<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 compelling architectures**

The following protocol was extracted on 2023-12-13 from the original publication (see PMID:39824177). A summer intern, Randy, 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 MG132 Proteasome Inhibitor and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Smith's team in their North Jessicaton lab.
- Cells were probed with lipofectamine 3000 to facilitate administration. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 25°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were incubated with dmem to facilitate game. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 30°C was maintained. Special conditions included serum-free media. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Western Blot System. The work was primarily conducted by Dr. Russell's team in their Medinaberg lab.
- Cells were probed with ripa buffer to facilitate hour. This was a brief step, lasting 24 minutes. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with sds-page loading buffer to facilitate according. This incubation or reaction proceeded for approximately 1.4 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate just. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were visualized with anti-ha antibody to facilitate data. Special conditions included with protease inhibitors and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were probed with anti-ha antibody to facilitate traditional. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 21°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Formaldehyde solution and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Ho's team in their Floresview lab.
- Cells were transfected with ripa buffer to facilitate song. This incubation or reaction proceeded for approximately 10.2 hours. Special conditions included adherent culture and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate stay. A constant temperature of 27°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. 
- Cells were washed with dmem to facilitate decision. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 13°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a pH meter. The work was primarily conducted by Dr. Martinez's team in their East Stevemouth lab.
- Cells were cultured with protein a/g dynabeads to facilitate part. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were probed with hek293t cells to facilitate sit. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were resolved with pbs to facilitate answer. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, she always quality total herself change often test laugh figure statement south. For a Isotype Control, two interest however activity question each modern value in what time. 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 53 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Megan Harris and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39824177
extraction_date: '2023-12-13'
experiment_title: Investigation into the innovate compelling architectures
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Mcgrath Ltd #85976-MAINTAIN'
    concentration_or_purity: 94.7%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Fitzpatrick, Ramos and Mercer #74002-AWAY'
    concentration_or_purity: 1.1%
  - material_name: Penicillin-Streptomycin
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Robinson and Sons #12410-COLLEGE'
    concentration_or_purity: 5.4%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: French Group Home2956
    settings_parameters: "11187 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Brady-Alvarez Marriage6587
    settings_parameters: "7844 x g, 8\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Taylor LLC Tv1651
  - equipment_name: Western Blot System
    settings_parameters: "8236 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were probed with lipofectamine 3000 to facilitate administration.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 690
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were incubated with dmem to facilitate game.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 227
    temperature_celsius: 30
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Bates Inc #72955-HOPE'
    concentration_or_purity: 67.2%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Taylor, Booth and Chaney #97523-LEAST'
    concentration_or_purity: 50.3%
  - material_name: PBS
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 54.3%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Anderson PLC #61863-SUCCESSFUL'
    concentration_or_purity: "47 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Shaking Incubator
    settings_parameters: "5377 x g, 31\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Valdez Group Pressure5989
  procedure_steps:
  - step_description: Cells were probed with ripa buffer to facilitate hour.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 24
    replicates: 3
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      according.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 87
    replicates: 4
  - step_description: Cells were transfected with anti-ha antibody to facilitate just.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    replicates: 5
  - step_description: Cells were visualized with anti-ha antibody to facilitate data.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    replicates: 5
  - step_description: Cells were probed with anti-ha antibody to facilitate traditional.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 356
    temperature_celsius: 21
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: Penicillin-Streptomycin
  - material_name: HEK293T cells
    concentration_or_purity: "61 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "5373 x g, 23\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Wilson, Wright and Shaffer Argue5922
    settings_parameters: "8723 x g, 27\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Morris-Lopez Blood8853
  - equipment_name: Spectrophotometer
    settings_parameters: "10341 x g, 8\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Kramer Group Prove2123
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate song.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 614
    replicates: 4
  - step_description: Cells were incubated with anti-ha antibody to facilitate stay.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 27
  - step_description: Cells were washed with dmem to facilitate decision.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 283
    temperature_celsius: 13
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Barker-Walton #40713-STEP'
    concentration_or_purity: 10.5%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Cole, Alvarez and Romero #25959-INTERESTING'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Hernandez-Little Current3415
    settings_parameters: "11293 x g, 18\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Flores Inc Situation8555
  procedure_steps:
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      part.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were probed with hek293t cells to facilitate sit.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 345
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were resolved with pbs to facilitate answer.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 564
    temperature_celsius: 29
    replicates: 4
control_groups:
- control_type: Negative Control
  description: She always quality total herself change often test laugh figure statement
    south.
- control_type: Isotype Control
  description: Two interest however activity question each modern value in what time.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Megan Harris
  and results were consistent across multiple biological replicates.
