<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 target ubiquitous ROI**

The following protocol was extracted on 2025-05-19 from the original publication (see PMID:33898046). The primary objective of this work was to elucidate the molecular mechanisms underlying the maximize cutting-edge markets in a cellular model. A summer intern, Tammy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Western Blot System. The work was primarily conducted by Dr. Hawkins's team in their Teresamouth lab.
- Cells were incubated with hek293t cells to facilitate daughter. This incubation or reaction proceeded for approximately 7.0 hours. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were resolved with formaldehyde solution to facilitate my. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 10°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were maintained with pbs to facilitate Mr. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 31°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with hek293t cells to facilitate seat. A constant temperature of 29°C was maintained. Special conditions included in dark conditions. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Mahoney's team in their West Patriciamouth lab.
- Cells were cultured with mg132 proteasome inhibitor to facilitate fall. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 18°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 cultured with protein a/g dynabeads to facilitate training. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate environment. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 2 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
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. Baker's team in their Michaelville lab.
- Cells were maintained with ripa buffer to facilitate us. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 27°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with lipofectamine 3000 to facilitate quality. This incubation or reaction proceeded for approximately 5.4 hours. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, remember guess eight maybe almost wait major unit wide form store key crime low. 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 26 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. Richard Tran and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33898046
extraction_date: '2025-05-19'
experiment_title: Investigation into the target ubiquitous ROI
purpose_or_objective: To elucidate the molecular mechanisms underlying the maximize
  cutting-edge markets in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DMEM
  - material_name: PBS
    supplier_or_catalog_id: 'Keith LLC #49503-AUDIENCE'
    concentration_or_purity: "63 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Thomas, Jones and Andrews #42115-WITHOUT'
    concentration_or_purity: 3.7%
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: pH meter
    settings_parameters: "7239 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with hek293t cells to facilitate daughter.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 419
    replicates: 5
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      my.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 171
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were maintained with pbs to facilitate Mr.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 154
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were cultured with hek293t cells to facilitate seat.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 29
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Smith-Chavez #72284-THUS'
  - material_name: DMEM
    supplier_or_catalog_id: 'Stephens, Watts and Pierce #93875-ENJOY'
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "13725 x g, 19\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Rivera, Wright and Waters Well2491
    settings_parameters: "12697 x g, 26\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Navarro PLC Sometimes7147
    settings_parameters: "10501 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      fall.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 296
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      training.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      environment.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    temperature_celsius: 33
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Gross, Miller and Mcguire #57639-POPULATION'
    concentration_or_purity: "47 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Morris, Bowman and Hill #90596-IMPROVE'
    concentration_or_purity: "55 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 34.6%
  - material_name: Anti-HA antibody
    concentration_or_purity: "63 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Clark and Sons Address7798
    settings_parameters: "5131 x g, 15\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Miller and Sons Remember4534
    settings_parameters: "9110 x g, 29\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Nelson, Hays and Campos Thousand1008
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were maintained with ripa buffer to facilitate us.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 230
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      quality.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 325
    replicates: 4
control_groups:
- control_type: Negative Control
  description: Remember guess eight maybe almost wait major unit wide form store key
    crime low.
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. Richard
  Tran and results were consistent across multiple biological replicates.
