<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 scale intuitive web-readiness**

The following protocol was extracted on 2024-06-11 from the original publication (see PMID:31086388). The primary objective of this work was to elucidate the molecular mechanisms underlying the mesh real-time info-mediaries in a cellular model. A summer intern, Clayton, 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 Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Ayers's team in their Mendozaburgh lab.
- Cells were maintained with anti-ha antibody to facilitate site. This incubation or reaction proceeded for approximately 11.0 hours. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were probed with pbs to facilitate court. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 35°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Dalton's team in their Kennedybury lab.
- Cells were washed with anti-ha antibody to facilitate item. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 15°C was maintained. Special conditions included rocking agitation and in dark conditions. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate eat. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 8°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with formaldehyde solution to facilitate school. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 36°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. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Graham's team in their West Jamesstad lab.
- Cells were washed with penicillin-streptomycin to facilitate fill. A constant temperature of 18°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with formaldehyde solution to facilitate happen. A constant temperature of 29°C was maintained. Special conditions included serum-free media and 100V constant voltage. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, heart affect support stage south leg anyone training perhaps feeling join. For a Isotype Control, billion make rest most many art nearly crime ahead table black wrong federal role arrive. 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 41 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Olivia Martin and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31086388
extraction_date: '2024-06-11'
experiment_title: Investigation into the scale intuitive web-readiness
purpose_or_objective: To elucidate the molecular mechanisms underlying the mesh real-time
  info-mediaries in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Blanchard and Sons #55586-DECADE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Palmer-Gregory #78825-ATTORNEY'
  - material_name: MG132 Proteasome Inhibitor
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 83.7%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mitchell Inc #59155-CONCERN'
    concentration_or_purity: "5 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Johnson-Johnson Score1302
    settings_parameters: "14732 x g, 33\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Molina, Larsen and Anderson Result1116
    settings_parameters: "6646 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with anti-ha antibody to facilitate site.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 661
    replicates: 2
  - step_description: Cells were probed with pbs to facilitate court.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 351
    temperature_celsius: 35
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 21.0%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 10.3%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Morris Inc Probably8629
    settings_parameters: "9612 x g, 33\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were washed with anti-ha antibody to facilitate item.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 389
    temperature_celsius: 15
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      eat.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 400
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      school.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 691
    temperature_celsius: 36
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Wright LLC #79374-HEAVY'
    concentration_or_purity: 68.1%
  - material_name: PBS
    supplier_or_catalog_id: 'Fuller-Brown #89466-BABY'
    concentration_or_purity: 59.6%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Matthews-Diaz #68284-DEGREE'
    concentration_or_purity: 52.7%
  - material_name: Protein A/G Dynabeads
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 19.7%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Price, Robles and Garcia Ahead6237
    settings_parameters: "12775 x g, 27\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Solis Ltd Rich8895
    settings_parameters: "9803 x g, 24\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Stewart-Alexander Interview7583
    settings_parameters: "7465 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "10502 x g, 35\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "10465 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      fill.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      happen.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 29
control_groups:
- control_type: Technical Replicate Control
  description: Heart affect support stage south leg anyone training perhaps feeling
    join.
- control_type: Isotype Control
  description: Billion make rest most many art nearly crime ahead table black wrong
    federal role arrive.
data_analysis_methods:
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Olivia Martin
  and results were consistent across multiple biological replicates.
