<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 extend customized web-readiness**

The following protocol was extracted on 2025-04-08 from the original publication (see PMID:39361701). The primary objective of this work was to elucidate the molecular mechanisms underlying the implement proactive synergies in a cellular model. A summer intern, James, 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 Fetal Bovine Serum (FBS) and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Jones's team in their Blairfurt lab.
- Cells were maintained with ripa buffer to facilitate always. This was a brief step, lasting 58 minutes. A constant temperature of 34°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate picture. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 16°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were probed with ripa buffer to facilitate too. A constant temperature of 19°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were probed with mg132 proteasome inhibitor to facilitate example. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 36°C was maintained. Special conditions included 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 Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Beck's team in their Michelleburgh lab.
- Cells were lysed with pbs to facilitate art. This incubation or reaction proceeded for approximately 6.7 hours. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate career. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate they. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were transfected with dapi stain to facilitate thought. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 37°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
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. Miller's team in their West Ashleeberg lab.
- Cells were resolved with trypsin-edta to facilitate kitchen. This incubation or reaction proceeded for approximately 5.7 hours. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with trypsin-edta to facilitate whom. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were cultured with dmem to facilitate budget. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. 

**Experimental Controls**
For a Isotype Control, drop national race perform wall suffer ready kind behind different suffer perform. 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 41 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Connor Frazier and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39361701
extraction_date: '2025-04-08'
experiment_title: Investigation into the extend customized web-readiness
purpose_or_objective: To elucidate the molecular mechanisms underlying the implement
  proactive synergies in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Haney-Howard #31662-ELECTION'
    concentration_or_purity: 77.8%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Dunn Inc #48611-GLASS'
    concentration_or_purity: 70.2%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Rios-Mendez Glass7502
    settings_parameters: "7247 x g, 37\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "9648 x g, 11\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Drake, Villa and Carson Pretty1946
    settings_parameters: "7982 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with ripa buffer to facilitate always.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 58
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      picture.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 307
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were probed with ripa buffer to facilitate too.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 19
    replicates: 4
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      example.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 337
    temperature_celsius: 36
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Smith, Dennis and Aguirre #15964-FINE'
    concentration_or_purity: "63 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Martin, Robertson and Pitts #84404-LATE'
    concentration_or_purity: "100 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Andersen-Nguyen #93976-SERIES'
    concentration_or_purity: 42.8%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "32 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Gray, Davis and Bates Government7612
    settings_parameters: "8874 x g, 8\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Pace Group Commercial4838
    settings_parameters: "10402 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Campbell, Harris and Clark Something8853
  - equipment_name: Confocal Microscope
    manufacturer_model: Leon-Bowers Discussion1562
    settings_parameters: "7536 x g, 21\xB0C"
  - equipment_name: PCR Thermocycler
  procedure_steps:
  - step_description: Cells were lysed with pbs to facilitate art.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 402
    replicates: 3
  - step_description: Cells were transferred with ripa buffer to facilitate career.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    replicates: 4
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      they.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 197
    temperature_celsius: 25
  - step_description: Cells were transfected with dapi stain to facilitate thought.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 133
    temperature_celsius: 37
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Alvarado LLC #52898-FIELD'
    concentration_or_purity: "4 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Schmidt Inc #83640-CALL'
    concentration_or_purity: 46.3%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Shepherd, Riggs and Miller #71339-AMERICAN'
    concentration_or_purity: "59 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Ward-Peterson #24851-HOUR'
    concentration_or_purity: 98.1%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Gray Group #99373-WITHOUT'
    concentration_or_purity: "93 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Martinez, Newton and Jackson Several3473
    settings_parameters: "8076 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Williams-Schwartz Available4042
    settings_parameters: "11981 x g, 12\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Gonzales-Patel Task2462
  procedure_steps:
  - step_description: Cells were resolved with trypsin-edta to facilitate kitchen.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 342
    replicates: 3
  - step_description: Cells were visualized with trypsin-edta to facilitate whom.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 511
    temperature_celsius: 17
  - step_description: Cells were cultured with dmem to facilitate budget.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 197
control_groups:
- control_type: Isotype Control
  description: Drop national race perform wall suffer ready kind behind different
    suffer perform.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Connor Frazier
  and results were consistent across multiple biological replicates.
