markdown-output/3-level-sci-rna-seq-with-facs-buxdnxi6.md

```markdown
# Goal/Experiment:
The goal of this experiment is to perform a 3-level sci RNA-Seq (single-cell combinatorial indexing RNA sequencing) with the addition of Fluorescence Activated Cell Sorting (FACS) to decrease background noise during the library preparation stage.

## 3-level sci RNA-Seq with FACS

**David Fraser Read¹, Cole Trapnell¹**  
¹University of Washington, Dept. of Genome Sciences  

**DOI:** [dx.doi.org/10.17504/protocols.io.buxdnxi6](https://dx.doi.org/10.17504/protocols.io.buxdnxi6)

### Abstract
This protocol is a variant of "3 level sci RNA-Seq" which includes a FACS sorting step before the PCR stage. This notable addition helps to decrease background in the library preparation.

### Guidelines
This protocol is an adaptation and includes:
- Addition of FACS sorting to reduce background noise.
- Omission of the USER enzyme reaction step.
- Modified reverse transcription temperature ramp to enhance the number of unique molecular identifiers (UMIs) recovered per nucleus.

### Materials

#### Supplies
- **Nuclease-free water** (Ambion, AM 9937)
- **Snap Cap FACS Tube** (Corning, 08-771-23)
- **SUPERase In RNase Inhibitor 20 U/μL** (Thermo Fisher Scientific, AM2696)
- **BSA 20 mg/mL** (NEB, B9000S)
- **1M Tris-HCl (pH 7.4)** (Thermo Fisher Scientific, AM9759)
- **5M NaCl** (Thermo Fisher Scientific, AM9759)
- **1M MgCl2** (Thermo Fisher Scientific, AM9530G)
- **Triton X-100 for molecular biology** (Sigma Aldrich, 93443-100ML)
- **10mM dNTP** (Thermo Fisher Scientific, R0192)
- Indexed oligo-dT primers (100uM, 5'/5Phos/CAGACGNNNNNNNNNNT10bp barcode)
- **Superscript IV RNase Inhibitor** (Invitrogen, 10777019)
- **Quick ligation kit** (NEB, M2200L)
- **Elution buffer** (Qiagen, 19086)
- **NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module** (NEB, E7550S)
- **DNA binding buffer** (Zymo Research, D4004-1-L)
- **AMPure XP beads** (Beckman Coulter, A63882)
- **Ethanol** (Sigma Aldrich, 459844-4L)
- **Qubit dsDNA HS kit** (Invitrogen, Q32854)
- **Qubit tubes** (Invitrogen, Q32856)
- **Nextera 96 plate** (Illumina)
- Various falcon tubes and tips
- **BrightLine™ Hemacytometer** (Sigma Aldrich)
- **LoBind clear 1.5 mL PCR clean** (Eppendorf, 03-395-565; 22343102)

#### Equipment
- **FACS Aria II Sorter** with 96 well plate holder
- **Ice buckets**
- **Refrigerated centrifuge** with 15 mL tube holders
- **ScreenTape** (Agilent)
- **Qubit** (Thermo)

#### N7-loaded Tn5
The original use of the protocol involved custom Tn5 loaded with Nextera N7 adapters (commercial equivalent example: Illumina FC-121-1030). Alternatively, unloaded Tn5 can be purchased and adapters loaded per the method described [here](https://www.biorxiv.org/content/10.1101/2019.12.17.879304v1.full.pdf).

## Protocol

### Buffer Preparation

1. **Nuclei Buffer:**
   - Combine: 
     - 10 mM Tris-HCl (pH 7.4)
     - 10 mM NaCl
     - 3 mM MgCl2  
   - Store at 4°C.

2. **Nuclei Suspension Buffer (NSB):**
   - 1 mL Nuclei Buffer  
   - 10 μL BSA  
   - 10 μL SUPERaseIn  
   - Chill on ice.

3. **Nuclei Buffer with BSA (NBB):**
   - 1 mL Nuclei Buffer
   - 10 μL BSA
   - Chill on ice.

4. **10% Triton X-100 Stock:**
   - 1 mL Triton X-100  
   - 9 mL Nuclease-free water.  
   - Store at 4°C.

5. **Permeabilization Buffer:**
   - 500 μL per sample:
   - 12.5 μL of 10% Triton X-100
   - 487.5 μL NSB
   - Pre-chill on ice.

### Permeabilization

6. **Thaw**
   - Thaw frozen aliquots at 37°C in water bath.

7. **Buffer Addition**
   - Add 400 μL of Permeabilization Buffer. Mix gently.

8. **Incubate**
   - Incubate for 3 minutes on ice.

9. **Pellet and Resuspend**
   - Pellet at 500g for 5 min (4°C), discard supernatant and resuspend.

10. **Recentrifuge**
    - Pellet at 500g for 5 min (4°C), discard supernatant.

11. **Resuspend**
    - Resuspend in 300 μL NSB and count nuclei with hemocytometer.

### Reverse Transcription

12. **Setup RT reaction**
    - 30,000 nuclei in 22 μL Nuclei buffer
    - 2 μL 10mM dNTP
    - 2 μL indexed oligo-dT primer (100uM)
    - Incubate at 55°C for 5 min, then cool on ice.

13. **Prepare RT Mix**
    - 8 μL SuperScript IV First-Strand Buffer
    - 2 μL 100mM DTT
    - 2 μL SuperScript IV reverse transcriptase
    - 2 μL RNaseOUT RNase Inhibitor

14. **Distribute RT mix and Incubate**
    - Distribute 14 μL to each well. Incubate at following steps:
      - 4°C for 2 mins
      - 10°C for 2 mins
      - 20°C for 2 mins
      - 30°C for 2 mins
      - 40°C for 2 mins
      - 50°C for 2 mins
      - 53°C for 15 mins
      - 55°C for 10 mins
    - Add 60 μL ice-cold NBB post reaction.

15. **Pool Nuclei**
    - Pool Nuclei, pellet at 600 RCF for 10 min (4°C).

### Ligation

16. **Resuspend Nuclei**
    - Resuspend nuclei in 1 mL NSB.

17. **Distribute and Add Indexing Oligos**
    - Distribute 10 μL to each well, add 8 μL indexing oligos (100uM).

18. **Prepare Ligation Mix**
    - Combine:  
      - 2 μL Quick Ligase
      - 20 μL Quick Ligase buffer  
    - Distribute 22 μL to each well.

19. **Mix and Ligate**
    - Mix by pipetting, then incubate at 25°C for 10 min.  
    - Add 60 μL NBB, pool all wells.

20. **Spin and Resuspend**
    - Add 10 mL NBB, spin at 600 RCF, 10 min (4°C), supernatant discarded.  
    - Resuspend in 1 mL Elution Buffer.

21. **Add DAPI and Filter**
    - Add 10 μL of 300 μM DAPI, mix gently.
    - Filter through a 35 μM FACS tube.

### FACS Sorting

22. **Sort Nuclei**
    - Add 4 μL Elution Buffer to each well, sort based on DAPI.

### Second Strand Synthesis

23. **Volume Check**
    - Ensure volume in well is ~12 μL. Adjust input volumes if necessary.

24. **Prepare and Add Second Strand Mix**
    - For each well, prepare:
      - 1.33 μL second strand buffer
      - 0.67 μL enzyme mix  
    - Add 2 μL per well.

25. **Incubate**
    - Incubate at 16°C for 3 hours.

### Tagmentation

26. **Make TD Buffer**
    - 1.2 mL tagmentation salt buffer
    - 300 μL dimethylformamide

27. **Prepare Mix**
    - 12.5 μL 2x TD buffer,  
    - 12.5 μL second tagmentation mix 
    - (optional: 0.02 μL N7 loaded Tn5)
    - Incubate 5 min at 55°C.

### Ampure Bead Purification

28. **Add 50 μL of Ampure Beads**
    - Incubate 5 min, transfer to magnet, incubate 3 min more.

29. **Wash beads**
    - Twice with ~150 μL 80% ethanol.

30. **Resuspend Beads**
    - Add 17 μL EB.

### Post-Bead Cleanup

31. **Bead Cleanup**
    - With .7 volumes bead volume, wash with 80% ethanol.

### PCR

32. **Setup PCR**
    - 2 μL indexed P5 PCR primer (10uM)
    - 2 μL P7 primer (10uM)
    - 20 μL NEBNext master mix
    - PCR setting:  
      - 72°C 5 min
      - 98°C 30 secs
      - 17 cycles: 98°C 10 secs, 66°C 30 secs, 72°C 30 secs
      - 72°C 5 min

### Quantify and Sequence

33. **Quantify & Sequence Sample**
    - Quantified using Qubit and Agilent ScreenTape.
    - Sequenced on Illumina Nextseq 2000, 100 bp kit.
  
    - Read settings:
      - Read 1: 34 bases
      - Read 2: 66 bases
      - Index 1: 10 bases
      - Index 2: 10 bases

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```