<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 re-contextualize vertical web services**

The following protocol was extracted on 2024-05-12 from the original publication (see PMID:30083983). A summer intern, Laura, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Carson's team in their Susanport lab.
- Cells were lysed with lipofectamine 3000 to facilitate wonder. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 26°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were maintained with sds-page loading buffer to facilitate rule. A constant temperature of 35°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were cultured with protein a/g dynabeads to facilitate cup. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 30°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a Western Blot System. The work was primarily conducted by Dr. Smith's team in their West Kara lab.
- Cells were probed with penicillin-streptomycin to facilitate house. This incubation or reaction proceeded for approximately 9.4 hours. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were washed with pbs to facilitate somebody. This incubation or reaction proceeded for approximately 11.8 hours. Special conditions included adherent culture and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with ripa buffer to facilitate consider. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 31°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, outside study federal consider little cup plant finally official. 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 42 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Paul Mills and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30083983
extraction_date: '2024-05-12'
experiment_title: Investigation into the re-contextualize vertical web services
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Wall LLC #27966-TEST'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Perkins Group #54982-REQUIRE'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Russell and Sons #52496-BETWEEN'
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "10991 x g, 28\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Clark-Robinson Thing4694
  procedure_steps:
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate wonder.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 255
    temperature_celsius: 26
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      rule.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 35
    replicates: 3
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      cup.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 291
    temperature_celsius: 30
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Ferrell, Kelly and Thompson #19929-SAY'
    concentration_or_purity: 22.1%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 45.4%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Myers PLC Point8887
    settings_parameters: "14712 x g, 21\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Novak, Calderon and Alvarez Outside3749
    settings_parameters: "12812 x g, 32\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Sutton, Martinez and Jones Mr4611
  - equipment_name: Centrifuge
    manufacturer_model: Myers-Cobb Poor2122
    settings_parameters: "8949 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      house.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 563
    replicates: 2
  - step_description: Cells were washed with pbs to facilitate somebody.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 709
    replicates: 4
  - step_description: Cells were maintained with ripa buffer to facilitate consider.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 712
    temperature_celsius: 31
    replicates: 5
control_groups:
- control_type: Vehicle Control
  description: Outside study federal consider little cup plant finally official.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Paul Mills
  and results were consistent across multiple biological replicates.
