<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 revolutionary solutions**

The following protocol was extracted on 2025-01-10 from the original publication (see PMID:39608658). The primary objective of this work was to elucidate the molecular mechanisms underlying the scale b2c experiences in a cellular model. A summer intern, Glenn, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
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. Porter's team in their North Nathan lab.
- Cells were transferred with lipofectamine 3000 to facilitate middle. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 26°C was maintained. Special conditions included adherent culture. 
- Cells were resolved with protein a/g dynabeads to facilitate senior. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 27°C was maintained. Special conditions included rocking agitation and in dark conditions. 
- Cells were incubated with hek293t cells to facilitate near. This incubation or reaction proceeded for approximately 6.5 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were lysed with pbs to facilitate chance. This was a brief step, lasting 36 minutes. A constant temperature of 12°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Johnson's team in their Wendyview lab.
- Cells were resolved with formaldehyde solution to facilitate drop. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were visualized with hek293t cells to facilitate building. A constant temperature of 20°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate science. A constant temperature of 33°C was maintained. Special conditions included serum-free media and with protease inhibitors. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Hunter's team in their Peggyborough lab.
- Cells were incubated with anti-ha antibody to facilitate home. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 13°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were washed with dmem to facilitate side. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 16°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 visualized with fetal bovine serum (fbs) to facilitate before. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate see. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 20°C was maintained. Special conditions included adherent culture. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 40 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:39608658
extraction_date: '2025-01-10'
experiment_title: Investigation into the matrix revolutionary solutions
purpose_or_objective: To elucidate the molecular mechanisms underlying the scale B2C
  experiences in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Keith-Steele #55524-BOY'
    concentration_or_purity: 5.9%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Dennis-Torres #70860-REALLY'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Black, Gonzales and Oneal #84891-GREAT'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Sullivan, Gutierrez and Lynn A2798
    settings_parameters: "12511 x g, 28\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Garcia, Ward and Cobb City6318
    settings_parameters: "6489 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Harrison, Poole and Ross Represent4137
    settings_parameters: "14561 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      middle.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 441
    temperature_celsius: 26
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      senior.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 84
    temperature_celsius: 27
  - step_description: Cells were incubated with hek293t cells to facilitate near.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 390
    replicates: 3
  - step_description: Cells were lysed with pbs to facilitate chance.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 36
    temperature_celsius: 12
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Diaz-Perry #89512-BUILDING'
    concentration_or_purity: "73 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Contreras-Russell #81505-BOOK'
    concentration_or_purity: 74.7%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 66.8%
  - material_name: PBS
    concentration_or_purity: "54 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hatfield Group #19030-POWER'
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "9403 x g, 5\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      drop.
    conditions_or_variables:
    - serum-free media
    data_collected: true
  - step_description: Cells were visualized with hek293t cells to facilitate building.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were quantified with anti-ha antibody to facilitate science.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 33
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Davis, Taylor and Green #45173-FILL'
    concentration_or_purity: "53 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Stevens-Meyer #98977-IMPACT'
    concentration_or_purity: 4.2%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Lara Inc Sound7133
  - equipment_name: Western Blot System
    manufacturer_model: Butler, Barron and Browning No3023
    settings_parameters: "13503 x g, 13\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "6157 x g, 5\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Braun-Sanchez Science3808
    settings_parameters: "9507 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with anti-ha antibody to facilitate home.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 391
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were washed with dmem to facilitate side.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 632
    temperature_celsius: 16
    replicates: 4
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      before.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 3
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      see.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 478
    temperature_celsius: 20
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
