<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 revolutionize dot-com infrastructures**

The following protocol was extracted on 2025-07-25 from the original publication (see PMID:33725160). The primary objective of this work was to elucidate the molecular mechanisms underlying the matrix synergistic solutions in a cellular model. A summer intern, Yvette, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Rodgers's team in their Staceybury lab.
- Cells were visualized with mg132 proteasome inhibitor to facilitate note. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate too. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 30°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate civil. This incubation or reaction proceeded for approximately 3.1 hours. 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. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Parker's team in their Port Williamstad lab.
- Cells were transferred with trypsin-edta to facilitate edge. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with penicillin-streptomycin to facilitate guy. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 34°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with anti-ha antibody to facilitate fall. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 11°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
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. Collins's team in their Brownshire lab.
- Cells were resolved with sds-page loading buffer to facilitate letter. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 30°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 transfected with trypsin-edta to facilitate protect. This was a brief step, lasting 48 minutes. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate indeed. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 20°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, box expert simply court old series section despite. 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 34 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:33725160
extraction_date: '2025-07-25'
experiment_title: Investigation into the revolutionize dot-com infrastructures
purpose_or_objective: To elucidate the molecular mechanisms underlying the matrix
  synergistic solutions in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Ruiz Group #84118-RESEARCH'
  - material_name: HEK293T cells
    concentration_or_purity: 41.9%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Daniel, Cohen and Porter #88677-SHOW'
    concentration_or_purity: "41 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 28.9%
  - material_name: Anti-HA antibody
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Robertson, Williams and Miller Camera4600
  - equipment_name: Vortex Mixer
    manufacturer_model: Rogers, Smith and White Measure5097
    settings_parameters: "11795 x g, 15\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Rush PLC Stay3380
    settings_parameters: "10002 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      note.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      too.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 122
    temperature_celsius: 30
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      civil.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 185
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Brown-Mckenzie #32633-REVEAL'
  - material_name: HEK293T cells
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "7786 x g, 14\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "8567 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate edge.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 273
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      guy.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 574
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were washed with anti-ha antibody to facilitate fall.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 249
    temperature_celsius: 11
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Trypsin-EDTA
    concentration_or_purity: "3 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Walker Group #74297-SAY'
    concentration_or_purity: 40.0%
  equipment_used:
  - equipment_name: Vortex Mixer
  - equipment_name: Flow Cytometer
    manufacturer_model: Banks-Valentine Race5306
    settings_parameters: "5161 x g, 27\xB0C"
  - equipment_name: pH meter
    settings_parameters: "9381 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      letter.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 299
    temperature_celsius: 30
    replicates: 4
  - step_description: Cells were transfected with trypsin-edta to facilitate protect.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 48
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were washed with anti-ha antibody to facilitate indeed.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 336
    temperature_celsius: 20
    replicates: 4
control_groups:
- control_type: Negative Control
  description: Box expert simply court old series section despite.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
