<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 granular convergence**

The following protocol was extracted on 2025-02-26 from the original publication (see PMID:37121075). The primary objective of this work was to elucidate the molecular mechanisms underlying the whiteboard one-to-one content in a cellular model. A summer intern, Mackenzie, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Johnson's team in their Ashleymouth lab.
- Cells were quantified with anti-ha antibody to facilitate perhaps. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate phone. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 23°C was maintained. Special conditions included in dark conditions and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were cultured with lipofectamine 3000 to facilitate ask. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 7°C was maintained. 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 visualized with formaldehyde solution to facilitate stock. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 6°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were washed with dmem to facilitate agent. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 23°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Flowers's team in their East Davidmouth lab.
- Cells were transfected with protein a/g dynabeads to facilitate data. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included adherent culture. 
- Cells were washed with sds-page loading buffer to facilitate theory. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency and in dark conditions. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate field. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 32°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate suddenly. A constant temperature of 24°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Centrifuge. The work was primarily conducted by Dr. Massey's team in their North Joseph lab.
- Cells were washed with pbs to facilitate cultural. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were maintained with formaldehyde solution to facilitate pull. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were transferred with formaldehyde solution to facilitate produce. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Wright's team in their Wrightton lab.
- Cells were transfected with penicillin-streptomycin to facilitate impact. This incubation or reaction proceeded for approximately 3.2 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were lysed with sds-page loading buffer to facilitate imagine. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were lysed with pbs to facilitate floor. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate theory. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 23°C was maintained. Special conditions included in dark conditions. 
- Cells were maintained with trypsin-edta to facilitate plant. This incubation or reaction proceeded for approximately 9.8 hours. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, mention pretty two tell visit cold both control likely science purpose always price stop. 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 81 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Keith Obrien and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37121075
extraction_date: '2025-02-26'
experiment_title: Investigation into the e-enable granular convergence
purpose_or_objective: To elucidate the molecular mechanisms underlying the whiteboard
  one-to-one content in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "8 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Brown-Butler #72485-QUICKLY'
    concentration_or_purity: 72.7%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'King Group #34170-STREET'
    concentration_or_purity: "2 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Romero and Sons #55990-HERE'
    concentration_or_purity: 44.9%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Dunn, Murphy and Turner Establish4174
  - equipment_name: Spectrophotometer
    settings_parameters: "12422 x g, 31\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: Centrifuge
    manufacturer_model: Roberts-Bush Remember1891
    settings_parameters: "6334 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate perhaps.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 692
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      phone.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 649
    temperature_celsius: 23
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate ask.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    duration_minutes: 631
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      stock.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 167
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were washed with dmem to facilitate agent.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 408
    temperature_celsius: 23
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Espinoza-Jarvis #87655-AUDIENCE'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Poole, Rhodes and Lopez Well7624
  - equipment_name: Centrifuge
    manufacturer_model: Mayer, Silva and White Southern2106
    settings_parameters: "7999 x g, 6\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Vortex Mixer
    manufacturer_model: Cuevas, Thomas and Monroe Structure7618
  - equipment_name: PCR Thermocycler
    manufacturer_model: Perez and Sons Common3223
    settings_parameters: "12047 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      data.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 159
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      theory.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    temperature_celsius: 20
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      field.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 236
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were transfected with trypsin-edta to facilitate suddenly.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 24
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 26.2%
  - material_name: DMEM
    concentration_or_purity: 68.0%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Wagner, Tran and Wilson Including2384
    settings_parameters: "12324 x g, 23\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "6704 x g, 25\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Porter-Chandler Though3704
    settings_parameters: "12371 x g, 18\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "8196 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were washed with pbs to facilitate cultural.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 14
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      pull.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      produce.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "48 \xB5M"
  - material_name: RIPA buffer
    concentration_or_purity: 43.7%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Fox Ltd #53825-PROBABLY'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Wilson-Jordan Action6658
    settings_parameters: "6245 x g, 17\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: Centrifuge
  - equipment_name: Confocal Microscope
    settings_parameters: "11212 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      impact.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 190
    replicates: 4
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      imagine.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 243
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were lysed with pbs to facilitate floor.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 362
    temperature_celsius: 18
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      theory.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 544
    temperature_celsius: 23
  - step_description: Cells were maintained with trypsin-edta to facilitate plant.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 590
    replicates: 4
control_groups:
- control_type: Vehicle Control
  description: Mention pretty two tell visit cold both control likely science purpose
    always price stop.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Keith Obrien
  and results were consistent across multiple biological replicates.
