Feb 07, 2024
Sinai SCENT TMC - Single Cell Assay for Transposase Accessible Chromatin (ATAC-seq)
- Travis Dawson1
- 1Icahn School of Medicine
Protocol Citation: Travis Dawson 2024. Sinai SCENT TMC - Single Cell Assay for Transposase Accessible Chromatin (ATAC-seq). protocols.io https://dx.doi.org/10.17504/protocols.io.j8nlkoqo1v5r/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: February 02, 2024
Last Modified: February 07, 2024
Protocol Integer ID: 94625
Keywords: accessible chromatin, determination of nucleosome positioning, common entry point for epigenomic analysis, open chromatin state, genomic regions with open chromatin state, single cell assay for transposase, chromatin state, chromatin immunoprecipitation, chromatin states in cell, nucleosome positioning, initial findings from atac, seq assay, epigenomic analysis, identification of transcription factor, single cell assay, dna methylation, assay for transposase, genome, transcription factor, sinai scent tmc, genomic region, atac, based assay, sequencing
Abstract
The Assay for Transposase Accessible Chromatin (ATAC)-Seq method is a genome-wide, next-generation sequencing (NGS)-based assay that characterizes chromatin states in cell and tissue samples. Specifically, ATAC-Seq is utilized to identify genomic regions with open chromatin states, typically associated with actively transcribing sites, facilitating the identification of transcription factors and determination of nucleosome positioning. As a common entry point for epigenomic analysis, ATAC-Seq probes the molecular mechanisms regulating various cellular processes. Initial findings from ATAC-Seq assays can be further validated and expanded through complementary techniques such as reporter assays, chromatin immunoprecipitations, and DNA methylation assays.
Safety warnings
- All personnel must have completed the necessary training, including annual refresher training, on the safe handling of potentially infectious material.
- Personal protective equipment (PPE), which includes gowns, gloves, and protective goggles.
Procedure
52m
Prepare Transposition Mix
Prepare Transposition Mix (see below) On ice . Pipette mix 10x and centrifuge briefly.
Add 10 µL Transposition Mix to a tube of a PCR 8-tube strip for each sample. Centrifuge briefly and maintain 0 °C .
Refer to Nuclei Concentration Guidelines (see below) to calculate the volume of Nuclei Stock and Diluted Nuclei Buffer for a total volume of 5 µL .
Add the calculated volume of Diluted Nuclei Buffer to the Transposition Mix. Pipette mix.
Centrifuge briefly.
Gently pipette mix the Nuclei Stock. Add the calculated volume of Nuclei Stock to the tube
containing the Transposition Mix. Gently pipette mix 6x (pipette set to 10 uL). DO NOT CENTRIFUGE
THE TUBE.
Incubate in a thermal cycler using the following protocol:
GEM Generation and Barcoding
Prepare master mix On ice . Pipette mix 10x and centrifuge briefly.
Place the PCR strip containing Transposed Nuclei on a cooling block.
Assemble Chromium Next GEM Chip H:
Load 50% Glycerol into Unused Chip Wells (if <8 samples per chip):
i. 70 ul to unused wells in row labeled 1.
ii. 50 ul to unused wells in row labeled 2.
iii. 40 ul to unused wells in row labeled 3.
Aliquot 60 µL Master Mix to each tube containing Transposed Nuclei for a total of 75 µL in each tube
Using P200 multi-channel set to 70 ul, gently mix 5x On ice
00:00:30 Transfer 70 µL of cell mix to row 1, wait 00:00:30 for cells to prime before adding Gel Beads. Proceed with next step during 00:00:30 priming.
1m 30s
Vortex Gel Bead Strip for 30 seconds
Centrifuge the Gel Bead strip for ~5 seconds. Confirm there are no bubbles at the bottom of the tubes and the liquid levels are even. Place the Gel Bead sstrip back in the holder. Secure the holder lid.
Puncture the foil seal of the Gel Bead tubes. Slowly aspirate 50 ul Gel Beads. Dispense into the wells in row labeled 2 without introducing bubbles.
Wait 00:00:30
30s
Add 40 µL of Partitioning Oil to row 3. Remove bubbles
Attach gasket (notch on top left)
Place the assembled chip with the gasket into the tray of the Chromium Controller, ensuring the chip stays horizontal. Close the tray and press the play button to begin run (00:18:00 ). Complete next steps during run.
18m
Place a PCR 8-tube strip On ice
When chip run is complete, press the eject button of the Controller to remove the chip. Discard the gasket, open chip holder, and fold the lid back until it clicks to expose the wells at a 45 degree angle.
Transfer 100 µL of GEMs into PCR strip tube. Pipette slowly. It should take ~20 seconds to pipette GEMs.
If multiple chips are run back-to-back, cover the GEM-containing strip tube and place On ice for no more than 1 hour.
Run the following thermocycler program:
NOTE: PCR product can be stored at 15°C for up to 18 hours or at −20°C for up to a week, or proceed to the next step immediately.
Post GEM Incubation Cleanup
Add 125 µL Recovery Agent to each sample at room temperature. DO NOT pipette mix or vortex the biphasic mixture. Gently invert tube 10x to mix. Centrifuge briefly.
Slowly remove and discard 125 µL Recovery Agent/Partitioning Oil (pink) from the bottom of the tube. DO NOT aspirate any aqueous sample.
Prepare Dynabeads Cleanup Mix:
Vortex and add 200 µL of Dynabeads Cleanup Mix to each sample. Pipette mix 5x (pipette set to 200 ul).
Incubate 00:10:00 Room temperature
10m
Prepare Elution Solution I. Vortex and centrifuge briefly:
At the end of 10 min incubation, place on the 10x Magnetic Separator, high position (Magnet – High) until the solution clears.
Remove the supernatant.
Add 300 µL freshly prepared 80% ethanol to the pellet while on the magnet – High. Wait 00:00:30
30s
Remove the ethanol.
Add 200 µL 80% ethanol to the pellet. Wait 00:00:30
30s
Remove the ethanol.
Centrifuge briefly. Place on the magnet – Low.
Remove the remaining ethanol.
Remove from the magnet. Immediately add 40.5 µL Elution Solution I to avoid clumping.
Pipette mix 15x (pipette set to 40 ul) without introducing bubbles.
Incubate 00:01:00 Room temperature
1m
centrifuge briefly. Place on the magnet – Low until the solution clears.
Transfer 40 µL sample to a new tube strip.
Vortex the SPRIselect reagent until fully resuspended. Add 48 µL SPRIselect reagent to each sample. Pipette mix thoroughly.
Incubate 00:05:00 Room temperature
5m
Centrifuge briefly. Place on the magnet – High until the solution clears.
Remove the supernatant.
Add 200 µL 80% ethanol to the pellet. Wait 00:00:30
30s
Remove the ethanol.
Repeat steps 3.24 and 3.25 for a total of 2 washes.
Centrifuge briefly. Place on the magnet – Low.
Remove any remaining ethanol.
Remove the tube strip from the magnet. Immediately add 40.5 µL Elution Solution I.
Pipette mix 15x (pipette set to 30 ul) without introducing bubbles.
Incubate 00:02:00 Room temperature
2m
Centrifuge briefly. Place on the magnet – Low until the solution clears.
Transfer 40 µL sample to a new strip tube.
NOTE: Samples can be stored at 4°C up to 72 hours or at -20°C for up to 1 week, or proceed to the next step.
Library Construction
Prepare Sample Index PCR Mix On ice
Add 57.5 µL of Sample Index PCR Mix to 40 µL sample.
Add 2.5 µL of an individual Single Index N Set A to each well and record assignment
Mix by pipetting 15x and centrifuge briefly.
Run the following thermocycler program:
NOTE: Samples can be stored at 4°C up to 72 hours, or proceed to the next step.
Vortex to resuspend SPRIselect reagent. Add40 µL SPRIselect reagent to each sample. Pipette
to mix 15x.
Incubate 00:05:00 Room temperature
5m
Place on the magnet – High until the solution clears.
Transfer 130 µL supernatant to a new strip tube. DO NOT discard the supernatant.
Vortex to resuspend SPRIselect reagent. Add 74 µL SPRIselect reagent to each sample. Pipette to mix 15x.
Incubate 00:05:00 Room temperature
5m
Place on the magnet – High until the solution clears.
Discard the supernatant
Add 200 µL 80% ethanol to the pellet. Wait 00:00:30
30s
Remove the ethanol.
Repeat steps 4.14 and 4.15 for a total of 2 washes.
Centrifuge briefly. Place on the magnet – Low.
Remove remaining ethanol.
Remove from the magnet. Immediately add 20.5 µL Buffer EB. Pipette mix 15x
Incubate 00:02:00 Room temperature
2m
Centrifuge briefly. Place on the magnet – Low.
Transfer 20 µL sample to a new tube strip.
NOTE: Samples can be stored at 4°C up to 72 hours or -20°C for long-term storage.
LIBRARY QUANTIFICATION
Qubit - Run 1 µL sample at 1:5 dilution on the Qubit dsDNA HS Assay Kit
BioAnalyzer/Tapestation
1. EITHER Run 1 µL sample diluted to 3 ng/ul on the Agilent Bioanalyzer High Sensitivity DNA chip to determine fragment size. Lower molecular weight product (<150 bp) may be present. This does not affect sequencing.
2. OR Run 2 µL sample diluted to 1 ng/ul on the Agilent Tapestation High Sensitivity D1000 ScreenTape to determine fragment size.
qPCR
1. Thaw KAPA Library Quantification Kit for Illumina Platforms
2. Dilute 1 µL sample with deionized water to appropriate dilutions that fall within the linear detection range of the KAPA Library Quantification Kit for Illumina Platforms. (For more accurate quantification, make the dilution(s) in duplicate).
3. Make enough Quantification Master Mix for the DNA dilutions per sample and the DNA Standards (plus 10% excess) using the guidance for 1 reaction volume below:
4. Dispense 16 µL Quantification Master Mix for sample dilutions and DNA Standards into a 96 well PCR plate.
5. Add 4 µL sample dilutions and 4 µL DNA Standards to appropriate wells. Centrifuge briefly.
6. Incubate in a thermal cycler with the following protocol.
7. Follow the manufacturer’s recommendations for qPCR-based quantification. For library quantification for sequencer clustering, determine the concentration using the average size in the region of 175 – 1,000 bp.
Sequencing
Sequencing Libraries:
Chromium Single Cell ATAC libraries comprise double stranded DNA fragments which begin with P5 and end with P7. Sequencing these libraries produces a standard Illumina BCL data output folder.
The BCL data for Single Cell ATAC libraries include:
- Paired-end Read 1N containing insert sequence only
- Read 2N containing insert sequence, starting from the opposite end of fragment
- 8 bp sample index in the i7 read
- 16bp 10x barcode sequence in the i5 read
Illumina Sequencer Compatibility:
The compatibility of the listed sequencers has been verified by 10x Genomics. Some variation in assay performance is expected based on sequencer choice.
- MiSeq
- NextSeq 500/550 (High Output)
- NextSeq 1000/2000
- HiSeq 2500 (Rapid Run)
- HiSeq 3000.4000
- NovaSeq
Sample Indices
Each i7 sample index in the Single Index Plate Kit N Set A (PN-3000427) is a mix of 4 different sequences to balance across all 4 nucleotides. If multiple samples are pooled in a sequence lane, the sample index name (i.e. Single Index Plate N Set A well ID) is needed in the sample sheet used for generating FASTQs with “cellranger scATAC mkfastq”.
Sequencing Depth & Run Parameters
Library Pooling
Pooling dissimilar libraries may compromise the ability to pool effectively due to differences in insert sizes. DO NOT pool Single Cell ATAC libraries with other 10x Genomics libraries.