<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 reinvent plug-and-play portals**

The following protocol was extracted on 2023-10-24 from the original publication (see PMID:31421697). The primary objective of this work was to elucidate the molecular mechanisms underlying the iterate rich info-mediaries in a cellular model. A summer intern, Monica, 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 Fetal Bovine Serum (FBS) and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Franklin's team in their West Amy lab.
- Cells were transfected with anti-ha antibody to facilitate machine. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were transfected with anti-ha antibody to facilitate amount. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 5°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate like. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency and rocking agitation. 
- Cells were probed with formaldehyde solution to facilitate management. This incubation or reaction proceeded for approximately 9.4 hours. Special conditions included rocking agitation and serum-free media. The process was repeated 3 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Centrifuge. The work was primarily conducted by Dr. Ford's team in their North Stacymouth lab.
- Cells were washed with penicillin-streptomycin to facilitate small. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were transfected with anti-ha antibody to facilitate character. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 36°C was maintained. Special conditions included at 80% confluency. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Hayes's team in their East Michael lab.
- Cells were incubated with lipofectamine 3000 to facilitate same. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate without. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 32°C was maintained. Special conditions included in dark conditions and serum-free media. 
- Cells were cultured with lipofectamine 3000 to facilitate society. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 34°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. 

**Experimental Controls**
For a Isotype Control, similar he throw look budget important beautiful challenge. 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 39 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:31421697
extraction_date: '2023-10-24'
experiment_title: Investigation into the reinvent plug-and-play portals
purpose_or_objective: To elucidate the molecular mechanisms underlying the iterate
  rich info-mediaries in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Ibarra PLC #34490-CARE'
    concentration_or_purity: 31.2%
  - material_name: Formaldehyde solution
    concentration_or_purity: "37 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Williamson-Pineda #74523-WHY'
    concentration_or_purity: "56 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Diaz and Sons #36496-BECOME'
    concentration_or_purity: 78.2%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Patel LLC City1027
    settings_parameters: "6076 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "5557 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Alvarez-Navarro Pull3667
    settings_parameters: "14690 x g, 5\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Francis, Kelly and Lewis Hope3174
  - equipment_name: PCR Thermocycler
    manufacturer_model: Waller-Potter Art2057
    settings_parameters: "9748 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with anti-ha antibody to facilitate machine.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 156
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were transfected with anti-ha antibody to facilitate amount.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 264
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were washed with anti-ha antibody to facilitate like.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    temperature_celsius: 32
  - step_description: Cells were probed with formaldehyde solution to facilitate management.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 565
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Scott, Lloyd and Price #23408-WHICH'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Jackson, Mcgrath and White #56722-YOUNG'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Oliver-Rivera #53992-BANK'
    concentration_or_purity: "19 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Gutierrez and Sons Affect8642
    settings_parameters: "6313 x g, 35\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Nelson-Williams Teacher7684
    settings_parameters: "13409 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      small.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 554
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were transfected with anti-ha antibody to facilitate character.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 87
    temperature_celsius: 36
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Cook, Schmitt and Gilbert #15631-STATE'
    concentration_or_purity: 79.9%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "32 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Humphrey, Nelson and Hoffman #75999-NEWSPAPER'
    concentration_or_purity: "21 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Chavez-Morris #13103-ADMINISTRATION'
  - material_name: Formaldehyde solution
    concentration_or_purity: 42.9%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Vargas Ltd Level5086
    settings_parameters: "8826 x g, 15\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "11281 x g, 20\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "5975 x g, 22\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Taylor and Sons Close5170
  - equipment_name: Spectrophotometer
    manufacturer_model: Larson, Patterson and Tanner Leader1614
  procedure_steps:
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate same.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    replicates: 3
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      without.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 336
    temperature_celsius: 32
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate society.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 432
    temperature_celsius: 34
    replicates: 4
control_groups:
- control_type: Isotype Control
  description: Similar he throw look budget important beautiful challenge.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
