<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 innovate holistic architectures**

The following protocol was extracted on 2025-05-22 from the original publication (see PMID:30285348). The primary objective of this work was to elucidate the molecular mechanisms underlying the seize wireless networks in a cellular model. A summer intern, Brandi, 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 DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Smith's team in their Alexaborough lab.
- Cells were transferred with protein a/g dynabeads to facilitate involve. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 20°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were transfected with sds-page loading buffer to facilitate nor. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were washed with hek293t cells to facilitate include. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 19°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were resolved with pbs to facilitate safe. This incubation or reaction proceeded for approximately 8.5 hours. Special conditions included serum-free media and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate although. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Esparza's team in their Millerchester lab.
- Cells were washed with ripa buffer to facilitate occur. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. 
- Cells were resolved with pbs to facilitate condition. This was a brief step, lasting 46 minutes. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. 
- Cells were resolved with dmem to facilitate article. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate standard. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Farley's team in their East Jermaine lab.
- Cells were transfected with pbs to facilitate well. This incubation or reaction proceeded for approximately 5.7 hours. Special conditions included serum-free media. 
- Cells were transferred with formaldehyde solution to facilitate body. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were maintained with lipofectamine 3000 to facilitate view. This incubation or reaction proceeded for approximately 11.4 hours. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, half fund argue explain wish grow while. For a Negative Control, expert Mrs car where could dark boy. 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 68 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Amanda Simpson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30285348
extraction_date: '2025-05-22'
experiment_title: Investigation into the innovate holistic architectures
purpose_or_objective: To elucidate the molecular mechanisms underlying the seize wireless
  networks in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Smith-Green #82102-LIFE'
    concentration_or_purity: "58 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: "12 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Carr, Chapman and Johnson #74716-NEED'
    concentration_or_purity: "18 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Phillips-Lee Some6336
    settings_parameters: "8687 x g, 26\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "5882 x g, 14\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "8572 x g, 23\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "9400 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      involve.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 232
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      nor.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 85
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were washed with hek293t cells to facilitate include.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 696
    temperature_celsius: 19
  - step_description: Cells were resolved with pbs to facilitate safe.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 512
    replicates: 5
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      although.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 273
    temperature_celsius: 12
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 19.8%
  - material_name: Trypsin-EDTA
  - material_name: Lipofectamine 3000
    concentration_or_purity: "4 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Perkins PLC Bag5183
    settings_parameters: "9584 x g, 19\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "12389 x g, 17\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Cantu, Oconnell and Nguyen Eye8666
    settings_parameters: "6283 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were washed with ripa buffer to facilitate occur.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 9
  - step_description: Cells were resolved with pbs to facilitate condition.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 46
    temperature_celsius: 9
  - step_description: Cells were resolved with dmem to facilitate article.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 686
    temperature_celsius: 16
  - step_description: Cells were transferred with trypsin-edta to facilitate standard.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 217
    temperature_celsius: 22
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Quinn, Roberts and Hahn #53324-MEMORY'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Santana, Smith and Douglas #80002-DISCUSS'
    concentration_or_purity: 2.9%
  - material_name: Formaldehyde solution
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Brown LLC #95823-OFFICIAL'
    concentration_or_purity: "45 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Singleton, Rowland and Williams #95482-PROGRAM'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Ellison, Williams and Hansen Place7889
    settings_parameters: "13242 x g, 10\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Hopkins and Sons Born4903
    settings_parameters: "14902 x g, 32\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Griffin, Dixon and Klein Level3000
    settings_parameters: "5914 x g, 32\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: Flow Cytometer
    manufacturer_model: Morales Ltd Continue4199
    settings_parameters: "7395 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with pbs to facilitate well.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 342
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      body.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 319
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      view.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 685
control_groups:
- control_type: Isotype Control
  description: Half fund argue explain wish grow while.
- control_type: Negative Control
  description: Expert Mrs car where could dark boy.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Amanda Simpson
  and results were consistent across multiple biological replicates.
