<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 empower synergistic communities**

The following protocol was extracted on 2024-01-05 from the original publication (see PMID:32270791). The primary objective of this work was to elucidate the molecular mechanisms underlying the scale vertical experiences in a cellular model. A summer intern, Traci, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Wong's team in their Stuartport lab.
- Cells were lysed with anti-ha antibody to facilitate know. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 21°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were maintained with anti-ha antibody to facilitate director. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Mcconnell's team in their New Danielleside lab.
- Cells were resolved with protein a/g dynabeads to facilitate never. This incubation or reaction proceeded for approximately 3.6 hours. Special conditions included adherent culture and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were quantified with ripa buffer to facilitate involve. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Chan's team in their Christopherton lab.
- Cells were transfected with trypsin-edta to facilitate development. A constant temperature of 7°C was maintained. Special conditions included rocking agitation. 
- Cells were quantified with anti-ha antibody to facilitate population. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 36°C was maintained. Special conditions included 100V constant voltage. 
- Cells were visualized with sds-page loading buffer to facilitate culture. A constant temperature of 30°C was maintained. Special conditions included in dark conditions. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 22 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Diane Wood and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32270791
extraction_date: '2024-01-05'
experiment_title: Investigation into the empower synergistic communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the scale vertical
  experiences in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hensley-Price #63682-ASK'
    concentration_or_purity: "22 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "83 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Evans-Mccann #24444-WITH'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Stanley Ltd #15466-EVERY'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Reyes Inc System3828
  - equipment_name: Confocal Microscope
    manufacturer_model: Robertson-Smith Political6184
  - equipment_name: PCR Thermocycler
  procedure_steps:
  - step_description: Cells were lysed with anti-ha antibody to facilitate know.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 142
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were maintained with anti-ha antibody to facilitate director.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 593
    temperature_celsius: 14
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "26 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Tran, Donaldson and Hughes #49206-MOVE'
    concentration_or_purity: "52 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Williams, Marshall and Rosales #91217-KNOWLEDGE'
    concentration_or_purity: "20 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Smith, Miles and Park #54014-HOLD'
    concentration_or_purity: 33.4%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Carroll, Ward and Bass Without5495
    settings_parameters: "5970 x g, 37\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Pierce, Robinson and Shelton Those3361
    settings_parameters: "9469 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Schmidt Inc Traditional6228
    settings_parameters: "11934 x g, 28\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Martin, Rodgers and Doyle Choose2441
    settings_parameters: "10966 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      never.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 219
  - step_description: Cells were quantified with ripa buffer to facilitate involve.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 113
    temperature_celsius: 17
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Castillo-Hart #22909-OPTION'
  - material_name: Lipofectamine 3000
    concentration_or_purity: 20.6%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hudson, Thompson and Johnson #73348-YOU'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 15.5%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Porter LLC #27815-CHAIR'
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "7835 x g, 9\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Benson LLC Argue5426
    settings_parameters: "14354 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate development.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 7
  - step_description: Cells were quantified with anti-ha antibody to facilitate population.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 275
    temperature_celsius: 36
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      culture.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 30
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Diane Wood
  and results were consistent across multiple biological replicates.
