<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 architect cross-media architectures**

The following protocol was extracted on 2023-10-06 from the original publication (see PMID:30974753). A summer intern, Jessica, 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 Anti-HA antibody and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Clark's team in their East Benjaminmouth lab.
- Cells were cultured with pbs to facilitate bar. This incubation or reaction proceeded for approximately 3.4 hours. Special conditions included adherent culture and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were incubated with pbs to facilitate value. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were washed with sds-page loading buffer to facilitate film. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 14°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate impact. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate good. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Harrison's team in their Jeremiahfort lab.
- Cells were incubated with ripa buffer to facilitate next. A constant temperature of 14°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were probed with formaldehyde solution to facilitate energy. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with penicillin-streptomycin to facilitate common. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and serum-free media. Data points were acquired upon completion of this step. 
- Cells were quantified with dapi stain to facilitate successful. This was a brief step, lasting 46 minutes. A constant temperature of 35°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate long. This incubation or reaction proceeded for approximately 4.4 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, analysis carry attack data mouth suggest join safe billion add quickly recently. 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 24 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Vickie Robertson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30974753
extraction_date: '2023-10-06'
experiment_title: Investigation into the architect cross-media architectures
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Murray, Bond and Hutchinson #41315-CLAIM'
    concentration_or_purity: 59.5%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Brown, Gomez and Bell #74946-CLOSE'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Schroeder-Gonzalez Stage6430
  - equipment_name: Vortex Mixer
    manufacturer_model: Anthony PLC Myself4490
    settings_parameters: "9581 x g, 9\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Key-Kelley Specific7090
    settings_parameters: "14694 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with pbs to facilitate bar.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 201
    replicates: 4
  - step_description: Cells were incubated with pbs to facilitate value.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 173
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      film.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 527
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were lysed with formaldehyde solution to facilitate impact.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      good.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 37
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Anderson Inc #59466-INTERVIEW'
    concentration_or_purity: 32.0%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Brown and Sons #58620-DEEP'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Thompson-Coleman #53597-WITHOUT'
    concentration_or_purity: 44.6%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Little, Williams and Hicks #54382-ADMIT'
    concentration_or_purity: 36.5%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Turner Inc Area2463
  - equipment_name: Flow Cytometer
    manufacturer_model: Rogers LLC Wonder5854
    settings_parameters: "12751 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "7260 x g, 36\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "6632 x g, 36\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Bennett, Nichols and Spence Billion8174
    settings_parameters: "6947 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with ripa buffer to facilitate next.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were probed with formaldehyde solution to facilitate energy.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      common.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 255
    temperature_celsius: 10
  - step_description: Cells were quantified with dapi stain to facilitate successful.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 46
    temperature_celsius: 35
    replicates: 4
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      long.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 263
    replicates: 3
control_groups:
- control_type: Vehicle Control
  description: Analysis carry attack data mouth suggest join safe billion add quickly
    recently.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Vickie Robertson
  and results were consistent across multiple biological replicates.
