Jun 29, 2026

FLEX FFPE sample preparation and chromium fixed RNA profiling protocol

DOI
https://dx.doi.org/10.17504/protocols.io.5jyl835w6v2w/v1
  • 1Washington University in St. Louis, School of Medicine
Xiang Li
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DOI: https://dx.doi.org/10.17504/protocols.io.5jyl835w6v2w/v1
Protocol Citation: Xiang Li, Feng Chen, Li Ding 2026. FLEX FFPE sample preparation and chromium fixed RNA profiling protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.5jyl835w6v2w/v1
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 29, 2026
Last Modified: June 29, 2026
Protocol  Integer ID: 320004
Keywords: 10x genomics chromium fixed rna profiling, cell suspension suitable for downstream flex probe hybridization, gene expression flex, flex ffpe sample preparation, downstream flex probe hybridization, rna profiling protocol, rna profiling protocol this protocol, fixed nuclei, cell suspension, preparation of nuclei, cellular material, cells from formalin, ffpe, nuclei, intact cell, cell, small fraction of intact cell
Abstract
This protocol describes the preparation of nuclei/cells from formalin-fixed paraffin-embedded (FFPE) tissue sections for 10x Genomics Chromium Fixed RNA Profiling, also referred to as Gene Expression Flex. The resulting output is a fixed nuclei/cell suspension suitable for downstream FLEX probe hybridization. Throughout this protocol, the isolated material is referred to as “nuclei/cells”; however, the final suspension may primarily consist of nuclei, with a small fraction of intact cells, dissociated cellular material, and debris.
Important blocks handling notes before starting sectioning
2d
FFPE nuclei/cells yield is highly variable and depends on following, so DV 200 QC is needed and only use FFPE tissue scrolls cut from a well preserved FFPE block:
o FFPE block age.
o Tissue type.
o Tissue density.
o Tissue area in the section.
o Fixation quality.
o Pre-fixation tissue quality.
For both human and mouse FFPE tissue, start with at least:
o Two 25 µm sections.
If the tissue is expected to have low cellularity, small tissue area, or poor recovery, increase the number of scrolls.
If more tissue is required, try to reduce the paraffin by scoring the blocks.
FFPE sectioning and scroll transfer
2d
Before sectioning, make sure the FFPE block is well hydrated by placing the FFPE blocks in an ice water with the tissue block facing the water surface until sufficiently rehydrated.
Sectioning the blocks in 25 µm, the sectioned tissue ribbons should automatically form into compact scrolls, always cut and discard the first section.
Use forceps to transfer scrolls into a 1.5 ml low-bind microcentrifuge tube without damage or fragment the scrolls.
Proceed immediately to deparaffinization, or store scrolls at 4°C if needed.
During all liquid handling steps, pipette reagents along the side wall of the tube.
Do not pipette directly onto the scrolls.
Keep scrolls intact during deparaffinization and rehydration to reduce tissue loss.
Use low-binding tubes when possible.
Use a swinging-bucket rotor for centrifugation when possible to improve nuclei/cells recovery.
If the sample has low nuclei/cells numbers, do not over-dry or completely remove all residual liquid from the pellet; leaving a small volume of supernatant can help prevent pellet loss.
Prepare Liberase TH stock solution
10m
Add 1 ml nuclease-free water to 5 mg Liberase TH.
Invert the tube until the powder is fully dissolved.
Only prepare single-use aliquots.
Unused aliquots can store at -20°C.
Final stock concentration: 5 mg/ml.
Prepare dissociation enzyme mix before starting the dissociation
5m
Prepare dissociation enzyme mix fresh every time.
o Liberase TH stock, 5 mg/ml: 210 µl.
o RPMI: 840 µl.
o Total volume: 1050 µl.
Incubate the prepared enzyme mix at 37°C for 10 min before adding it to tissue.
Deparaffinization and rehydration
35m
Important notes:
During all liquid handling steps, pipette reagents along the side wall of the tube.
Do not pipette directly onto the scrolls.
Keep scrolls intact during deparaffinization and rehydration to reduce tissue loss.
If the sample supposed to has low nuclei/cells numbers, do not over dry or completely remove all residual liquid from the pellet; leaving a small volume of supernatant can help prevent pellet loss.
Xylene washes
30m
Add 1 ml xylene.
Incubate for 10 min at room temperature.
Carefully remove the liquid.
Repeat the xylene wash two additional times.
Total: three xylene washes.
Ethanol and water rehydration
5m
Add 1 ml 100% ethanol.
Incubate for 30 sec at room temperature.
Carefully remove the liquid.
Add 1 ml 100% ethanol.
Incubate for 30 sec at room temperature.
Carefully remove the liquid.
Add 1 ml 70% ethanol.
Incubate for 30 sec at room temperature.
Carefully remove the liquid.
Add 1 ml 50% ethanol.
Incubate for 30 sec at room temperature.
Carefully remove the liquid.
Add 1 ml nuclease-free water.
Incubate for 30 sec at room temperature.
Carefully remove the liquid.
Add 1 ml ice-cold PBS.
Keep the sample on ice until ready for dissociation.
Immediately before dissociation, remove PBS carefully without disrupting the tissue scrolls.
Pestle dissociation of FFPE tissue
1h 10m
Prepare quenching buffer right before the incubation step done, keep on ice 500 µl per Reaction：
o Nuclease-free water: 434.5 µl.
o 8X Concentrated Quench Buffer: 62.5 µl.
o RNase inhibitor, 40 U/µl: 3 µl.
o Total volume: 500 µl.
Remove PBS carefully.
Add 100 µl pre-warmed Dissociation Enzyme Mix.
Insert an RNase-free disposable pellet pestle into the tube, then gently trap the scrolls between the pestle and the tube wall, then rotate the pestle clockwise and counterclockwise 10-20 times and move the pestle gently up and down while rotating.
Continue until the scrolls are broken into similarly sized small pieces.
Add 900 µl Dissociation Enzyme Mix to the tube.
While adding the enzyme mix, rinse the pestle tip to recover tissue pieces stuck to the pestle.
Pipette mix gently.
Incubate at 37°C for 45 min in a thermomixer at 800 rpm.
After incubation, triturate the sample using a 1000 µl pipette by pipetting up and down 10-20 times.
Place a 30 µm filter on a chilled 5 ml collection tube.
Pass the suspension through the 30 µm filter.
Rinse the original 1.5 ml tube with 1 ml chilled PBS.
Pass this rinse through the same filter.
Rinse the filter with an additional 1 ml chilled PBS.
Collect all filtrate in the same collection tube.
Centrifuge at 850 rcf for 5 min at 4°C.
Carefully remove the supernatant without disturbing the pellet.
Resuspend the pellet in 0.5 ml chilled Tissue Resuspension Buffer or Quenching Buffer.
Pipette mix gently 5 times.
Keep the nuclei/cells suspension on ice.
Proceed to nuclei/cells counting.
Nuclei/cells counting
15m
Prepare a working aliquot with Ethidium Homodimer-1 staining solution by dilution (1:100) in 100% glycerol.
Mix the nuclei/cells suspension gently and mixing with Ethidium Homodimer-1 working solution by 1:1 dilution.
Add 10 ul of mix suspension into cell counter slides and avoid bubbles during pipetting.
Count using an automated fluorescent cell counter.
Focus nuclei/cells under brightfield first.
Switch to the fluorescent channel.
Visually inspect the counted objects to confirm that nuclei/cells are counted and no cell clumps present.
Record:
o Nuclei/cells concentration.
o Cell viability level.
If large debris or clumps remain, pass the suspension through a new 30 µm filter and recount if necessary.
Storage of fixed nuclei/cells suspension
Short-term storage at 4°C
Use nuclei/cells resuspended in Quenching Buffer as described above.
Thaw Enhancer at 65°C for 10 min.
Vortex and briefly centrifuge Enhancer.
Keep Enhancer warm at 42°C and confirm that no precipitate is present.
Do not keep thawed Enhancer on ice.
Add 0.1 volume pre-warmed Enhancer to the nuclei/cells suspension.
o Example: add 50 µl Enhancer to 500 µl nuclei/cells suspension.
Pipette mix gently.
Store at 4°C for up to 1 week.
Long-term storage at -80°C
Use nuclei/cells resuspended in Quenching Buffer.
Thaw Enhancer at 65°C for 10 min.
Vortex and briefly centrifuge Enhancer.
Keep Enhancer warm at 42°C and confirm that no precipitate is present.
Add 0.1 volume pre-warmed Enhancer to the nuclei/cells suspension.
o Example: add 50 µl Enhancer to 500 µl nuclei/cells suspension.
Pipette mix gently.
Add 50% glycerol to a final glycerol concentration of 10%.
o Example: add 137.5 µl 50% glycerol to 550 µl nuclei/cells suspension containing Enhancer.
Pipette mix gently.
Store at -80°C for up to 6 months.
Post-storage processing
Use 4°C sample or thaw -80°C samples at room temperature until no ice remains.
Centrifuge at 850 rcf for 5 min at room temperature.
Carefully remove the supernatant without disturbing the pellet.
Resuspend the pellet in 0.5 ml Quenching Buffer.
Recommended input for performing chromium fixed RNA profiling / FLEX
After counting, immediately proceed to the FLEX Probe Hybridization step.
Keep the nuclei suspension on ice before starting the assay.
Notes: recommended Input for FLEX Probe Hybridization:
For multiplex FLEX:
o Optimal input: 100,000-2 × 10⁶ nuclei/cells per hybridization.
o Do not exceed 2 × 10⁶ cells/nuclei in one hybridization reaction.
o Assign each biological sample to one unique Probe Barcode.
o For 4-plex assays, each sample is typically assigned one of four Probe Barcodes kit.
o For 16-plex assays, each sample is typically assigned one of sixteen Probe Barcodes kit.
If nuclei/cells input is low, expect higher risk of:
o Unequal pooling between samples.
o Lower usable data and complexity.
o Insufficient cells or nuclei/cells after post-hybridization washes.
o Lower final cell recovery.
If one sample needs higher cell recovery, it can be divided into multiple sub-pools and hybridized with multiple Probe Barcodes. These sub-pools can later be combined bioinformatically.
Probe Hybridization
1d
Prepare thermocycler
Set a thermocycler with heated lid to 42°C.
Use the following incubation program:
o Lid temperature: 42°C.
o Reaction volume: 100 µl.
o Pre-equilibration: 42°C hold.
o Probe hybridization: 42°C for 16-24 h.
Prepare Hyb Mix
Prepare reagents as below:
Thaw Hyb Buffer B at 42°C.
Vortex and briefly centrifuge.
Keep Hyb Buffer B warm.
If Hyb Buffer B looks milky, return it to 42°C until clear.
Heat Enhancer at 65°C for 10 min.
Vortex Enhancer and keep the enhancer at 42°C, also to confirm that no precipitate remains.
Prepare Hyb Mix at room temperature as below (per sample):
o Hyb Buffer B: 70 µl.
o Enhancer: 10 µl.
o Total: 80 µl.
Add warm Enhancer to the Hyb Mix.
Pipette mix Hyb Mix 10 times.
Incubate Hyb Mix at 42°C for 5 min before use.
Do not place thawed Hyb Buffer B, Enhancer or Hyb Mix back on ice due precipitation will form.
Pellet FFPE-dissociated nuclei
Transfer the required number of nuclei/cells (100,000-2 × 10⁶) in quenching buffer into a 1.5ml tube.
Centrifuge at 850 rcf for 5 min at 4°C.
Carefully remove the supernatant without disturbing the pellet.
For low-input samples, complete removal of supernatant is not required.
Up to approximately 15 µl residual supernatant may be left behind to avoid pellet loss.
Add Hyb Mix and WTA probe barcode
Resuspend each nuclei pellet in 80 µl Hyb Mix.
Transfer the sample to PCR tube strips.
Keep the sample at room temperature and do not place it on ice after resuspension in Hyb Mix.
Add 20 µl of one unique Human or Mouse WTA Probe Barcode to each 80 µl sample + Hyb Mix.
Pipette mix gently 10 times with the pipette set to 80 µl.
Record the Probe Barcode name, PN number, and sample identity.
Use only one WTA Probe Barcode per sample tube.
Hybridize Probes
Incubate sample mixtures at 42°C for 16-24 h.
Incubation for less than 16 h is not recommended.
All samples in the same project should have the same hybridization duration.
GEM generation and barcoding
3h 8m
Prepare Post-Hyb Wash Buffer
15m
Prepare Post-Hyb Wash Buffer fresh at room temperature, thaw Enhancer as described in step 41 and thaw concentrated Post-Hyb Buffer at room temperature, then keep it on ice.
Post-Hyb Wash Buffer, for FLEX 4:
o Nuclease-free water: 4.95 ml.
o Concentrated Post-Hyb Buffer: 0.275 ml.
o Enhancer: 0.275 ml.
o Total: 5.5 ml.
Post-Hyb Wash Buffer, for FLEX 16:
o Nuclease-free water: 13.86 ml.
o Concentrated Post-Hyb Buffer: 0.77 ml.
o Enhancer: 0.77 ml.
o Total: 15.4 ml.
Vortex briefly and keep at room temperature.
Do not keep Post-Hyb Wash Buffer at 4°C.
Dilute hybridized samples and count
1h
Remove tubes from the thermocycler after overnight hybridization.
Add 175 µl Post-Hyb Wash Buffer to each sample.
Pipette mix 5 times.
Take 10 µl diluted sample for counting using Ethidium Homodimer-1.
Count using a fluorescent counter.
Calculate and record the total number of cells/nuclei in each tube.
Pool samples
20m
Pool an equal number (based on the samples with lowest nuclei/cells output) of nuclei/cells from each hybridization reaction.
For 4-sample multiplexing, pool into a 5 ml centrifuge tube.
For 16-sample multiplexing, pool into a 15 ml centrifuge tube.
Calculate the volume of each sample to add based on post-hybridization counts.
For 4-plex pooling, add 2.3 ml Post-Hyb Wash Buffer after pooling.
For 16-plex pooling, add 9.2 ml Post-Hyb Wash Buffer after pooling.
Mix by inversion 5 times.
Wash Pooled Samples
1h
Centrifuge pooled samples at 850 rcf for 5 min at room temperature.
Carefully remove the supernatant without disturbing the pellet.
Resuspend the pellet in 1 ml Post-Hyb Wash Buffer.
Transfer to a 1.5 ml microcentrifuge tube.
Incubate at 42°C for 10 min in a thermomixer.
Centrifuge at 850 rcf for 5 min at room temperature.
Remove the supernatant.
Resuspend the pellet in 0.5 ml Post-Hyb Wash Buffer.
Pipette mix 5 times.
Incubate at 42°C for 10 min.
Centrifuge at 850 rcf for 5 min at room temperature.
Remove the supernatant.
Resuspend the pellet in 0.5 ml Post-Hyb Wash Buffer.
Pipette mix 5 times.
Incubate at 42°C for 10 min.
Centrifuge at 850 rcf for 5 min at room temperature.
Remove the supernatant carefully.
Prepare Post-Hyb Resuspension Buffer
3m
Prepare chilled Post-Hyb Resuspension Buffer and maintain at 4°C.
For 1 Pool + 10%
o Nuclease-free water: 1567.5 µl.
o Concentrated Post-Hyb Buffer: 82.5 µl.
o Total: 1650 µl.
Resuspend washed pool
30m
Resuspend the pellet in the appropriate volume of chilled Post-Hyb Resuspension Buffer.
o For < 1 × 10⁶ cells, resuspend in 500 µL Post-Hyb Resuspension Buffer.
o For 1 × 10⁶-4 × 10⁶ cells, resuspend in 750 µL Post-Hyb Resuspension Buffer.
o For 5 × 10⁶-8 × 10⁶ cells, resuspend in 1,000 µL Post-Hyb Resuspension Buffer.
o For 9 × 10⁶-12 × 10⁶ cells, resuspend in 1,250 µL Post-Hyb Resuspension Buffer.
o For 13 × 10⁶-16 × 10⁶ cells, resuspend in 1,500 µL Post-Hyb Resuspension Buffer.

Pipette mix 20 times to fully resuspend the pellet and break up small clumps.
Maintain the sample on ice.
Filter the pooled samples through a 30 µm filter and count the final pooled sample.
If the concentration is too far for the desired recovery target, concentrate the sample by centrifugation and resuspension in a proper volume.
Recount after concentration.
GEM chip loading
2h 38m
Prepare reagents
5m
Thaw Single Cell TL v1 Gel Beads to room temperature for at least 30 min before loading the chip.
Thaw Vortex Reducing Agent B at room temperature, verify no precipitate, and briefly centrifuge.
Thaw GEM Reagent Mix at room temperature, vortex, verify no precipitate, briefly centrifuge, and keep on ice.
Keep GEM Enzyme Mix on ice right before preparing the master mix.
Obtain Partitioning Oil, Chromium Next GEM Chip Q, chip Holder, and gasket.
Prepare GEM Master Mix
3m
Prepare GEM Master Mix as below, pipette mix 15 times, centrifuge briefly and keep on ice.
GEM Master Mix per 1 GEM Reaction：
o GEM Reagent Mix: 20.9 µl.
o Reducing Agent B: 1.7 µl.
o GEM Enzyme Mix: 12.4 µl.
o Total: 35 µl.
Prepare sample suspension for chip loading
5m
Add the appropriate volume of Post-Hyb Resuspension Buffer to the required volume of washed pooled sample.
Use the cell suspension volume calculator or chip loading table from the 10x guide to determine exact sample and buffer volumes.
Keep diluted sample on ice.
Add 35 µl GEM Master Mix to each tube containing diluted sample.
Do not pipette mix at this step as it will be done during chip loading step.
Proceed immediately to Chip Q loading.
Load Chromium Next GEM Chip Q
5m
Assemble Chromium Next GEM Chip Q in the holder.
Keep the chip horizontal.
Avoid bubbles during loading!
Fill unused chip wells with 50% glycerol solution:
o Row labeled 1: add 70 µl to each unused well.
o Row labeled 2: add 50 µl to each unused well.
o Row labeled 3: add 150 µl to each unused well.
Vortex Gel Beads for 30 sec using the 10x Vortex Adapter.
Briefly centrifuge Gel Beads for approximately 5 sec.
Load row labeled 1:
o Mix GEM Master Mix + sample.
o Load 70 µl into row labeled 1.
Load row labeled 2:
o Load 50 µl Gel Beads into row labeled 2.
o Wait 60 sec after loading.
Load row labeled 3:
o Load 45 µl Partitioning Oil into row labeled 3.
Close the chip holder lid and put on the gasket.
Run Chromium X/iX and Transfer GEMs
10m
Run the loaded Chip Q on Chromium X/iX.
The chip run takes approximately 5.5 min.
After the run, transfer GEMs from the recovery wells at row labeled 3.
Transfer GEMs carefully with pipette tips against the side walls of the tubes to avoid disrupting emulsions.
Proceed immediately to GEM incubation.
GEM Incubation
2h 10m
Incubate GEMs in a thermal cycler using a 100 µl reaction volume setting.
Use the following program:
o Lid temperature: 80°C.
o 25°C for 60 min.
o 60°C for 45 min.
o 80°C for 20 min.
o Hold at 4°C.
Total run time is approximately 125 min.
After incubation, GEMs may be stored at 4°C for up to 1 week.
Do not store GEMs at -20°C.
Alternatively, proceed directly to GEM recovery.
GEM recovery and pre-Amplification
1h 26m
Prepare reagents
Use the Reducing Agent B thawed in previous step.
Thaw Pre-Amp Primers B before 30 mins of GEM incubation done, vortex and centrifuge briefly and keep in the room temperature.
Get Amp Mix right before preparing the Pre-Amplification Mix, vortex and centrifuge briefly and keep on ice.
Post-GEM Recovery
5m
Add 125 µl Recovery Agent to each sample at room temperature.
Do not pipette mix or vortex the biphasic mixture.
Firmly cap the tube.
Mix by inverting 5 times.
Wait 2 min.
Briefly centrifuge.
Slowly remove and discard 125 µl Recovery Agent / Partitioning Oil from the bottom pink phase.
Do not aspirate the top aqueous sample.
Proceed directly to pre-Amplification PCR.
No cleanup is required before pre-Amplification PCR.
Pre-Amplification PCR
Prepare Pre-Amplification Mix
3m
Prepare on ice, vortex and centrifuge briefly.
o Amp Mix: 25 µl per reaction.
o Pre-Amp Primers B: 10 µl per reaction.
o Total: 35 µl per reaction.
Add Pre-Amplification Mix
3m
Add 35 µl Pre-Amplification Mix to the aqueous sample from GEM recovery.
Cap firmly.
Invert 8 times to mix.
Briefly centrifuge.
Set and run Pre-Amplification PCR Program
25m
o Lid temperature: 105°C.
o Reaction volume: 100 µl.
o 98°C for 3 min.
o 98°C for 15 sec.
o 63°C for 20 sec.
o 72°C for 1 min.
o Repeat steps 98°C (15 sec)-72°C (1 min) for a total of 8 cycles.
o 72°C for 1 min.
o Hold at 4°C.
Store product at 4°C for up to 72 h, or at -20°C for up to 1 week.
Alternatively, proceed directly to DNA cleanup.
DNA cleanup with SPRIselect beads
25m
Prepare Elution Solution
For 1000 µl Elution Solution:
o Buffer EB: 980 µl.
o 10% Tween-20: 10 µl.
o Reducing Agent B: 10 µl.
o Total: 1000 µl.
Cleanup as below steps:
Centrifuge samples for 30 sec in a micocentrifuge.
Transfer 70 µl of the upper clear aqueous layer to a new tube.
Avoid transferring cloudy precipitate at the phase interface.
Vortex SPRIselect reagent for at 30 seconds to fully resuspend beads.
Add 126 µl SPRIselect reagent to each 70 µl sample.
Pipette mix 15 times with pipette set to 180 µl.
Incubate for 5 min at room temperature.
Place sample tubes on magnet high pattern until the solution clears (~3 mins).
Remove and discard the supernatant without disturbing beads.
Wash beads with 200 µl freshly prepared 80% ethanol.
Wait 30 sec.
Remove ethanol.
Repeat ethanol wash once more, for a total of two washes.
Briefly centrifuge and return to magnet low pattern.
Remove residual ethanol.
Do not over-dry the beads.
Remove from magnet.
Add 101 µl Elution Solution.
Pipette mix 15 times.
Incubate 2 min at room temperature.
Place on magnet high pattern until solution clears.
Transfer 100 µl eluate to a new tube.
Store at 4°C for up to 72 h or at -20°C for up to 4 weeks, or proceed to Sample library Index PCR.
Gene expression library construction
1h 7m
Prepare reagents
3m
Thaw Dual Index Plate TS Set A at room temperature, vortex and centrifuge briefly and keep at room temperature.
Get Amp Mix right before preparing the Pre-Amplification Mix, vortex and centrifuge briefly and keep on ice.
Sample Index PCR
Prepare sample index PCR mix
3m
For 1 reaction:
o Amp Mix: 50 µl.
o Nuclease-free water: 10 µl.
o Total: 60 µl.
Prepare sample mix
3m
Transfer only 20 µl cleaned DNA sample to a new tube strip.
Add 60 µl Sample Index PCR Mix to sample.
Add 20 µl of one Dual Index TS Set A sample index.
Pipette mix 5 times with pipette set to 90 µl.
Briefly centrifuge.
Record the Dual index well ID.
Do not reuse overlapping index for samples in the same sequencing pool.
Set and run sample Index PCR program
3m
o Lid temperature: 105°C.
o Reaction volume: 100 µl.
o 98°C for 45 sec.
o 98°C for 20 sec.
o 54°C for 30 sec.
o 72°C for 20 sec.
o Repeat steps 98°C (20 sec)-72°C (20 sec) according to below targeted cell recovery and sample type (we always do 10 cycles).
o 72°C for 1 min.
o Hold at 4°C.
Cycle number may require optimization depending on RNA content and FFPE sample quality.
Store indexed PCR product at 4°C for up to 72 h, or proceed to post-PCR clean up.
Post Sample Index PCR clean up
25m
Add 100 µl SPRIselect reagent to each sample.
Pipette mix 15 times with pipette set to 180 µl.
Incubate for 5 min at room temperature.
Place sample tubes on magnet high pattern until the solution clears (~3 mins).
Remove and discard the supernatant without disturbing beads.
Wash beads with 200 µl freshly prepared 80% ethanol.
Wait 30 sec.
Remove ethanol.
Repeat ethanol wash once more, for a total of two washes.
Briefly centrifuge and return to magnet low pattern.
Remove residual ethanol.
Do not over-dry the beads.
Remove from magnet.
Add 41 µl Buffer EB.
Pipette mix 15 times.
Incubate 2 min at room temperature.
Place on magnet high pattern until solution clears (~3 mins).
Transfer 40 µl eluate to a new tube.
Store at 4°C for up to 72 h or at -20°C for long-term storage.
Library QC
30m
Assess final library trace at 1:80 dilution on TapeStation.
Ideal library peak trace after indexing is approximately 200-300 nM.
Submitting library for sequencing