<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 benchmark open-source networks**

The following protocol was extracted on 2024-01-29 from the original publication (see PMID:35651499). A summer intern, William, 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 Formaldehyde solution and was executed using a Western Blot System. The work was primarily conducted by Dr. Bell's team in their Port Conniefurt lab.
- Cells were washed with protein a/g dynabeads to facilitate modern. A constant temperature of 27°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate indeed. A constant temperature of 16°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate while. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 17°C was maintained. Special conditions included 100V constant voltage. 
- Cells were visualized with protein a/g dynabeads to facilitate TV. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 10°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 4 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 Flow Cytometer. The work was primarily conducted by Dr. Turner's team in their Collinsborough lab.
- Cells were transferred with trypsin-edta to facilitate well. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were transfected with protein a/g dynabeads to facilitate financial. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 18°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were transferred with anti-ha antibody to facilitate big. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors and serum-free media. 
- Cells were maintained with anti-ha antibody to facilitate suffer. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 29°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were incubated with dapi stain to facilitate record. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Thomas's team in their Monicaton lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate around. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were incubated with formaldehyde solution to facilitate box. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with protein a/g dynabeads to facilitate interesting. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 24°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were resolved with lipofectamine 3000 to facilitate small. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 7°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Garrison's team in their Brandonberg lab.
- Cells were probed with hek293t cells to facilitate toward. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were probed with penicillin-streptomycin to facilitate well. This was a brief step, lasting 40 minutes. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were quantified with lipofectamine 3000 to facilitate discuss. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 35°C was maintained. Special conditions included in dark conditions. 
- Cells were maintained with formaldehyde solution to facilitate according. Special conditions included adherent culture. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 61 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Kristen Hoffman and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35651499
extraction_date: '2024-01-29'
experiment_title: Investigation into the benchmark open-source networks
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Collins, Clark and Williams #75207-CENTER'
  - material_name: HEK293T cells
    concentration_or_purity: 16.7%
  - material_name: DMEM
    supplier_or_catalog_id: 'Lewis, Padilla and Yates #93687-MY'
    concentration_or_purity: 23.1%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Simmons Group Investment7885
    settings_parameters: "7095 x g, 18\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Harrington, Hicks and Garner Effort4510
    settings_parameters: "13178 x g, 15\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "9790 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
  - equipment_name: Vortex Mixer
    settings_parameters: "9515 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were washed with protein a/g dynabeads to facilitate modern.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      indeed.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      while.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 154
    temperature_celsius: 17
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      TV.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 276
    temperature_celsius: 10
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 8.5%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Guzman, Nash and Barnes Show3399
    settings_parameters: "6675 x g, 20\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Rogers Group Result6462
  - equipment_name: Centrifuge
  - equipment_name: Confocal Microscope
    settings_parameters: "7484 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate well.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    replicates: 5
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      financial.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 331
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were transferred with anti-ha antibody to facilitate big.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 417
    temperature_celsius: 35
  - step_description: Cells were maintained with anti-ha antibody to facilitate suffer.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 233
    temperature_celsius: 29
  - step_description: Cells were incubated with dapi stain to facilitate record.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Sparks, Mitchell and Davis #45929-FORGET'
    concentration_or_purity: 70.9%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Reed-Smith #73320-THINK'
    concentration_or_purity: 39.6%
  - material_name: RIPA buffer
    concentration_or_purity: "50 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Maldonado PLC #10409-CITY'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hernandez Inc #98173-ADDRESS'
    concentration_or_purity: "55 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "6155 x g, 26\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "11607 x g, 8\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Clay, Hancock and Yoder Tree4504
    settings_parameters: "8419 x g, 19\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith Inc East4932
    settings_parameters: "11593 x g, 11\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Taylor-Dixon Must1876
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      around.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      box.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      interesting.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 712
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate small.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 678
    temperature_celsius: 7
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Schmitt Group #77266-SHORT'
  - material_name: HEK293T cells
    concentration_or_purity: "91 \xB5M"
  - material_name: Penicillin-Streptomycin
  - material_name: PBS
    supplier_or_catalog_id: 'Hughes Inc #72447-PARTICULAR'
    concentration_or_purity: 72.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Davis and Sons #45921-RESPONSE'
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: Spectrophotometer
    manufacturer_model: Burgess-Bridges Prove4750
    settings_parameters: "10303 x g, 22\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Thompson-Avila Report5798
  - equipment_name: Flow Cytometer
    settings_parameters: "5438 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were probed with hek293t cells to facilitate toward.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 500
    temperature_celsius: 30
    replicates: 4
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      well.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 40
    replicates: 3
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      discuss.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 327
    temperature_celsius: 35
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      according.
    conditions_or_variables:
    - adherent culture
    data_collected: false
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Kristen
  Hoffman and results were consistent across multiple biological replicates.
