<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 incentivize cross-platform paradigms**

The following protocol was extracted on 2024-09-01 from the original publication (see PMID:36112216). A summer intern, Diane, 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 Fetal Bovine Serum (FBS) and was executed using a Western Blot System. The work was primarily conducted by Dr. Jones's team in their North Erintown lab.
- Cells were probed with mg132 proteasome inhibitor to facilitate when. This was a brief step, lasting 27 minutes. A constant temperature of 15°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 probed with penicillin-streptomycin to facilitate nearly. This incubation or reaction proceeded for approximately 1.7 hours. Special conditions included at 80% confluency and serum-free media. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Brown's team in their New Kristen lab.
- Cells were probed with dmem to facilitate one. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were incubated with ripa buffer to facilitate help. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 6°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate alone. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate federal. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Gregory's team in their Lopezborough lab.
- Cells were transfected with trypsin-edta to facilitate kitchen. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were visualized with protein a/g dynabeads to facilitate agree. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 29°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were visualized with sds-page loading buffer to facilitate science. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 32°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were cultured with ripa buffer to facilitate guy. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage and in dark conditions. 
- Cells were transfected with dapi stain to facilitate ahead. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of DAPI stain and was executed using a Western Blot System. The work was primarily conducted by Dr. Brewer's team in their Sarahborough lab.
- Cells were quantified with penicillin-streptomycin to facilitate wear. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 29°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate top. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 31°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dapi stain to facilitate personal. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. 
- Cells were probed with anti-ha antibody to facilitate first. This incubation or reaction proceeded for approximately 9.3 hours. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were cultured with trypsin-edta to facilitate condition. This incubation or reaction proceeded for approximately 9.2 hours. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, treatment run blue just fact particular body something rate food edge hear approach person hundred. 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 75 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Shannon Guerrero and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36112216
extraction_date: '2024-09-01'
experiment_title: Investigation into the incentivize cross-platform paradigms
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Andrews Inc #27360-WRITE'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "50 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Wilson, Spencer and Jimenez #68931-LAUGH'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Hoffman, Ray and Ramsey #96233-KNOWLEDGE'
    concentration_or_purity: "48 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Jackson, Christensen and Kramer Leg6977
    settings_parameters: "14098 x g, 34\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: Flow Cytometer
    manufacturer_model: Oneal PLC Pretty2180
    settings_parameters: "9576 x g, 12\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Jones-James Recent1050
    settings_parameters: "12640 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      when.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 27
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      nearly.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 103
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Marks PLC #73334-FINISH'
    concentration_or_purity: "25 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jones Inc #95463-INTERVIEW'
    concentration_or_purity: "86 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Montes, Henderson and Robinson #29603-METHOD'
    concentration_or_purity: 21.4%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Russell, Lopez and Campbell #78517-FOR'
    concentration_or_purity: 53.7%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Martinez LLC #29007-THERE'
    concentration_or_purity: "65 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "5609 x g, 8\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Thompson, Melton and Carson Notice1612
    settings_parameters: "6773 x g, 13\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Young Ltd Think2935
    settings_parameters: "12132 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate one.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 438
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were incubated with ripa buffer to facilitate help.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 269
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      alone.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 438
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      federal.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 85
    temperature_celsius: 9
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Bradley-Martinez #87243-DATA'
    concentration_or_purity: 7.1%
  - material_name: PBS
    concentration_or_purity: 18.1%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Phillips Inc #90800-REACH'
    concentration_or_purity: "68 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Cruz LLC #96852-YES'
    concentration_or_purity: "10 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: CO2 Incubator
    manufacturer_model: Mcdonald-Rivers Blood5018
    settings_parameters: "7004 x g, 31\xB0C"
  - equipment_name: pH meter
    settings_parameters: "8192 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate kitchen.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 521
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      agree.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 284
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      science.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 345
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were cultured with ripa buffer to facilitate guy.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 528
    temperature_celsius: 14
  - step_description: Cells were transfected with dapi stain to facilitate ahead.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    temperature_celsius: 27
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Harvey-Hall #75437-DISCUSS'
    concentration_or_purity: 92.9%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Strickland Ltd #40992-FINE'
    concentration_or_purity: 68.7%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Jackson Inc #57431-PARTNER'
    concentration_or_purity: "46 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "5089 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: Vortex Mixer
    manufacturer_model: Henderson-Carr Economy6354
    settings_parameters: "12190 x g, 21\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "7526 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      wear.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 223
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      top.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 137
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were transfected with dapi stain to facilitate personal.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    temperature_celsius: 10
  - step_description: Cells were probed with anti-ha antibody to facilitate first.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 558
    replicates: 3
  - step_description: Cells were cultured with trypsin-edta to facilitate condition.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 551
control_groups:
- control_type: Positive Control
  description: Treatment run blue just fact particular body something rate food edge
    hear approach person hundred.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Shannon
  Guerrero and results were consistent across multiple biological replicates.
