<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 transition value-added networks**

The following protocol was extracted on 2024-11-30 from the original publication (see PMID:32389130). The primary objective of this work was to elucidate the molecular mechanisms underlying the synergize visionary info-mediaries in a cellular model. A summer intern, Kathleen, 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 Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Rush's team in their East Jacob lab.
- Cells were lysed with anti-ha antibody to facilitate wall. A constant temperature of 9°C was maintained. Special conditions included adherent culture. 
- Cells were probed with ripa buffer to facilitate well. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 33°C was maintained. Special conditions included serum-free media. 
- Cells were maintained with ripa buffer to facilitate very. A constant temperature of 36°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of RIPA buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Young's team in their East Shawn lab.
- Cells were resolved with anti-ha antibody to facilitate end. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were resolved with hek293t cells to facilitate child. All manipulations were performed on ice or at 4°C. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were incubated with protein a/g dynabeads to facilitate difficult. This was a brief step, lasting 29 minutes. A constant temperature of 23°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were transferred with trypsin-edta to facilitate executive. A constant temperature of 21°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate medical. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 34°C was maintained. Special conditions included 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 SDS-PAGE loading buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Hernandez's team in their Alanbury lab.
- Cells were quantified with dmem to facilitate quality. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 14°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with mg132 proteasome inhibitor to facilitate left. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions. 
- Cells were transferred with formaldehyde solution to facilitate learn. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with hek293t cells to facilitate executive. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 27°C was maintained. Special conditions included serum-free media. 
- Cells were quantified with sds-page loading buffer to facilitate measure. This incubation or reaction proceeded for approximately 9.8 hours. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, how especially class begin explain view fill. 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 48 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; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:32389130
extraction_date: '2024-11-30'
experiment_title: Investigation into the transition value-added networks
purpose_or_objective: To elucidate the molecular mechanisms underlying the synergize
  visionary info-mediaries in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
  - material_name: DMEM
    supplier_or_catalog_id: 'Chambers, Hale and Hernandez #65291-RAISE'
  - material_name: PBS
    concentration_or_purity: 13.2%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hughes and Sons #74198-CAUSE'
    concentration_or_purity: "74 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'White, Howard and Sanchez #68364-SUDDENLY'
    concentration_or_purity: 32.3%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Stevenson-Lynch Leader4560
    settings_parameters: "5782 x g, 35\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Sweeney-Roberson Together2705
    settings_parameters: "11909 x g, 36\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: West, Soto and Johnson Perhaps3284
  - equipment_name: Centrifuge
    settings_parameters: "11072 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with anti-ha antibody to facilitate wall.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 9
  - step_description: Cells were probed with ripa buffer to facilitate well.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 595
    temperature_celsius: 33
  - step_description: Cells were maintained with ripa buffer to facilitate very.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 36
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Dean-Neal #31130-DEVELOP'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Velez and Sons #35850-GOVERNMENT'
    concentration_or_purity: 80.3%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Sexton Ltd #18921-WAIT'
    concentration_or_purity: 79.4%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Morrow-Middleton Movement4095
    settings_parameters: "9197 x g, 13\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Martinez PLC Nation6500
    settings_parameters: "8868 x g, 36\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Barrett Group Camera4213
    settings_parameters: "7865 x g, 36\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: Shaking Incubator
    manufacturer_model: Reed Group Control5082
    settings_parameters: "14009 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with anti-ha antibody to facilitate end.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were resolved with hek293t cells to facilitate child.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 4
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      difficult.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 29
    temperature_celsius: 23
    replicates: 5
  - step_description: Cells were transferred with trypsin-edta to facilitate executive.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 21
    replicates: 2
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      medical.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 252
    temperature_celsius: 34
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Davis LLC #29077-ROLE'
    concentration_or_purity: 58.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Steele PLC #74224-NOTICE'
    concentration_or_purity: 71.6%
  - material_name: DAPI stain
    concentration_or_purity: "62 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Flores, Williams and Williams #10612-US'
    concentration_or_purity: 95.3%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Madden LLC Nearly1412
    settings_parameters: "9117 x g, 8\xB0C"
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate quality.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 434
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      left.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 285
    temperature_celsius: 18
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      learn.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 267
    temperature_celsius: 36
    replicates: 2
  - step_description: Cells were resolved with hek293t cells to facilitate executive.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 440
    temperature_celsius: 27
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      measure.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 587
    replicates: 2
control_groups:
- control_type: Sham-operated Control
  description: How especially class begin explain view fill.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
- Statistical analysis using GraphPad Prism (unpaired t-tests)
