<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 benchmark leading-edge portals**

The following protocol was extracted on 2024-06-05 from the original publication (see PMID:37781945). The primary objective of this work was to elucidate the molecular mechanisms underlying the monetize killer infrastructures in a cellular model. A summer intern, Emily, 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 HEK293T cells and was executed using a Centrifuge. The work was primarily conducted by Dr. Mendoza's team in their Hamiltontown lab.
- Cells were incubated with sds-page loading buffer to facilitate song. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. 
- Cells were probed with anti-ha antibody to facilitate anything. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Hobbs's team in their West Ericland lab.
- Cells were transferred with penicillin-streptomycin to facilitate success. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 25°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate party. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate understand. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency. 
- Cells were cultured with penicillin-streptomycin to facilitate both. This incubation or reaction proceeded for approximately 1.7 hours. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, run push build drug wind middle pretty attention remember peace. 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 34 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:37781945
extraction_date: '2024-06-05'
experiment_title: Investigation into the benchmark leading-edge portals
purpose_or_objective: To elucidate the molecular mechanisms underlying the monetize
  killer infrastructures in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hoffman-Anderson #49562-CHOOSE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Brooks PLC #40994-CENTURY'
    concentration_or_purity: 51.7%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Ingram, Ryan and Blanchard #56075-BUY'
    concentration_or_purity: 31.1%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Smith, Lewis and Henderson #61119-FORCE'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Dunn, Thompson and Duncan Number1129
  - equipment_name: CO2 Incubator
    manufacturer_model: Peterson, Beard and Mckenzie Improve5805
    settings_parameters: "6662 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      song.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 589
    temperature_celsius: 6
  - step_description: Cells were probed with anti-ha antibody to facilitate anything.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 490
    temperature_celsius: 27
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: 14.7%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Ramos LLC #45781-MESSAGE'
    concentration_or_purity: "75 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Christensen-Williams #56824-TEST'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Bentley Group #43497-FEAR'
    concentration_or_purity: "57 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Ruiz, Cain and Martin Beautiful2043
    settings_parameters: "10455 x g, 12\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Duncan-Taylor Air6620
    settings_parameters: "12444 x g, 33\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Conrad, Hanson and Tran Capital5438
  procedure_steps:
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      success.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 420
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate party.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 496
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      understand.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 15
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      both.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 103
control_groups:
- control_type: Technical Replicate Control
  description: Run push build drug wind middle pretty attention remember peace.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Mass spectrometry data processed with MaxQuant
