Page 1 Part Number 100-815-000 version 03 (June 2020)
Equipment and Materials Needed for Sequencing Quick Reference Card
This Quick Reference Card lists examples of third-party laboratory equipment and other materials that are recommended for running specific types of applications on PacBio Sequel System and Sequel II System instruments. Note that although vendor part numbers are listed herein, they may not always be up to date. Verify and obtain the latest part numbers and relevant documentation from the specific vendor or manufacturer’s website. Laboratory Equipment and Material Categories
A. DNA Sizing Analysis B. DNA Quantification Analysis C. DNA Purity Analysis D. DNA Shearing E. DNA Size Selection F. General Laboratory Equipment G. General Laboratory Reagents and Consumables
SMRT Sequencing Application Categories Whole Genome Sequencing (WGS)
• De Novo Assembly – HiFi Reads • De Novo Assembly – Low DNA Input • De Novo Assembly – Microbial Multiplexing • Variant Detection • Structural Variant Detection
RNA Sequencing (RNA) • Iso-Seq Method • Single-Cell Iso-Seq
Metagenomics Sequencing (META) • Full-length 16S rRNA Sequencing • Shotgun Metagenomic Profiling or Assembly
Targeted Sequencing (TARG) • Amplicon Sequencing • No-Amp Targeted Sequencing
Laboratory Equipment and Material Recommendations Guide
+ Compatible with a specific application
‒ Not recommended for a specific application
Highly Recommended Where multiple compatible equipment options may be available for a particular category, specific products that are highly recommended are also highlighted
Page 2 Part Number 100-815-000 version 03 (June 2020)
A. DNA Sizing Analysis
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sequ
enci
ng
Sing
le-C
ell I
so-
Seq
Sequ
enci
ng
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Bioanalyzer 2100 System for DNA Sizing Analysis Up To ~7 – 15 kb
Agilent Technologies
Bioanalyzer 2100 platform
Suitable for analysis of SMRTbell
libraries up to ~15 kb
G2939BA ‒ ‒ ‒ ‒ ‒ + + + ‒ + ‒
Agilent Technologies
DNA 7500 Kit for Bioanalyzer 2100
5067-1506 ‒ ‒ ‒ ‒ ‒ ‒ ‒ + ‒ + ‒
Agilent Technologies
DNA 12000 Kit for Bioanalyzer 2100
5067-1508 ‒ ‒ ‒ ‒ ‒ + + + ‒ + ‒
Agilent Technologies
High Sensitivity Analysis Kit for Bioanalyzer 2100
5067-4626 ‒ ‒ ‒ ‒ ‒ + + + ‒ + ‒
Page 3 Part Number 100-815-000 version 03 (June 2020)
A. DNA Sizing Analysis (Cont.)
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt
Det
ectio
n
Stru
ctur
al
Varia
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Fragment Analyzer System for DNA Sizing Analysis Up To ~50 kb
Agilent Technologies
Fragment Analyzer System
Suitable for analysis of SMRTbell
libraries up to ~50 kb
M5310AA ‒ ‒ ‒ ‒ ‒ + + + ‒ + ‒
Agilent Technologies
Large Fragment 50 kb Kit for Fragment Analyzer
DNF-464-0500 ‒ ‒ ‒ ‒ ‒ + + + ‒ + ‒
Pippin Pulse System for DNA Sizing Analysis Up To ~100 kb
Sage Science Pippin Pulse System
Suitable for analysis of SMRTbell
libraries and genomic DNA up to ~100 kb
PPI0200 + ‒ + + + ‒ ‒ ‒ + ‒ +
Galileo Bioscience
Gel Tank with Tray and Combo 80-1214 + ‒ + + + ‒ ‒ ‒ + ‒ +
Sage Science 10X KBB Buffer KBB1001 + ‒ + + + ‒ ‒ ‒ + ‒ +
Lonza SeaKem® Gold Agarose 50150 + ‒ + + + ‒ ‒ ‒ + ‒ +
Page 4 Part Number 100-815-000 version 03 (June 2020)
A. DNA Sizing Analysis (Cont.)
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Femto Pulse System for DNA Sizing Analysis Up To ~165 kb
Agilent Technologies
Femto Pulse System
Rapid analysis time (<1.5 hours) Requires <1 ng of sample Suitable for analysis of SMRTbell
libraries and genomic DNA up to ~165 kb
M5330AA + + + + + + + + + + +
Agilent Technologies
Genomic DNA 165 kb Kit for Femto Pulse
FP-1002-0275 + + + + + ‒ ‒ ‒ + ‒ +
CHEF Mapper XA System for DNA Sizing Analysis Up To ~10 Mb Bio-Rad Pulsed Field Gel Electrophoresis
System: CHEF Mapper® XA
Suitable for analysis of SMRTbell
libraries and genomic DNA up to ~10 Mb
170-3670 + ‒ + + + ‒ ‒ ‒ + ‒ +
Bio-Rad 10X TBE Electrophoresis Buffer
1610770 + ‒ + + + ‒ ‒ ‒ + ‒ +
Bio-Rad Pulsed Field Certified Agarose
1620137 + ‒ + + + ‒ ‒ ‒ + ‒ +
HIG
HLY
REC
OM
MEN
DED
Page 5 Part Number 100-815-000 version 03 (June 2020)
B. DNA Quantification Analysis
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Fluorometric Assay Systems Thermo Fisher
Scientific
Qubit 4 Fluorometer
Fluorometric-based assay method
Enables highly accurate and sensitive quantitation of dsDNA
Q33238 + + + + + + + + + + +
Thermo Fisher
Scientific
Qubit Assay Tubes Q32856 + + + + + + + + + + +
Thermo Fisher
Scientific
Qubit 1X dsDNA High Sensitivity (HS) Assay Kit
Q33230 + + + + + + + + + + +
C. DNA Purity Analysis
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Spectrophotometric Assay Systems Thermo Fisher
Scientific
NanoDrop™ 2000/2000c Spectrophotometer
ND-2000 + + + + + + + + + + +
Page 6 Part Number 100-815-000 version 03 (June 2020)
D. DNA Shearing
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
g-TUBE Devices for Shearing DNA to 6 – 20 kb Fragment Sizes Covaris g-TUBE
520079 + + + + + ‒ ‒ ‒ + ‒ ‒
Syringes & Needles for Shearing DNA to >30 kb Fragment Sizes Becton
Dickenson BD Luer-Lok™ 1-mL Syringe
309628 ‒ ‒ ‒ ‒ + ‒ ‒ ‒ ‒ ‒ ‒
SAI Infusion 26G Blunt End Needles
B26-150 ‒ ‒ ‒ ‒ + ‒ ‒ ‒ ‒ ‒ ‒
Megaruptor 2 System for Shearing DNA to 2 – 75 kb Fragment Sizes Diagenode Megaruptor 2 System
Long Hydropores for Megaruptor 2
Hydrotubes for Megaruptor 2
B06010002
E07010002
C30010018
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
‒ ‒ ‒
‒
‒ ‒
‒ ‒ ‒
+
+
+
‒ ‒ ‒
‒ ‒ ‒
Page 7 Part Number 100-815-000 version 03 (June 2020)
D. DNA Shearing (Cont.)
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Megaruptor 3 System for Shearing DNA to 2 – 75 kb Fragment Sizes
Diagenode Megaruptor 3 System
Up to 8 samples can be processed in parallel without additional user input
Eliminates cross-contamination without requiring additional wash steps by using disposable shearing elements in a completely closed-system
Megaruptor 3 Shearing Kit
B06010003
E07010003
+
+
+
+
+
+
+
+
+
+
‒ ‒
‒
‒
‒ ‒
+
+
‒ ‒
‒ ‒
HIG
HLY
REC
OM
MEN
DED
Page 8 Part Number 100-815-000 version 03 (June 2020)
E. DNA Size Selection
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
SageELF System for DNA Size Selection 100 bp – 40 kb Sage Science SageELF System
Separates DNA samples by size,
and then simultaneously fractionates the whole sample into 12 fractions
One sample is fractionated on a single precast agarose cassette, and one or two cassettes may be processed at one time
ELF0001 + ‒ + + + ‒ ‒ ‒ ‒ ‒ ‒
Sage Science 0.75% Agarose Cassette for SageELF, 1 – 18 kb
ELD7510 + ‒ + + + ‒ ‒ ‒ ‒ ‒ ‒
BluePippin System for DNA Size Selection 100 bp – 50 kb Sage Science BluePippin System
Separates DNA samples by size,
and collects all fragments above a size threshold set by the user
Up to four samples (plus a Size Marker) can be fractionated on a single precast agarose cassette, and only one cassette may be processed at one time
BLU0001 + ‒ + + + ‒ ‒ ‒ ‒ ‒ ‒
Sage Science 0.75% Agarose Cassette for BluePippin, 4 – 20 kb High Pass
(with S1 Marker)
BLF7510 + ‒ + + + ‒ ‒ ‒ ‒ ‒ ‒
HIG
HLY
REC
OM
MEN
DED
FO
R V
AR
IAN
T D
ETEC
TIO
N
HIG
HLY
REC
OM
MEN
DED
FO
R D
E N
OVO
ASS
EMB
LY
(HIF
I, M
ICR
OB
IAL)
AN
D S
V D
ETEC
TIO
N
Page 9 Part Number 100-815-000 version 03 (June 2020)
F. General Laboratory Equipment
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Benchtop Microcentrifuges Eppendorf See recommended models below
MiniSpin® Plus
Centrifuge 5425
022620100
5405000441
+ + + + + + + + + + +
Mini Microcentrifuges VWR Mini Microcentrifuge
10153-842 + + + + + + + + + + +
Plate Centrifuge VWR Plate Centrifuge
10144-214 + + + + + + + + + + +
Tube Rotators VWR Tube Rotator
10136-084 + + + + + + + + + + +
Page 10 Part Number 100-815-000 version 03 (June 2020)
F. General Laboratory Equipment (Cont.) WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Vortex Mixers VWR Digital Vortex Mixer
(or equivalent)
10153-842 + + + + + + + + + + +
VWR Microtube and microplate holder kit with insert retainer for vortex mixer
Q33230 + + + + + + + + + + +
Thermal Mixers Eppendorf
Eppendorf ThermoMixer® C
(or equivalent)
Provides stable incubation temperatures for SMRTbell library construction reactions
2231000667 + + + + + + + + + + +
Thermal Cyclers Bio-Rad S1000 Thermal Cycler
(or equivalent)
Provides stable incubation temperatures for SMRTbell library annealing and binding reactions Controllable heated lid preferred Compatible with 0.2 mL PCR
tubes 96-well capacity recommended
for high-throughput environments Minimum 60 minutes thermal
stability needed for 4ºC – 80ºC Overnight thermal stability
needed at 4ºC
1861096 + + + + + + + + + + +
Page 11 Part Number 100-815-000 version 03 (June 2020)
F. General Laboratory Equipment (Cont.)
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Heat Sealers and Foil Sheets Thermo Fisher
Scientific ALPS 50 V-Manual Heat Sealer
(or equivalent)
Note that if you already have a
heat sealer, it must be capable of maintaining temperatures between 160ºC to 178ºC. Heat sealers exceeding this range may have negative impacts on sequencing results.
AB-1443A + + + + + + + + + + +
Thermo Fisher Scientific
Pierceable Sealing Foil Sheets
AB-0757 + + + + + + + + + + +
Pipettes and Tips Gilson
PIPETMAN® P2, P10, P20, P100,
P200, P1000 Pipettes (or equivalent)
F144801 F144802 F123600 F123615 F123601 F123602
+ + + + + + + + + + +
Gilson Filter Tips for PIPETMAN® P2, P10, P20, P100, P200, P1000 Pipettes
(or equivalent)
F1731031 F1733031 F1735031 F172613
+ + + + + + + + + + +
F. General Laboratory Equipment (Cont.)
Page 12 Part Number 100-815-000 version 03 (June 2020)
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Pipettes and Tips (Cont.) Rainin Wide-Orifice Pipette Tips RT LTS
200 µL FLW 960A/10 (or equivalent)
30389241 + + + + + + + + + + +
Ice Makers VWR Flake Ice Maker with Bin
(or equivalent)
89166-534 + + + + + + + + + + +
Magnetic Separator Racks Thermo Fisher
Scientific DynaMag™-2 Magnet
Separation Stand for 1.5–2 mL Microcentrifuge Tubes (or
equivalent)
12321D + + + + + + + + + + +
V & P Scientific, Inc.
Low Profile Magnetic Separation Stand for 0.2 mL, 8-Strip PCR
Tubes (or equivalent)
VP772F4-1 + + + + + + + + + + +
Page 13 Part Number 100-815-000 version 03 (June 2020)
General Laboratory Equipment (Cont.)
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Lab Refrigerators (4ºC) VWR Standard Series Lab Refrigerator
(or equivalent)
76314-274 + + + + + + + + + + +
Lab Freezers (-20ºC) VWR Standard Series Lab Freezer
with Manual Defrost (or equivalent)
76314-276 + + + + + + + + + + +
Page 14 Part Number 100-815-000 version 03 (June 2020)
F. General Laboratory Reagents and Consumables
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Tubes* Eppendorf Eppendorf PCR Tubes, 0.2 mL,
PCR Clean, Colorless 0030124332 + + + + + + + + + + +
Eppendorf Eppendorf DNA LoBind Tube 0.5 mL, PCR clean
022431005 + + + + + + + + + + +
Eppendorf Eppendorf DNA LoBind Tube 1.5 mL, PCR clean
022431021 + + + + + + + + + + +
Eppendorf Eppendorf DNA LoBind Tube 2.0 mL, PCR clean
022431048 + + + + + + + + + + +
VWR Falcon™ Conical Centrifuge Tubes, PP (Polypropylene), 15 mL / 50 mL
21008-936 21008-940 + + + + + + + + + + +
* Corning® Axygen® consumables are not compatible with SMRT Sequencing and should not be used in the preparation of PCR amplicons or SMRTbell® templates.
Page 15 Part Number 100-815-000 version 03 (June 2020)
General Laboratory Reagents and Consumables (Cont.)
WGS RNA META TARG
Vendor Product PN
De
Nov
o –
HiF
i
De
Nov
o –
Low
DN
A In
put
De
Nov
o –
Mic
robi
al
Varia
nt D
etec
tion
Stru
ctur
al V
aria
nt
Det
ectio
n
Iso-
Seq
Sing
le-C
ell
Iso-
Seq
Full-
Leng
th 1
6S
Shot
gun
Met
a-G
Am
plic
on S
eq.
No-
Am
p Se
q.
Ethyl Alcohol, Pure Sigma-Aldrich Ethyl Alcohol, Pure, 200 Proof,
ACS Reagent, ≥99.5% (or equivalent)
459844 + + + + + + + + + + +
Molecular Biology Grade Water Sigma-Aldrich Nuclease-Free Water, for Molecular
Biology (or equivalent)
W4502 + + + + + + + + + + +
Sample and Buffer Plate Accessories for Agilent Fragment Analyzer and Femto Pulse Systems
Eppendorf twin.tec® PCR Plate 96, semi-skirted, 250 µL, PCR clean,
colorless plates (Recommended Sample Plate for Agilent Fragment Analyzer & Femto Pulse Systems)
951020303 + + + + + + + + + + +
Thermo Fisher Scientific
Fisherbrand™ 96-Well DeepWell™ Polypropylene Microplates, 1 mL (Recommended Buffer Plate for
Agilent Fragment Analyzer & Femto Pulse Systems)
12-566-120 + + + + + + + + + + +
For Research Use Only. Not for use in diagnostic procedures. © Copyright 2020, Pacific Biosciences of California, Inc. All rights reserved. Information in this document is subject to change without notice. Pacific Biosciences assumes no responsibility for any errors or omissions in this document. Certain notices, terms, conditions and/o r use restrictions may pertain to your use of Pacific Biosciences products and/or third p arty products. Please refer to the applicable Pacific Biosciences Terms and Conditions of S ale and to the applicable license terms at http://www.pacificbiosciences.com/lice nses.html. Pacific Biosciences, the Pacific Biosciences logo, PacBio, S MRT, SMRTbell, Iso-Seq and Sequel are trademarks of Pacific Biosciences. BluePippin and SageELF are trademarks of Sage Science, Inc. NGS-go and NGSengine are trademarks of GenDx. FEMTO Pulse and Fragment Analyzer are trademarks of Agilent Technologies. All other trademarks are the sole property of their respective owners.