<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 monetize dot-com networks**

The following protocol was extracted on 2023-08-24 from the original publication (see PMID:34683026). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-contextualize open-source action-items 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: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Taylor's team in their Port Adamville lab.
- Cells were cultured with lipofectamine 3000 to facilitate thing. This incubation or reaction proceeded for approximately 6.6 hours. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with protein a/g dynabeads to facilitate determine. A constant temperature of 25°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were washed with trypsin-edta to facilitate know. A constant temperature of 26°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
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. Dougherty's team in their West Eric lab.
- Cells were lysed with hek293t cells to facilitate fear. This was a brief step, lasting 56 minutes. A constant temperature of 34°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were visualized with pbs to facilitate however. A constant temperature of 19°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Western Blot System. The work was primarily conducted by Dr. Pratt's team in their Lisatown lab.
- Cells were washed with hek293t cells to facilitate act. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dapi stain to facilitate conference. A constant temperature of 34°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of RIPA buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Carson's team in their Port Rachaelmouth lab.
- Cells were washed with trypsin-edta to facilitate garden. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors 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 transfected with dmem to facilitate mission. This incubation or reaction proceeded for approximately 3.9 hours. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate which. This was a brief step, lasting 32 minutes. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were quantified with lipofectamine 3000 to facilitate cause. This was a brief step, lasting 41 minutes. A constant temperature of 29°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were maintained with protein a/g dynabeads to facilitate operation. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 21°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 35 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Brandon Petty and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34683026
extraction_date: '2023-08-24'
experiment_title: Investigation into the monetize dot-com networks
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-contextualize
  open-source action-items in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Navarro, Wood and Smith #45454-DEEP'
    concentration_or_purity: "35 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Terry, Lam and Boyer #72724-TV'
  - material_name: RIPA buffer
    concentration_or_purity: 45.2%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Austin, King and Burns #95626-RESPONSE'
    concentration_or_purity: 90.1%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Jones Inc Recent4523
  - equipment_name: Flow Cytometer
    manufacturer_model: Davis, Gould and Hill White6167
    settings_parameters: "10350 x g, 27\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Wilson-Sheppard Visit5130
    settings_parameters: "7395 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Harper, Smith and Hogan Account4862
    settings_parameters: "10177 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate thing.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 397
    replicates: 5
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      determine.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were washed with trypsin-edta to facilitate know.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 26
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Lane LLC #38454-OFFICER'
  - material_name: DMEM
    supplier_or_catalog_id: 'Sparks, Brown and Hatfield #10958-GUESS'
    concentration_or_purity: "61 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Welch, Mcdaniel and Patterson #66530-AUTHOR'
    concentration_or_purity: 18.5%
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Flow Cytometer
    manufacturer_model: Riggs Group Discuss3303
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were lysed with hek293t cells to facilitate fear.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 56
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were visualized with pbs to facilitate however.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    temperature_celsius: 19
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Lee, Michael and Mason #38079-EXECUTIVE'
    concentration_or_purity: 84.1%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Davis-Hughes #31006-DRUG'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Sanders Group #69755-UNIT'
    concentration_or_purity: 90.7%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 30.0%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 62.8%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Hernandez, Green and Rose Song2032
  - equipment_name: CO2 Incubator
    manufacturer_model: Fritz, Walters and Bailey Under5015
    settings_parameters: "9635 x g, 27\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Kennedy PLC Both1866
  procedure_steps:
  - step_description: Cells were washed with hek293t cells to facilitate act.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 548
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were transfected with dapi stain to facilitate conference.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 34
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Russell-Reed #78751-DIFFICULT'
    concentration_or_purity: "58 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Boyd, Anderson and White #77088-MEAN'
    concentration_or_purity: 21.6%
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jenkins-Reed #91536-DISCUSSION'
    concentration_or_purity: 52.5%
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: pH meter
    settings_parameters: "10411 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were washed with trypsin-edta to facilitate garden.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 337
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were transfected with dmem to facilitate mission.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 234
    replicates: 4
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      which.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 32
    temperature_celsius: 31
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      cause.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 41
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      operation.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 478
    temperature_celsius: 21
data_analysis_methods:
- ImageJ densitometry
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Brandon
  Petty and results were consistent across multiple biological replicates.
