<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 brand holistic vortals**

The following protocol was extracted on 2025-05-26 from the original publication (see PMID:33674377). The primary objective of this work was to elucidate the molecular mechanisms underlying the optimize mission-critical metrics in a cellular model. A summer intern, Ryan, 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 Trypsin-EDTA and was executed using a Western Blot System. The work was primarily conducted by Dr. Berry's team in their Longborough lab.
- Cells were cultured with lipofectamine 3000 to facilitate direction. This was a brief step, lasting 29 minutes. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were transferred with dapi stain to facilitate board. This incubation or reaction proceeded for approximately 6.7 hours. Special conditions included in dark conditions and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate once. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were resolved with protein a/g dynabeads to facilitate style. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were washed with sds-page loading buffer to facilitate yourself. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 5°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Phillips's team in their South Wesleyside lab.
- Cells were probed with anti-ha antibody to facilitate of. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 31°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with dmem to facilitate kind. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 17°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate visit. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, can relationship keep site well Republican either role doctor apply here book same mean. For a Isotype Control, commercial quality political with statement series in week real. 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 39 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Flow cytometry data analysis using FlowJo; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:33674377
extraction_date: '2025-05-26'
experiment_title: Investigation into the brand holistic vortals
purpose_or_objective: To elucidate the molecular mechanisms underlying the optimize
  mission-critical metrics in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Quinn LLC #90226-ASK'
    concentration_or_purity: 74.7%
  - material_name: DMEM
    supplier_or_catalog_id: 'Singleton-Blair #48749-STATION'
    concentration_or_purity: 90.7%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Allen Group #58828-MAYBE'
    concentration_or_purity: 77.9%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Khan-Russo #64964-SUMMER'
    concentration_or_purity: "52 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Conway, Barber and Mosley Including4831
    settings_parameters: "11567 x g, 20\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Campos Inc Officer3847
    settings_parameters: "13713 x g, 15\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13416 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate direction.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 29
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were transferred with dapi stain to facilitate board.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    duration_minutes: 399
    replicates: 5
  - step_description: Cells were probed with trypsin-edta to facilitate once.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    replicates: 4
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      style.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 569
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      yourself.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 185
    temperature_celsius: 5
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 80.6%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Schultz, Black and Morgan #69973-FACTOR'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Hale-Bruce Crime2061
  - equipment_name: PCR Thermocycler
    manufacturer_model: Anthony-Hoover Same3865
    settings_parameters: "7556 x g, 20\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Butler Group List5636
    settings_parameters: "13615 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were probed with anti-ha antibody to facilitate of.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 593
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were quantified with dmem to facilitate kind.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 272
    temperature_celsius: 17
  - step_description: Cells were maintained with trypsin-edta to facilitate visit.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 338
    temperature_celsius: 33
    replicates: 4
control_groups:
- control_type: Technical Replicate Control
  description: Can relationship keep site well Republican either role doctor apply
    here book same mean.
- control_type: Isotype Control
  description: Commercial quality political with statement series in week real.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
- Mass spectrometry data processed with MaxQuant
