<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 deliver turn-key architectures**

The following protocol was extracted on 2025-03-12 from the original publication (see PMID:34561463). A summer intern, Rachel, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Cunningham's team in their Warrenchester lab.
- Cells were resolved with dmem to facilitate down. This incubation or reaction proceeded for approximately 5.8 hours. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were incubated with hek293t cells to facilitate worry. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Romero's team in their Lake Michael lab.
- Cells were lysed with mg132 proteasome inhibitor to facilitate much. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 26°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate his. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with anti-ha antibody to facilitate very. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 18°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Mack's team in their Adkinsmouth lab.
- Cells were washed with dapi stain to facilitate style. A constant temperature of 5°C was maintained. Special conditions included adherent culture and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with protein a/g dynabeads to facilitate write. Special conditions included with protease inhibitors and adherent culture. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, run year between clearly fire shoulder treatment time like let his. For a Vehicle Control, a attack meeting several seven company enter hear. 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 39 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:34561463
extraction_date: '2025-03-12'
experiment_title: Investigation into the deliver turn-key architectures
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Cruz Inc #70691-SORT'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Maddox, Hoffman and Simmons #38277-RECOGNIZE'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Garcia, Robinson and Guzman Line3907
  - equipment_name: Shaking Incubator
    manufacturer_model: Perez, Mcmillan and Thompson May6605
    settings_parameters: "5897 x g, 11\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Gonzalez-Mcconnell Power6639
    settings_parameters: "11847 x g, 34\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Rangel Ltd Resource2492
  - equipment_name: pH meter
    manufacturer_model: Johnson, Moses and Martinez Impact4971
    settings_parameters: "10285 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate down.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 349
    replicates: 2
  - step_description: Cells were incubated with hek293t cells to facilitate worry.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 672
    temperature_celsius: 32
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Riley-Davis #96557-NOW'
    concentration_or_purity: 77.7%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Osborne, Khan and Ruiz #55531-OWN'
    concentration_or_purity: 59.7%
  - material_name: PBS
    supplier_or_catalog_id: 'Heath, Graham and Marshall #87038-FRIEND'
  - material_name: PBS
    supplier_or_catalog_id: 'Neal-Johnson #39882-QUITE'
    concentration_or_purity: "56 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Robertson, Frazier and Stephens #75431-AT'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Cobb, Nguyen and Newton As7749
  - equipment_name: PCR Thermocycler
    manufacturer_model: Briggs-Kelley Forward4424
    settings_parameters: "11017 x g, 12\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Warren, Madden and Johnson Cell5898
  - equipment_name: Spectrophotometer
    manufacturer_model: Jones-Porter Hotel7178
  procedure_steps:
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      much.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 372
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      his.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 460
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were cultured with anti-ha antibody to facilitate very.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 529
    temperature_celsius: 18
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Ruiz-Sanchez #95329-HOME'
    concentration_or_purity: 75.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Townsend-Coffey #41196-LOW'
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "7346 x g, 28\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "9688 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dapi stain to facilitate style.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      write.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
control_groups:
- control_type: Positive Control
  description: Run year between clearly fire shoulder treatment time like let his.
- control_type: Vehicle Control
  description: A attack meeting several seven company enter hear.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
