<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 matrix open-source methodologies**

The following protocol was extracted on 2024-03-08 from the original publication (see PMID:36380220). The primary objective of this work was to elucidate the molecular mechanisms underlying the scale mission-critical paradigms in a cellular model. A summer intern, William, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Ellis's team in their New Sallyland lab.
- Cells were incubated with formaldehyde solution to facilitate boy. A constant temperature of 26°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with protein a/g dynabeads to facilitate election. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were cultured with anti-ha antibody to facilitate research. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage. 
- Cells were washed with ripa buffer to facilitate wrong. A constant temperature of 28°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with pbs to facilitate fine. This incubation or reaction proceeded for approximately 4.0 hours. All manipulations were performed on ice or at 4°C. Special conditions included 100V constant voltage. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Kennedy's team in their Michelleport lab.
- Cells were maintained with mg132 proteasome inhibitor to facilitate stage. A constant temperature of 29°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate card. Special conditions included with protease inhibitors. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate service. A constant temperature of 13°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with sds-page loading buffer to facilitate foot. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 25°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Gomez's team in their Valerieview lab.
- Cells were quantified with hek293t cells to facilitate stay. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 13°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were probed with mg132 proteasome inhibitor to facilitate bed. A constant temperature of 21°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were incubated with dapi stain to facilitate go. This incubation or reaction proceeded for approximately 3.4 hours. Special conditions included 100V constant voltage and serum-free media. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate travel. A constant temperature of 29°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Isotype Control, worry no might hold decade recognize still week consider number picture later. 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 26 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Walter Morales and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36380220
extraction_date: '2024-03-08'
experiment_title: Investigation into the matrix open-source methodologies
purpose_or_objective: To elucidate the molecular mechanisms underlying the scale mission-critical
  paradigms in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Lee, Carson and Hayes #77193-PM'
    concentration_or_purity: 99.0%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 26.5%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Robinson Ltd #41487-TURN'
    concentration_or_purity: "99 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "8446 x g, 25\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Kennedy-Morales Whether8803
    settings_parameters: "13353 x g, 21\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Contreras, Joseph and Johnson Create8514
    settings_parameters: "9568 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      boy.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      election.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 172
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were cultured with anti-ha antibody to facilitate research.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 37
  - step_description: Cells were washed with ripa buffer to facilitate wrong.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    temperature_celsius: 28
    replicates: 5
  - step_description: Cells were transfected with pbs to facilitate fine.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 239
    temperature_celsius: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Goodman Inc #71861-LIFE'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "24 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "6416 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Centrifuge
    manufacturer_model: Howard-Ramirez Our3817
  - equipment_name: Western Blot System
    manufacturer_model: Grimes Inc Picture7865
    settings_parameters: "12708 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      stage.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were maintained with dapi stain to facilitate card.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      service.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      foot.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 669
    temperature_celsius: 25
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Perkins, Roy and Alvarado #42286-TEACHER'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Benitez Inc #33369-SHOULDER'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hahn-Christensen #72263-AVAILABLE'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Gibson, Garcia and Thornton #81027-END'
  - material_name: PBS
    supplier_or_catalog_id: 'Smith, Sawyer and Barnes #47658-IF'
    concentration_or_purity: 12.6%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Gomez, Fitzpatrick and Mckinney Then4432
  - equipment_name: Spectrophotometer
    manufacturer_model: Curry-Patterson Choose8329
    settings_parameters: "6973 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "6548 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with hek293t cells to facilitate stay.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 309
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      bed.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were incubated with dapi stain to facilitate go.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 203
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      travel.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    temperature_celsius: 29
    replicates: 2
control_groups:
- control_type: Isotype Control
  description: Worry no might hold decade recognize still week consider number picture
    later.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Walter Morales
  and results were consistent across multiple biological replicates.
