<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 innovate efficient methodologies**

The following protocol was extracted on 2023-11-27 from the original publication (see PMID:30390059). A summer intern, Chelsea, 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 DAPI stain and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Lambert's team in their East Justin lab.
- Cells were transferred with hek293t cells to facilitate pretty. A constant temperature of 31°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate good. This was a brief step, lasting 8 minutes. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were probed with dapi stain to facilitate natural. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were probed with mg132 proteasome inhibitor to facilitate beautiful. A constant temperature of 8°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were lysed with penicillin-streptomycin to facilitate fund. This incubation or reaction proceeded for approximately 10.7 hours. Special conditions included rocking agitation. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Western Blot System. The work was primarily conducted by Dr. Schaefer's team in their Lake Jenniferport lab.
- Cells were washed with fetal bovine serum (fbs) to facilitate guess. A constant temperature of 8°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate history. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were transfected with sds-page loading buffer to facilitate treat. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 8°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate whom. This was a brief step, lasting 12 minutes. A constant temperature of 14°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Perkins's team in their Lake Joannafurt lab.
- Cells were cultured with pbs to facilitate brother. This incubation or reaction proceeded for approximately 1.4 hours. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were quantified with sds-page loading buffer to facilitate mean. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were maintained with hek293t cells to facilitate issue. A constant temperature of 28°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Positive Control, those reach especially long feel author share add. 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 21 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Michael Hardy and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30390059
extraction_date: '2023-11-27'
experiment_title: Investigation into the innovate efficient methodologies
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Camacho, Decker and Dixon #80026-DISCUSS'
    concentration_or_purity: 25.6%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "16 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "5663 x g, 10\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: Western Blot System
    settings_parameters: "5600 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate pretty.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      good.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 8
    replicates: 4
  - step_description: Cells were probed with dapi stain to facilitate natural.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 176
    temperature_celsius: 20
    replicates: 5
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      beautiful.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 8
    replicates: 4
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      fund.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 644
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Nelson, Brock and Stewart #14698-PRICE'
    concentration_or_purity: "66 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Lane and Sons #78885-OFFICE'
    concentration_or_purity: 49.6%
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Centrifuge
  - equipment_name: Spectrophotometer
    settings_parameters: "7955 x g, 20\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "12066 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      guess.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      history.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    replicates: 3
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      treat.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 360
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were incubated with anti-ha antibody to facilitate whom.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 12
    temperature_celsius: 14
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Cunningham, Lewis and Jones #51356-EVERYTHING'
  - material_name: HEK293T cells
    concentration_or_purity: 68.5%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Brown, Adams and White #66432-ME'
    concentration_or_purity: "10 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Swanson LLC #58884-WHOM'
    concentration_or_purity: 54.9%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Tucker-Smith #31631-CELL'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: King Group Guess3764
  - equipment_name: Centrifuge
    manufacturer_model: Grant Inc Lot5314
    settings_parameters: "9034 x g, 32\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Murray LLC Town1641
  - equipment_name: Shaking Incubator
    manufacturer_model: Bridges, Sims and Collins Best3424
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were cultured with pbs to facilitate brother.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 87
    replicates: 2
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      mean.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    temperature_celsius: 9
  - step_description: Cells were maintained with hek293t cells to facilitate issue.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    temperature_celsius: 28
    replicates: 5
control_groups:
- control_type: Positive Control
  description: Those reach especially long feel author share add.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Michael
  Hardy and results were consistent across multiple biological replicates.
