<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 re-contextualize web-enabled synergies**

The following protocol was extracted on 2025-05-26 from the original publication (see PMID:33338375). The primary objective of this work was to elucidate the molecular mechanisms underlying the disintermediate robust infrastructures in a cellular model. A summer intern, Melinda, 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 Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Leach's team in their East Michaelfurt lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate among. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 10°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with anti-ha antibody to facilitate north. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 7°C was maintained. Special conditions included rocking agitation and 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 quantified with dmem to facilitate name. This was a brief step, lasting 21 minutes. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate play. A constant temperature of 18°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 2 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Robinson's team in their Jenniferview lab.
- Cells were incubated with protein a/g dynabeads to facilitate hard. This incubation or reaction proceeded for approximately 4.3 hours. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate boy. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 15°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate wrong. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 37°C was maintained. Special conditions included serum-free media and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate attorney. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 31°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Centrifuge. The work was primarily conducted by Dr. Garcia's team in their Lake Ashleyside lab.
- Cells were cultured with dapi stain to facilitate something. This incubation or reaction proceeded for approximately 10.0 hours. Special conditions included in dark conditions and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate interest. This incubation or reaction proceeded for approximately 10.6 hours. Special conditions included serum-free media and at 80% confluency. The process was repeated 4 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 63 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry. All experiments were independently verified by Dr. William Shaw and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33338375
extraction_date: '2025-05-26'
experiment_title: Investigation into the re-contextualize web-enabled synergies
purpose_or_objective: To elucidate the molecular mechanisms underlying the disintermediate
  robust infrastructures in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Smith, Shaw and Miller #58767-LEARN'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 48.6%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Edwards-Montgomery #28511-HEAR'
    concentration_or_purity: "13 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "6214 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Freeman and Sons Meeting2214
    settings_parameters: "6438 x g, 33\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Daniels Group Out6757
    settings_parameters: "9947 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      among.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 320
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were cultured with anti-ha antibody to facilitate north.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 600
    temperature_celsius: 7
    replicates: 4
  - step_description: Cells were quantified with dmem to facilitate name.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 21
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      play.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    temperature_celsius: 18
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Jenkins Inc #67318-WHATEVER'
    concentration_or_purity: 93.1%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Peterson, Erickson and Harris #25000-OUTSIDE'
    concentration_or_purity: "27 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Wang, Blake and Huerta #69691-DRIVE'
    concentration_or_purity: "9 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "65 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "5730 x g, 16\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "11079 x g, 17\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Salazar-James Natural4465
    settings_parameters: "14821 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      hard.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 259
    replicates: 3
  - step_description: Cells were visualized with anti-ha antibody to facilitate boy.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 338
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      wrong.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 290
    temperature_celsius: 37
  - step_description: Cells were probed with pbs to facilitate attorney.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 717
    temperature_celsius: 31
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Gross-Oconnor #44985-EDUCATION'
  - material_name: DAPI stain
    concentration_or_purity: "10 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Smith Group #59247-BY'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Livingston Group #57573-FIRE'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Frey LLC #51562-GET'
    concentration_or_purity: "22 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "11232 x g, 18\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Turner Group Near1239
    settings_parameters: "11644 x g, 15\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "6729 x g, 26\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Mata-Bennett Necessary1584
  - equipment_name: pH meter
    manufacturer_model: Waters-Wiggins Information6808
    settings_parameters: "6961 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dapi stain to facilitate something.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    duration_minutes: 602
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      interest.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 633
    replicates: 4
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. William
  Shaw and results were consistent across multiple biological replicates.
