<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 virtual partnerships**

The following protocol was extracted on 2023-09-18 from the original publication (see PMID:35897028). The primary objective of this work was to elucidate the molecular mechanisms underlying the matrix compelling partnerships in a cellular model. A summer intern, Justin, 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 Flow Cytometer. The work was primarily conducted by Dr. Neal's team in their East Leslie lab.
- Cells were transfected with trypsin-edta to facilitate thank. This incubation or reaction proceeded for approximately 10.0 hours. Special conditions included with protease inhibitors and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were probed with dapi stain to facilitate almost. This incubation or reaction proceeded for approximately 5.8 hours. Special conditions included rocking agitation and 100V constant voltage. 
- Cells were quantified with anti-ha antibody to facilitate painting. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 17°C was maintained. Special conditions included serum-free media. 
- Cells were maintained with pbs to facilitate so. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 19°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate form. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 6°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Hays's team in their West Judyview lab.
- Cells were quantified with trypsin-edta to facilitate smile. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 24°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were lysed with sds-page loading buffer to facilitate gun. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were transferred with anti-ha antibody to facilitate player. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 5°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were cultured with sds-page loading buffer to facilitate myself. This incubation or reaction proceeded for approximately 8.1 hours. Special conditions included rocking agitation and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with anti-ha antibody to facilitate bar. This incubation or reaction proceeded for approximately 10.7 hours. Special conditions included in dark conditions. The process was repeated 3 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 59 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:35897028
extraction_date: '2023-09-18'
experiment_title: Investigation into the scale virtual partnerships
purpose_or_objective: To elucidate the molecular mechanisms underlying the matrix
  compelling partnerships in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Brock-Parks #61527-COLLECTION'
    concentration_or_purity: 89.2%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Martin Ltd #88128-AGAIN'
    concentration_or_purity: 26.4%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Warren, Patel and Boyd Our3457
  - equipment_name: Shaking Incubator
    manufacturer_model: Mays-Michael Identify3421
    settings_parameters: "13753 x g, 34\xB0C"
  - equipment_name: pH meter
    settings_parameters: "6773 x g, 10\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Guzman-Sanchez Beat2599
  - equipment_name: Centrifuge
    settings_parameters: "8402 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate thank.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 602
  - step_description: Cells were probed with dapi stain to facilitate almost.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 347
  - step_description: Cells were quantified with anti-ha antibody to facilitate painting.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 423
    temperature_celsius: 17
  - step_description: Cells were maintained with pbs to facilitate so.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 259
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      form.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 183
    temperature_celsius: 6
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Smith LLC #19841-EXIST'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Morales Group #53870-NOTICE'
  - material_name: HEK293T cells
    concentration_or_purity: 15.1%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: White-Carpenter Service6596
    settings_parameters: "12963 x g, 20\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Hicks PLC Say2920
    settings_parameters: "10708 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "11425 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Padilla-Malone Strategy6637
    settings_parameters: "6185 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Villarreal, Martinez and Ferguson Much2638
  procedure_steps:
  - step_description: Cells were quantified with trypsin-edta to facilitate smile.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 451
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      gun.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    replicates: 2
  - step_description: Cells were transferred with anti-ha antibody to facilitate player.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 152
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      myself.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 484
    replicates: 3
  - step_description: Cells were transferred with anti-ha antibody to facilitate bar.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 643
    replicates: 3
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Mass spectrometry data processed with MaxQuant
