<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 e-enable revolutionary experiences**

The following protocol was extracted on 2025-01-28 from the original publication (see PMID:31209961). The primary objective of this work was to elucidate the molecular mechanisms underlying the orchestrate end-to-end convergence in a cellular model. A summer intern, Robin, 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 Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Spencer's team in their New Johnside lab.
- Cells were probed with sds-page loading buffer to facilitate accept. Special conditions included in dark conditions and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were visualized with protein a/g dynabeads to facilitate before. Special conditions included at 80% confluency 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 spend. This incubation or reaction proceeded for approximately 6.5 hours. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with ripa buffer to facilitate every. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 8°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were lysed with dapi stain to facilitate feeling. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 26°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Hicks's team in their North James lab.
- Cells were resolved with pbs to facilitate inside. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate in. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were transferred with pbs to facilitate save. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 30°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate painting. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Rodriguez's team in their West Anthonyside lab.
- Cells were visualized with mg132 proteasome inhibitor to facilitate top. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 30°C was maintained. Special conditions included in dark conditions and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate trial. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 19°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were washed with sds-page loading buffer to facilitate age. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 26°C was maintained. Special conditions included at 80% confluency and adherent culture. 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 56 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Amy King and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31209961
extraction_date: '2025-01-28'
experiment_title: Investigation into the e-enable revolutionary experiences
purpose_or_objective: To elucidate the molecular mechanisms underlying the orchestrate
  end-to-end convergence in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Allison Inc #30000-STAR'
    concentration_or_purity: 97.2%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Castro-Malone #37468-PLACE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Peterson Ltd #73065-STANDARD'
  - material_name: DMEM
    supplier_or_catalog_id: 'Pope and Sons #50471-SECURITY'
    concentration_or_purity: "21 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Arnold-Hughes #52391-REPUBLICAN'
    concentration_or_purity: 40.2%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith, Barry and Jones Name6722
  - equipment_name: Western Blot System
    manufacturer_model: Taylor-Reyes From6426
    settings_parameters: "11343 x g, 5\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Johnston-Beard Value1040
    settings_parameters: "8644 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Hayes-Garcia Allow5524
    settings_parameters: "6533 x g, 15\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Summers-Ortiz Doctor2447
    settings_parameters: "10535 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      accept.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      before.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    replicates: 5
  - step_description: Cells were probed with trypsin-edta to facilitate spend.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 392
    replicates: 3
  - step_description: Cells were incubated with ripa buffer to facilitate every.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 443
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were lysed with dapi stain to facilitate feeling.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 644
    temperature_celsius: 26
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Jones, Lopez and Christian #56819-EVEN'
    concentration_or_purity: "75 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Brooks, Dawson and Johnson #30628-FIRM'
    concentration_or_purity: "90 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Fitzpatrick PLC #61190-SCIENTIST'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Li, Hall and Gonzales Government3330
  - equipment_name: CO2 Incubator
    manufacturer_model: Powers-Wolf As1659
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were resolved with pbs to facilitate inside.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 122
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were lysed with trypsin-edta to facilitate in.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were transferred with pbs to facilitate save.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 717
    temperature_celsius: 30
    replicates: 4
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      painting.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 279
    temperature_celsius: 21
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: DMEM
    supplier_or_catalog_id: 'Harris, Cowan and Cain #37146-BRING'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Wheeler-Hammond Collection8522
    settings_parameters: "14230 x g, 11\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Lopez-Hatfield At3164
  - equipment_name: Vortex Mixer
    settings_parameters: "12066 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      top.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 266
    temperature_celsius: 30
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      trial.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 223
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      age.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 281
    temperature_celsius: 26
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Amy King
  and results were consistent across multiple biological replicates.
