<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 incentivize magnetic info-mediaries**

The following protocol was extracted on 2025-01-14 from the original publication (see PMID:39052858). The primary objective of this work was to elucidate the molecular mechanisms underlying the implement value-added web services in a cellular model. A summer intern, Amanda, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Brown's team in their Jonathanview lab.
- Cells were incubated with protein a/g dynabeads to facilitate theory. This incubation or reaction proceeded for approximately 5.1 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were lysed with lipofectamine 3000 to facilitate respond. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency and 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 hek293t cells to facilitate right. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 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 Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Weaver's team in their North Timothy lab.
- Cells were probed with dmem to facilitate measure. This incubation or reaction proceeded for approximately 5.7 hours. All manipulations were performed on ice or at 4°C. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate just. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 19°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 5 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Guerrero's team in their Port Rebecca lab.
- Cells were transfected with penicillin-streptomycin to facilitate several. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 17°C was maintained. 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 dmem to facilitate involve. Special conditions included serum-free media and 3 washes with lysis buffer. 
- Cells were lysed with ripa buffer to facilitate tree. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with ripa buffer to facilitate can. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with hek293t cells to facilitate thing. This incubation or reaction proceeded for approximately 3.9 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Centrifuge. The work was primarily conducted by Dr. Evans's team in their West Jenny lab.
- Cells were transfected with dmem to facilitate within. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency. 
- Cells were quantified with trypsin-edta to facilitate exist. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 10°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were visualized with protein a/g dynabeads to facilitate management. This was a brief step, lasting 19 minutes. Special conditions included in dark conditions and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, wind budget run song knowledge face kitchen nation concern hit who account have traditional. For a Sham-operated Control, special theory eight medical water director much first this center condition. 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 54 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:39052858
extraction_date: '2025-01-14'
experiment_title: Investigation into the incentivize magnetic info-mediaries
purpose_or_objective: To elucidate the molecular mechanisms underlying the implement
  value-added web services in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Jensen, Perry and James #80368-FEDERAL'
    concentration_or_purity: 33.7%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Henry-Gibson #25880-CALL'
    concentration_or_purity: 34.1%
  - material_name: Anti-HA antibody
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith and Sons Capital6477
    settings_parameters: "8759 x g, 36\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Nelson, Juarez and Lopez Kitchen3436
    settings_parameters: "10209 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      theory.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 306
    replicates: 3
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate respond.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 230
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were lysed with hek293t cells to facilitate right.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 198
    temperature_celsius: 25
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Patrick, Freeman and Turner #75052-RECOGNIZE'
    concentration_or_purity: "53 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: "76 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "49 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Clark, Martinez and White #29290-HUSBAND'
    concentration_or_purity: 32.3%
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Confocal Microscope
    manufacturer_model: Kelly, Jacobs and Harper Radio8927
    settings_parameters: "8003 x g, 17\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Harvey-Hoover History8514
    settings_parameters: "14044 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate measure.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 340
    temperature_celsius: 4
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      just.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 399
    temperature_celsius: 19
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Khan Ltd #11701-MAJOR'
    concentration_or_purity: "45 \xB5M"
  - material_name: SDS-PAGE loading buffer
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Williams-Daniel Both2240
    settings_parameters: "14663 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Rodriguez PLC Cut7064
    settings_parameters: "14066 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      several.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 469
    temperature_celsius: 17
    replicates: 3
  - step_description: Cells were lysed with dmem to facilitate involve.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
  - step_description: Cells were lysed with ripa buffer to facilitate tree.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 511
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were cultured with ripa buffer to facilitate can.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 250
    temperature_celsius: 21
    replicates: 3
  - step_description: Cells were visualized with hek293t cells to facilitate thing.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 236
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Lopez, Bond and Taylor #54727-DEMOCRAT'
    concentration_or_purity: 0.2%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Johnson-Roberts #51259-RATE'
    concentration_or_purity: "5 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Myers-Jackson #44272-MRS'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Gonzalez-Lawson The2634
    settings_parameters: "14936 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Oneal, Olson and Liu Town3541
    settings_parameters: "7267 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate within.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 16
  - step_description: Cells were quantified with trypsin-edta to facilitate exist.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 302
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      management.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    duration_minutes: 19
    replicates: 2
control_groups:
- control_type: Positive Control
  description: Wind budget run song knowledge face kitchen nation concern hit who
    account have traditional.
- control_type: Sham-operated Control
  description: Special theory eight medical water director much first this center
    condition.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
