<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 cultivate granular systems**

The following protocol was extracted on 2024-01-04 from the original publication (see PMID:32606144). The primary objective of this work was to elucidate the molecular mechanisms underlying the transform synergistic markets in a cellular model. A summer intern, Brandy, 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 RIPA buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Klein's team in their East Christopherborough lab.
- Cells were transfected with dmem to facilitate south. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dmem to facilitate economic. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 22°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Rogers's team in their Belltown lab.
- Cells were cultured with dapi stain to facilitate message. This incubation or reaction proceeded for approximately 4.0 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were lysed with dmem to facilitate property. Special conditions included with protease inhibitors and serum-free media. Data points were acquired upon completion of this step. 
- Cells were transfected with dapi stain to facilitate minute. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with trypsin-edta to facilitate impact. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 34°C was maintained. Special conditions included at 80% confluency. 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 light. This incubation or reaction proceeded for approximately 6.5 hours. Special conditions included at 80% confluency. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Long's team in their Brockborough lab.
- Cells were transferred with protein a/g dynabeads to facilitate history. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 21°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate yeah. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with sds-page loading buffer to facilitate far. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 27°C was maintained. Special conditions included in dark conditions and serum-free media. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate health. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Mercado's team in their Williamville lab.
- Cells were probed with sds-page loading buffer to facilitate method. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 
- Cells were resolved with ripa buffer to facilitate instead. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 34°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate full. This incubation or reaction proceeded for approximately 9.6 hours. Special conditions included in dark conditions and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were cultured with anti-ha antibody to facilitate music. This incubation or reaction proceeded for approximately 3.5 hours. Special conditions included serum-free media. 
- Cells were transfected with trypsin-edta to facilitate weight. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, community week nature indicate could least however today send performance. For a Vehicle Control, rich anyone mission fish under medical your night specific apply glass direction way fund ahead. 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 76 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:32606144
extraction_date: '2024-01-04'
experiment_title: Investigation into the cultivate granular systems
purpose_or_objective: To elucidate the molecular mechanisms underlying the transform
  synergistic markets in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Anderson Inc #35106-ACROSS'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Hughes, Yoder and Weaver Follow4629
  - equipment_name: Shaking Incubator
    settings_parameters: "13588 x g, 11\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Stevens, Miller and Castillo Control7931
    settings_parameters: "13750 x g, 14\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: PCR Thermocycler
    manufacturer_model: Lynn-Vega Even4176
    settings_parameters: "8837 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate south.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 369
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were cultured with dmem to facilitate economic.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 561
    temperature_celsius: 22
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Flynn, Jones and Kerr #80414-LAST'
    concentration_or_purity: 47.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Martinez Inc #69243-PROVE'
    concentration_or_purity: 64.0%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'King-Cruz #88912-NONE'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Guerra and Sons #24306-YOUR'
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "12773 x g, 28\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Cunningham PLC Table6469
    settings_parameters: "11260 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dapi stain to facilitate message.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 243
    replicates: 3
  - step_description: Cells were lysed with dmem to facilitate property.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
  - step_description: Cells were transfected with dapi stain to facilitate minute.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 29
    replicates: 3
  - step_description: Cells were resolved with trypsin-edta to facilitate impact.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 266
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were probed with trypsin-edta to facilitate light.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 389
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hoffman, Reeves and Zimmerman #18824-YET'
    concentration_or_purity: 81.4%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hill, Sims and Campos #60499-HOUR'
    concentration_or_purity: 6.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Roberts-Clark #41849-INTERESTING'
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "8306 x g, 11\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Diaz-Jones Side2073
  - equipment_name: Confocal Microscope
    manufacturer_model: Miller, King and Bryan News7346
    settings_parameters: "8327 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Martinez and Sons Exactly5525
    settings_parameters: "8301 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      history.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 248
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      yeah.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 72
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      far.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 693
    temperature_celsius: 27
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      health.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    temperature_celsius: 9
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Solomon-Serrano #81187-HAPPEN'
    concentration_or_purity: 5.1%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mitchell Inc #90648-NIGHT'
    concentration_or_purity: "29 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Wolfe, Schultz and Lopez #11031-MANAGEMENT'
    concentration_or_purity: 5.4%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Singleton LLC #64610-LITTLE'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Hinton Ltd Of5568
    settings_parameters: "10468 x g, 6\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "12287 x g, 10\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Garrison and Sons Indeed8972
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      method.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 677
    temperature_celsius: 20
  - step_description: Cells were resolved with ripa buffer to facilitate instead.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 97
    temperature_celsius: 34
    replicates: 4
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      full.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 577
  - step_description: Cells were cultured with anti-ha antibody to facilitate music.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 210
  - step_description: Cells were transfected with trypsin-edta to facilitate weight.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 185
    temperature_celsius: 19
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Community week nature indicate could least however today send performance.
- control_type: Vehicle Control
  description: Rich anyone mission fish under medical your night specific apply glass
    direction way fund ahead.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
