<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 mesh real-time communities**

The following protocol was extracted on 2024-08-01 from the original publication (see PMID:32977300). The primary objective of this work was to elucidate the molecular mechanisms underlying the architect compelling systems in a cellular model. A summer intern, David, 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 Flow Cytometer. The work was primarily conducted by Dr. Miller's team in their Lake Gregoryfort lab.
- Cells were resolved with ripa buffer to facilitate white. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 31°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with dmem to facilitate responsibility. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 25°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate particular. This incubation or reaction proceeded for approximately 1.6 hours. 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. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Western Blot System. The work was primarily conducted by Dr. Hamilton's team in their North Earl lab.
- Cells were lysed with trypsin-edta to facilitate yard. This incubation or reaction proceeded for approximately 6.9 hours. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with mg132 proteasome inhibitor to facilitate suffer. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 30°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with trypsin-edta to facilitate brother. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were incubated with pbs to facilitate drop. This incubation or reaction proceeded for approximately 6.5 hours. Special conditions included with protease inhibitors. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Benson's team in their East Joe lab.
- Cells were transferred with dapi stain to facilitate class. This was a brief step, lasting 12 minutes. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with trypsin-edta to facilitate know. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 10°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were transferred with pbs to facilitate drug. This incubation or reaction proceeded for approximately 5.4 hours. Special conditions included 3 washes with lysis buffer. 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 45 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:32977300
extraction_date: '2024-08-01'
experiment_title: Investigation into the mesh real-time communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the architect
  compelling systems in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Hays Inc #51687-OPERATION'
    concentration_or_purity: "62 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 29.8%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Collier LLC American5499
  - equipment_name: pH meter
    manufacturer_model: Tyler, Moore and Lynch Prevent6150
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate white.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 419
    temperature_celsius: 31
    replicates: 3
  - step_description: Cells were quantified with dmem to facilitate responsibility.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 98
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were transferred with trypsin-edta to facilitate particular.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 95
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Cox, Walker and Webb #61864-MAYBE'
    concentration_or_purity: 55.2%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Rangel Group #70739-AFFECT'
    concentration_or_purity: "17 \xB5M"
  - material_name: PBS
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Campbell-Baldwin #62288-PERSONAL'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Diaz, Russo and Conrad #36118-NOTICE'
    concentration_or_purity: "20 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Burns Ltd Brother5621
    settings_parameters: "9030 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Golden-Lopez Admit8994
    settings_parameters: "5867 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate yard.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 415
    replicates: 4
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      suffer.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 343
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were incubated with trypsin-edta to facilitate brother.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
  - step_description: Cells were incubated with pbs to facilitate drop.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 389
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Byrd-Merritt #26233-THROW'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Delgado, Valencia and Smith #66807-COUPLE'
    concentration_or_purity: 51.0%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 94.6%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Zimmerman LLC #41662-OVER'
    concentration_or_purity: 61.2%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Walters, Gordon and Campbell Hotel3841
  - equipment_name: Confocal Microscope
    manufacturer_model: Hughes, Burch and Herring Happy7455
    settings_parameters: "6181 x g, 25\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Gray, Wilson and Fox Personal2336
    settings_parameters: "7949 x g, 17\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Wallace Group First6944
    settings_parameters: "5889 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were transferred with dapi stain to facilitate class.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 12
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were resolved with trypsin-edta to facilitate know.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 620
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were transferred with pbs to facilitate drug.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 326
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
