspend completely. DO NOT centrifuge before use. | 2000048 | 8 | 35 | 70 | |
Reducing Agent B | 2000087 | 5 | 22 | 44 | |
Nuclease-free Water | 5 | 22 | 44 |
Elution Solution I Add reagents in the order listed | PN | 1X (µl) | 10X (µl) | |
Buffer EB | 98 | 980 | ||
10% Tween 20 | 1 | 10 | ||
Reducing Agent B | 2000087 | 1 | 10 | |
Total | 100 | 1000 |
DNA Amplification Reaction Mix Add reagents in the order listed | PN | 1X (µl) | 4X + 10% (µl) | 8X + 10% (µl) | |
Amp Mix | 2000047/ 2000103 | 50 | 220 | 440 | |
cDNA Primers | 2000089 | 15 | 66 | 172 | |
total | 65 | 286 | 572 |
Lid Temperature | Reaction Volume | Run Time | |
105°C | 100 µl | ~30-45 min |
Step | Temperature | Time | |
1 | 98°C | 00:03:00 | |
2 | 98°C | 00:00:15 | |
3 | 63°C | 00:00:20 | |
4 | 72°C | 00:01:00 | |
5 | Go to Step 2, see table below for total # of cycles | ||
6 | 72°C | 00:01:00 | |
7 | 4°C | Hold |
Cell Load | Total Cycles | |
˂500 | 13 | |
500–6,000 | 12 | |
>6,000 | 11 |
Lid Temperature | Reaction Volume | Run Time | |
65°C | 50 µl | ~35 min |
Step | Temperature | Time | |
Pre-cool block Pre-cool block prior to preparing the Fragmentation Mix | 4°C | Hold | |
Fragmentation | 32°C | 00:05:00 | |
End Repair & A-tailing | 65°C | 00:30:00 | |
Hold | 4°C | Hold |
Fragmentation Mix Add reagents in the order listed | PN | 1X (µl) | 4X + 10% (µl) | 8X + 10% (µl) | |
Fragmentation Buffer | 2000091 | 5 | 22 | 44 | |
Fragmentation Enzyme | 2000090/ 2000104 | 10 | 44 | 88 | |
Total | 15 | 66 | 132 |
Adaptor Ligation Mix Add reagents in the order listed | PN | 1X (µl) | 4X + 10% (µl) | 8X + 10% (µl) | |
Ligation Buffer | 2000092 | 20 | 88 | 176 | |
DNA Ligase | 220110/ 220131 | 10 | 44 | 88 | |
Adaptor Oligos | 2000094 | 20 | 88 | 176 | |
Total | 50 | 220 | 440 |
Lid Temperature | Reaction Volume | Run Time | |
30°C | 100 µl | 15 min |
Step | Temperature | Time | |
1 | 20°C | 00:15:00 | |
2 | 4°C | Hold |
Lid Temperature | Reaction Volume | Run Time | |
105°C | 100 µl | ~25-40 min |
Step | Temperature | Time | |
1 | 98°C | 00:00:45 | |
2 | 98°C | 00:00:20 | |
3 | 54°C | 00:00:30 | |
4 | 72°C | 00:00:20 | |
5 | Go to step 2, see below for # of cycles | ||
6 | 72°C | 00:01:00 | |
4°C | Hold |
cDNA Input | Total Cycles | |
1-25 ng | 14-16 | |
25-150 ng | 12-14 | |
150-500 ng | 10-12 | |
500-1,000 ng | 8-10 | |
1,000-1,500 ng | 6-8 |
Sequencing Read | Recommended Number of Cycles | |
Read 1 i7 Index i5 Index Read 2 | 28 cycles 10 cycles 10 cycles 90 cycles |