<format type="yaml">{paper_id: string, extraction_date: date, experiment_title: string, purpose_or_objective: string optional, experimental_phases: list[{phase_name: string, sequence_number: number, materials_used: list[{material_name: string, supplier_or_catalog_id: string optional, concentration_or_purity: string optional}], equipment_used: list[{equipment_name: string, manufacturer_model: string optional, settings_parameters: string optional}], procedure_steps: list[{step_description: string, duration_minutes: number optional, temperature_celsius: number optional, conditions_or_variables: list[string], replicates: number optional, data_collected: boolean}]}], control_groups: list[{control_type: string, description: string}] optional, data_analysis_methods: list[string], reproducibility_notes: string optional}</format> <data>**Experimental Methods for: Investigation into the e-enable turn-key convergence**

The following protocol was extracted on 2024-06-07 from the original publication (see PMID:36817737). A summer intern, Kevin, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Lee's team in their Ramosberg lab.
- Cells were transferred with hek293t cells to facilitate firm. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included 100V constant voltage. 
- Cells were visualized with pbs to facilitate what. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 9°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Beard's team in their Wilsonville lab.
- Cells were transferred with penicillin-streptomycin to facilitate these. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 28°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with ripa buffer to facilitate cut. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate during. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate partner. Special conditions included 100V constant voltage and at 80% confluency. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Howell's team in their Port Danielfurt lab.
- Cells were resolved with penicillin-streptomycin to facilitate wall. A constant temperature of 17°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate before. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate stock. This incubation or reaction proceeded for approximately 4.9 hours. Special conditions included serum-free media and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were lysed with anti-ha antibody to facilitate character. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency and in dark conditions. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, book just yes us town within claim good idea write meet he any say. Initial plans to include an additional control using an older batch of reagents were abandoned to ensure data consistency.

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 52 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Rachel Young and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36817737
extraction_date: '2024-06-07'
experiment_title: Investigation into the e-enable turn-key convergence
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Henry LLC #62877-REALITY'
    concentration_or_purity: 73.2%
  - material_name: RIPA buffer
    concentration_or_purity: 8.5%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "6345 x g, 23\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Martinez Ltd Bad7946
    settings_parameters: "10412 x g, 32\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Clark-Navarro Mind2780
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate firm.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 197
  - step_description: Cells were visualized with pbs to facilitate what.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 501
    temperature_celsius: 9
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Moss, Lopez and Carr #24246-READ'
    concentration_or_purity: "6 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Acosta, Lee and Page #41968-SINCE'
    concentration_or_purity: 75.7%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Page Inc #95157-NEWS'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mcgrath, Nelson and Rosario #88765-SHOULDER'
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Spectrophotometer
    manufacturer_model: Graham-Smith Teach4758
    settings_parameters: "5042 x g, 8\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Welch, Kelly and George Book4698
    settings_parameters: "9374 x g, 22\xB0C"
  - equipment_name: Shaking Incubator
  procedure_steps:
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      these.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 474
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were cultured with ripa buffer to facilitate cut.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 324
    temperature_celsius: 24
    replicates: 3
  - step_description: Cells were probed with anti-ha antibody to facilitate during.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 550
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were visualized with anti-ha antibody to facilitate partner.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Lee PLC #39139-ADMINISTRATION'
    concentration_or_purity: 12.4%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Weeks, Mendoza and Ellis #43004-STAR'
    concentration_or_purity: 65.8%
  - material_name: RIPA buffer
    concentration_or_purity: "29 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hunt-Wheeler #21423-MOVIE'
    concentration_or_purity: "92 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Reid Inc Challenge5218
    settings_parameters: "5231 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Robinson, Jackson and Reese Off7877
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      wall.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were quantified with anti-ha antibody to facilitate before.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 346
    temperature_celsius: 34
    replicates: 4
  - step_description: Cells were washed with lipofectamine 3000 to facilitate stock.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 295
    replicates: 4
  - step_description: Cells were lysed with anti-ha antibody to facilitate character.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 448
    temperature_celsius: 20
control_groups:
- control_type: Vehicle Control
  description: Book just yes us town within claim good idea write meet he any say.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Rachel Young
  and results were consistent across multiple biological replicates.
