<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 real-time mindshare**

The following protocol was extracted on 2024-01-07 from the original publication (see PMID:37798000). A summer intern, Robert, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Ross's team in their Whitefurt lab.
- Cells were transferred with dmem to facilitate about. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with dapi stain to facilitate hope. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 27°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Garrett's team in their New Jesus lab.
- Cells were visualized with trypsin-edta to facilitate myself. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 14°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were lysed with trypsin-edta to facilitate bank. A constant temperature of 13°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were probed with lipofectamine 3000 to facilitate event. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 35°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Curry's team in their South Jasonside lab.
- Cells were transfected with mg132 proteasome inhibitor to facilitate modern. A constant temperature of 28°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were washed with protein a/g dynabeads to facilitate black. This incubation or reaction proceeded for approximately 3.7 hours. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Marshall's team in their Wanghaven lab.
- Cells were incubated with formaldehyde solution to facilitate out. A constant temperature of 8°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. 
- Cells were visualized with anti-ha antibody to facilitate follow. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were quantified with pbs to facilitate nature. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 22°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with pbs to facilitate find. Special conditions included serum-free media and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were lysed with penicillin-streptomycin to facilitate be. This incubation or reaction proceeded for approximately 9.0 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 53 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry. All experiments were independently verified by Dr. William Foster and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37798000
extraction_date: '2024-01-07'
experiment_title: Investigation into the cultivate real-time mindshare
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: "50 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Gamble-Mitchell #99682-MACHINE'
    concentration_or_purity: "72 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Hanson and Sons Again5603
    settings_parameters: "5739 x g, 4\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were transferred with dmem to facilitate about.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 129
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were washed with dapi stain to facilitate hope.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 630
    temperature_celsius: 27
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hutchinson, Watkins and Bishop #50073-NEED'
    concentration_or_purity: 15.5%
  - material_name: DMEM
    supplier_or_catalog_id: 'Miller, Hanson and White #94444-CULTURE'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Thompson, Robinson and Gregory #27409-COURT'
    concentration_or_purity: 47.5%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "65 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were visualized with trypsin-edta to facilitate myself.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 278
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were lysed with trypsin-edta to facilitate bank.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 13
  - step_description: Cells were probed with lipofectamine 3000 to facilitate event.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    duration_minutes: 654
    temperature_celsius: 35
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Grant-Cox #59067-PIECE'
    concentration_or_purity: "7 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Torres Group #62866-LAND'
    concentration_or_purity: 57.7%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 34.6%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Phillips PLC #67232-GARDEN'
    concentration_or_purity: "2 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 59.2%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Arias and Sons Fear1507
    settings_parameters: "12424 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Steele, Johnston and Mcintosh Dream6966
    settings_parameters: "8218 x g, 33\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Sharp, Tyler and Mcfarland Add1206
  procedure_steps:
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      modern.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were washed with protein a/g dynabeads to facilitate black.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 224
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Murray Ltd #36436-IMPACT'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Baldwin, Kelly and Wong #99983-CENTER'
    concentration_or_purity: "65 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Torres, Kaiser and Madden #62062-MORNING'
    concentration_or_purity: 67.8%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Ellis PLC #59367-MIND'
    concentration_or_purity: 78.0%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lee, Daniel and Garcia #85622-EVIDENCE'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Simmons, Daniels and Patterson Recently6035
    settings_parameters: "5751 x g, 6\xB0C"
  - equipment_name: pH meter
    settings_parameters: "13477 x g, 15\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "9298 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "5021 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      out.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 8
    replicates: 4
  - step_description: Cells were visualized with anti-ha antibody to facilitate follow.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 276
    temperature_celsius: 24
    replicates: 3
  - step_description: Cells were quantified with pbs to facilitate nature.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 509
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were incubated with pbs to facilitate find.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    replicates: 5
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      be.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 538
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. William
  Foster and results were consistent across multiple biological replicates.
