EXPERIMENT CHECKLISTFOR Stereo-seq OMNIFFPE SOLUTIONS

Updated: June 2024

Purpose

Category

Description

Recommended brandCat. No.

NotesCheckbox

For FFPE block slicing, section scooping and section baking - for the same item, please choose from either one of the recommended brands
Or other equipment thatcan perform paraffin
sectioning

Hand-operated rotary slicer

Leica

HistoCore BIOCUT

Dakota is a rotary slicer

DakeweMT1Feather Microtome Blade

FEATHER

R35

Low-profile Blades Disposable 819

Leica819

Equipment///

Needs to satisfy thefollowing temperatures:
42 ° C; 37 ° C; 60 ° C

Equipment

Tissue Floating Bath, LightedGeyer

19424235 ° C ~ 48 ° C

4484073

Microtome

Equipment

Microtome blade

Equipment

Slide warmer/dryer
Water BathTM

PROFLEX PCR 3X 32-well PCR system Applied biosystem
T100 PCR instrument

Bio-Rad1861096

Need Stereo-seq PCR
AdaptorConsumableForceps

Deli

DL396003

Straight-tipped forceps

Dust-free paper

Consumable

Kimtech dust-free wipe paper

KIMBERLY (KIMTECH)

0130-10Microscope Slide

Consumable

The surface is positively charged andadheres to the slide

CITOTEST80302-3161-16

BladeConsumable

One-sided security blade

FLYING EAGLE BRAND

137011

Anhydrous ethanol

Reagent

Anhydrous ethanol (CAS: 64-17-5)

XILONG Scientific

1280340101601

Or other brands, AR purity

Slide Box

Consumable

5-piece mail folder

Beyotime

FBX005Or other brands

PCR Thermal Cycler

EquipmentForceps

TM

Other reagents and consumables without recommended brands - for FFPE block slicing, section scooping and section baking.
Large containers for holding liquids
ddH2O/Milli-Q Water
Cardstock paper
Ice Box, or cooling station (e. g. Leica cooling station HistoCore Arcadia C)
Histology brushes
2Purpose

Category

Description

Recommended brandCat. No.

Notes

Checkbox

For FFPE block quality test (DV200) - for the same item, please choose from either one of the recommended brandRNA quality controlAgilent

RNA Quality ControlQsep

Equipment

2100 bioanalyzer/Agilent 2100

Agilent

Equipment

Ika Vortex Mixer

IKA

Kit

Agilent RNA 6000 Pico
QSEP high-throughput biologicalfragment analyzer

Agilent

5067-1513

Bioptic Inc.

Qsep400

Equipment

5065-4401

C105110/C105210/
C1058105418R/5420/5425/5425R

Kit

RNA Kit (R 1)

Bioptic Inc.

High speed
microcentrifuge

Equipment

Microcentrifuge

Eppendorf

RNA extraction kit

Kit

RNeasy FFPE Kit (50)

Qiagen73504

Deparaffinization Solution

Qiagen19093

RNaseZap RNase Decontamination
Solution

Thermo Fisher ScientificAM9780Paraffin wax remover Reagent
RNase
decontamination
Reagent
reagent
Nuclease-free water

Reagent

Nuclease-free water (not DEPCtreated)

Thermo Fisher ScientificAM9937RNA Quantification

Equipment

NanoDrop Eight photometer

Thermo Fisher Scientific

NanoDrop Eight

1.5 mL DNase/RNase
Free centrifuge tube

Consumable

1.5 mL DNase/RNase Free centrifuge
tube

Eppendorf/Axygen-

2.0 mL DNase/RNase
Free centrifuge tube

Consumable

2.0 mL DNase/RNase Free centrifuge
tube

Eppendorf/Axygen-

1000 μL pipette tips

Consumable

1000 μL suction

Eppendorf/Axygen-

200 μL pipette tips

Consumable

200 μL suction head

Eppendorf/Axygen-

10 μL pipette tips

Consumable

10 μL suction

Eppendorf/Axygen-

Agilent or QSEP

Or other similarequipment

Contains supporting
software

Other reagents and consumables without recommended brands - for FFPE block quality test (DV200)
EP tube rack
Metal Bath (for heating 1.5 mL centrifugal tube)
Vortex oscillator
Handheld centrifuge
Pipettes (1000µL; 200µL; 10µL; 2.5µL)
3

Purpose

Category

Description

Recommended brandCat. No.

Notes

Checkbox

For FFPE section dewaxing - for the same item, please choose from either one of the recommended brands
Slide warmer/dryer

Equipment///

Slide Box

Consumable

For holding or storing glass slides

Beyotime

FBX005Dust-free paper

Consumable

Kimtech dust-free wipe paper

KIMBERLY(KIMTECH)

0130-10Deparaffinization
agent

Reagent

Anhydrous ethanol

Reagent

Needs to satisfy thefollowing temperatures:
42 ° C; 37 ° C; 60 ° C
Instead, use a 50 mL
centrifuge tube

Environmental Dewaxing agent Histo- HEAD(BeiJing)
clear
Biotechnology

H6025

Environmental organizationtransparent dewaxing agent

Solarbio

G2150

Anhydrous ethanol (CAS: 64-17-5)

XILONG Scientific

1280340101601

Or other brands, AR purity-Or similar consumables

Other reagents and consumables without recommended brands - for FFPE section dewaxing
Slides staining jar

Consumable

Staining jar that can hold 5-10 slides/ddH2O/Milli-Q Water
EP Tube Rack
50 mL centrifugal rack
50 mL centrifuge tube4Purpose

Category

Description

Recommended brandCat. No.

Notes

Checkbox

For FFPE section H&E staining - for the same item, please choose from either one of the recommended brands
Mayer hematoxylin

Solarbio		

G4470

Hematoxylin solution according toMayer

Sigma

51275

Hematoxylin

Reagent

Bluing reagent

Reagent

Dako Bluing Buffer

DakoS3309

Eosin

Reagent

Eosin y Solution (Modified Alcoholic)Abcam

AB246824

Anhydrous ethanol

Reagent

Anhydrous ethanol (CAS: 64-17-5)

XILONG Scientific

1280340101699

20X SSC

Reagent

Ambion 20X SSC, no RNase

Invitrogen

AM9770

Nuclease-free waterReagent

Nuclease-free water (not DEPCtreated)

Thermo Fisher ScientificAM9937

Compressed air duster Reagent

Air Duster

Vlogger-Slide Box

Consumable

5-piece mail folder

Beyotime

FBX005

Cover slip

Consumable

Cover slip

CITOTEST10212450C

Dust-free paper

Consumable

Kimtech dust-free wipe paper

KIMBERLY(KIMTECH)

0130-10Mayer

Or other brands, AR purity

For blow-drying chips

Other reagents and consumables without recommended brands - for FFPE H&E staining
50 mL centrifuge tube

5Purpose

Category

Description

Recommended brandCat. No.

Notes

Checkbox

For FFPE section decolorization & decrosslinking - for the same item, please choose from either one of the recommended brands
Applied biosystem

4484073

T100 PCR instrument

Bio-Rad1861096

Reagent

Tris-EDTA antigen repair solution (1X)
pH 9.0

Solarbio

C1037

1000 μL pipette tips

Consumable

1000 μL suction

Eppendorf/Axygen-200 μL pipette tips

Consumable

200 μL suction head

Eppendorf/Axygen-

Slide BoxConsumable

5-piece mail folder

Beyotime

FBX005

20X SSC

ReagentAmbion® 20X SSC, RNase-free

Invitrogen

AM9770Dust-free paper

Consumable

Kimtech dust-free wipe paper

KIMBERLY(KIMTECH)

0130-10

PCR Thermal Cycler

Equipment

TE buffer (pH 9.0)

PROFLEX PCR 3X 32-well PCR system
TM

Other reagents and consumables without recommended brands - for FFPE section decolorization & decrosslinking
Pipettes (1000µL; 200µL; 10µL; 2.5µL)
Slides staining jar

Consumable

Staining jar that can hold 5-10 slides/-6Purpose

Category

DescriptionRecommended brandCat. No.

Notes

Checkbox

Notes

Checkbox

For FFPE ssDNA staining - for the same item, please choose from either one of the recommended brands
Nuclear staining
reagent

Kit

Qubit ssDNA Assay Kit

Invitrogen

TM

Q10212

20X SSC

Reagent

Ambion® 20X SSC, no RNase

Invitrogen

TMAM9770

Nuclease-free water

Reagent

Nuclease-free water (not DEPCtreated)

Thermo Fisher ScientificAM9937

Slide Box

Consumable

5-piece mail folder

Beyotime

FBX005

Cover slip

Consumable

Microscope cover

CITOTEST10212450C

Dust-free paper

Consumable

Kimtech dust-free wipe paper/delicate
KIMBERLY(KIMTECH)
task wipes

0130-10

Other reagents and consumables without recommended brands - for FFPE ssDNA staining
Pipettes (1000µL; 200µL; 10µL; 2.5µL)
Petri dishPurposeCategory

Description

Recommended brandCat. No.

For FFPE decrosslinking (post ssDNA stianing) - for the same item, please choose from either one of the recommended brands
20X SSC

Reagent

Ambion® 20X SSC, no RNase

Invitrogen

Slide Box

Consumable

5-piece mail folder

Beyotime

TMAM9770
FBX005Or, use a 50 ml centrifuge
tubeOther reagents and consumables without recommended brands - for FFPE decrosslinking (post ssDNA stianing)
Slide staining jar

Consumable

Staining jar that can hold 5-10 slides/-Pipettes (1000µL; 200µL; 10µL; 2.5µL)

7Purpose

Category

Description

Recommended brandCat. No.

Notes

Checkbox

For FFPE tissue fixation - for the same item, please choose from either one of the recommended brands
Methanol

Reagent

Methanol AR500mL (CAS: 67-56-1)

XILONG Scientific1280100101600

Or other brands, AR purity

Slide Box

Consumable

5-piece mail folder

BeyotimeFBX005

50mL centrifuge tube canbe used instead

Dust-free paper

Consumable

Kimtech dust-free wipe paper

KIMBERLY(KIMTECH)

0130-10

PurposeCategory

Description

Recommended brandCat. No.

Notes

Checkbox

For FFPE tissue permeabilization - for the same item, please choose from either one of the recommended brands
PCR Thermal Cycler

Equipment

PROFLEX PCR 3X 32-well PCR system
TM

T100 PCR instrument

Applied biosystem

4484073

Bio-Rad1861096

Hydrochloric acid solution (CAS: 7647Sigma01-0)

Safs 2104-50 mL

Hydrochloric acid

SINOPHARM

7647-01-0

Nuclease-free water (not DEPCtreated)

Thermo Fisher ScientificAM9937

1.5 mL DNase-/RNaseConsumablefree centrifuge tube

1.5 mL DNase-/RNase-free centrifuge
tube

Eppendorf/Axygen-

1000 μL Pipette Tips

Consumable

1000 μL Pipette Tips

Eppendorf/Axygen-

200 μL Pipette Tips

Consumable

200 μL Pipette Tips

Eppendorf/Axygen-

10 μL Pipette Tips

Consumable

10 μL Pipette Tips

Eppendorf/Axygen-

Hydrochloric acid

Nuclease-free water

Equipment

Reagent

Other reagents and consumables without recommended brands-for FFPE tissue permeabilization
Pipettes (1000µL; 200µL; 10µL; 2.5µL)

8Purpose

Category

Description

Recommended brandCat. No.

Notes

Checkbox

For FFPE mix overnight reaction - for the same item, please choose from either one of the recommended brands
Applied biosystem

4484073

T100 PCR instrument

Bio-Rad1861096

1.5 mL DNase-/RNaseConsumablefree centrifuge tube

1.5 mL enzyme-free centrifuge tube

Eppendorf/Axygen-

1000 μL Pipette Tips

Consumable

1000 μL Pipette Tips

Eppendorf/Axygen-

200 μL Pipette Tips

Consumable

200 μL Pipette Tips

Eppendorf/Axygen-

10 μL Pipette Tips

Consumable

10 μL Pipette Tips

Eppendorf/Axygen-

PCR Thermal Cycler

Equipment

PROFLEX PCR 3X 32-well PCR system
TM

Other reagents and consumables without recommended brands - for FFPE mix overnight reaction
Pipettes (1000µL; 200µL; 10µL; 2.5µL)

9Purpose

Category

Description

Recommended brandCat. No.

Notes

Checkbox

For FFPE cDNA release & cDNA amplification - for the same item, please choose from either one of the recommended brands

DNA Quantification

cDNA library
detection-Agilent

Kit

Qubit dsDNA Quantification Assay kit

Invitrogen

TMQ32854

Equipment

Qubit 4 fluorometer

Invitrogen

TMQ33238

TMQ32856

Consumable

Qubit Assay tube

Invitrogen

Equipment

2100 bioanalyzer/Agilent 2100

Agilent

Equipment

IKA Vortex Mixer

IKA

Kit

Bioanalyzer High Sensitivity DNAAnalysis
QSEP high-throughput biologicalfragment analyzer
High Sensitivity Cartridge Kit (N1)

Equipment

Kit

5065-4401

Agilent

5067-4626

BiOptic Inc.

QSEP400

BiOptic Inc.

C105105/C102205

Mini Metal Bath (MJY-100D)

Absin

ABS72022-1EA

ReagentAgencourt AMPure XP 450mL Kit

Beckman

A63882

Reagent

Vahts DNA Clean Beads

VazymeN411-01/N411-02/
N411-03

Consumable

DynaMag -2 Magnetic separation rack Invitrogen

Consumable

NEBNext Magnetic separation rack

NEB

S1515sNuclease-free water

Reagent

Nuclease-free water (not DEPCtreated)

Thermo Fisher ScientificAM9937

Anhydrous ethanol

Reagent

Absolute ethyl alcohol (CAS: 64-17-5)

XILONG Scientific

1280340101601

2.0 mL enzyme-free centrifuge tube

Eppendorf/Axygen-

1.5 mL enzyme-free centrifuge tube

Eppendorf/Axygen-cDNA library
detection-Qsep
Metal BathSPRI Beads
Magnetic separationrack(2.0 mL)
Magnetic separation
rack (0.2 mL)

Equipment

2.0 mL DNase-/RNaseConsumableFree centrifuge tube
1.5 mL DNase-/RNaseConsumableFree centrifuge tube

TMTM

12321D

PCR tube (0.2 mL)

Consumable

Axygen PCR cassette tube

AxygenPCR-0208-AD-C

1000 μL Pipette Tips

Consumable

1000 μL Pipette Tips

Eppendorf/Axygen-

200 μL Pipette Tips

Consumable

200 μL Pipette Tips

Eppendorf/Axygen-10 μL Pipette Tips

Consumable

10 μL Pipette Tips

Eppendorf/Axygen-Agilent or Qsep

For 37 ° C and 55 ° C heating;Or other similar devices

Or other consumables of thesame typeOr other consumables of thesame typeOr other brands, AR purity

Or other enzyme-free PCR
tubes

10

Other reagents and consumables without recommended brands -for FFPE cDNA release & cDNA amplification
PCR Thermal Cycler (any PCR Thermal Cycler that can be used for routine nucleic acid amplification)
Pipettes (1000µL; 200µL; 10µL; 2.5µL)

11