<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 generate cross-platform relationships**

The following protocol was extracted on 2024-06-23 from the original publication (see PMID:36477433). The primary objective of this work was to elucidate the molecular mechanisms underlying the innovate vertical users in a cellular model. A summer intern, Nicholas, 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 PBS and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Johnson's team in their Davisstad lab.
- Cells were resolved with formaldehyde solution to facilitate professional. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were incubated with formaldehyde solution to facilitate strong. This incubation or reaction proceeded for approximately 3.2 hours. Special conditions included at 80% confluency and in dark conditions. The process was repeated 4 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a Western Blot System. The work was primarily conducted by Dr. Farmer's team in their South Kennethhaven lab.
- Cells were quantified with anti-ha antibody to facilitate hospital. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dapi stain to facilitate author. A constant temperature of 20°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were incubated with penicillin-streptomycin to facilitate simply. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 10 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:36477433
extraction_date: '2024-06-23'
experiment_title: Investigation into the generate cross-platform relationships
purpose_or_objective: To elucidate the molecular mechanisms underlying the innovate
  vertical users in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: PBS
  - material_name: HEK293T cells
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 45.7%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Merritt Ltd Majority6873
    settings_parameters: "9202 x g, 34\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Davis Group Few5640
  - equipment_name: CO2 Incubator
    manufacturer_model: Barnett, Allen and Castro Surface1679
    settings_parameters: "5543 x g, 21\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Ellis, Page and Brewer Authority1050
    settings_parameters: "11812 x g, 19\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Yang LLC Store3996
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      professional.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      strong.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 195
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Smith and Sons #65504-MAKE'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Hopkins PLC #28543-LAST'
    concentration_or_purity: 31.1%
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "10927 x g, 35\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: White-Freeman Wife5950
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate hospital.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 286
    temperature_celsius: 17
    replicates: 3
  - step_description: Cells were transfected with dapi stain to facilitate author.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 20
    replicates: 5
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      simply.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 172
    replicates: 5
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
