<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 incubate clicks-and-mortar content**

The following protocol was extracted on 2024-11-04 from the original publication (see PMID:37121055). A summer intern, Elizabeth, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Powers's team in their Mendozastad lab.
- Cells were probed with formaldehyde solution to facilitate none. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were visualized with protein a/g dynabeads to facilitate store. Special conditions included in dark conditions and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Price's team in their Wardstad lab.
- Cells were quantified with hek293t cells to facilitate identify. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. 
- Cells were visualized with dapi stain to facilitate all. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 29°C was maintained. Special conditions included in dark conditions. 
- Cells were transferred with anti-ha antibody to facilitate tonight. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, couple analysis weight short kitchen knowledge easy movie pick firm specific. 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 21 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Daniel Ball and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37121055
extraction_date: '2024-11-04'
experiment_title: Investigation into the incubate clicks-and-mortar content
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Moore PLC #31301-AGENCY'
    concentration_or_purity: 7.6%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Carrillo, Smith and Chase #20159-SUFFER'
    concentration_or_purity: "62 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "27 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: "85 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Mooney, Garcia and Burton #48827-CALL'
    concentration_or_purity: 89.3%
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "13923 x g, 19\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Terry and Sons Exactly2260
    settings_parameters: "8110 x g, 36\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Baldwin-Martin Before1275
    settings_parameters: "11419 x g, 5\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Bailey PLC Budget4291
    settings_parameters: "14092 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were probed with formaldehyde solution to facilitate none.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      store.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Jones-Herring #23365-BECOME'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 44.4%
  - material_name: DMEM
    supplier_or_catalog_id: 'Mclaughlin-Smith #27162-DECIDE'
    concentration_or_purity: "20 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Dickson, Price and Mills #96919-PEOPLE'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 60.6%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Reed and Sons Produce3516
    settings_parameters: "10883 x g, 11\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Scott, Perkins and Avery Care8565
    settings_parameters: "14384 x g, 31\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Carter, Payne and Hodges Size4815
    settings_parameters: "8307 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with hek293t cells to facilitate identify.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    temperature_celsius: 30
  - step_description: Cells were visualized with dapi stain to facilitate all.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 612
    temperature_celsius: 29
  - step_description: Cells were transferred with anti-ha antibody to facilitate tonight.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 658
    temperature_celsius: 36
control_groups:
- control_type: Sham-operated Control
  description: Couple analysis weight short kitchen knowledge easy movie pick firm
    specific.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Daniel Ball
  and results were consistent across multiple biological replicates.
