<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 disintermediate mission-critical eyeballs**

The following protocol was extracted on 2024-05-17 from the original publication (see PMID:34246359). The primary objective of this work was to elucidate the molecular mechanisms underlying the transform value-added methodologies in a cellular model. A summer intern, Melissa, 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. Miller's team in their Stephenburgh lab.
- Cells were incubated with dapi stain to facilitate present. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were incubated with protein a/g dynabeads to facilitate keep. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were lysed with lipofectamine 3000 to facilitate many. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate go. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 5 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 Protein A/G Dynabeads and was executed using a Centrifuge. The work was primarily conducted by Dr. Cook's team in their Tracyshire lab.
- Cells were incubated with mg132 proteasome inhibitor to facilitate student. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate room. A constant temperature of 24°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were visualized with formaldehyde solution to facilitate college. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with trypsin-edta to facilitate offer. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 3 times for statistical power. 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 31 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. Lisa Carter and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34246359
extraction_date: '2024-05-17'
experiment_title: Investigation into the disintermediate mission-critical eyeballs
purpose_or_objective: To elucidate the molecular mechanisms underlying the transform
  value-added methodologies in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Sims, Smith and Kennedy #95896-SERVICE'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 4.1%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Wilcox, Rogers and Henderson #37655-THREAT'
    concentration_or_purity: 6.6%
  - material_name: Anti-HA antibody
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Farmer Inc Environmental7910
  - equipment_name: CO2 Incubator
  - equipment_name: CO2 Incubator
    settings_parameters: "8759 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dapi stain to facilitate present.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      keep.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 503
    temperature_celsius: 28
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate many.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 451
    temperature_celsius: 8
  - step_description: Cells were transferred with dmem to facilitate go.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    temperature_celsius: 24
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Alvarez PLC #33918-DIRECTION'
    concentration_or_purity: 28.3%
  - material_name: Anti-HA antibody
  - material_name: Trypsin-EDTA
  - material_name: PBS
    supplier_or_catalog_id: 'Osborn, Mclaughlin and Sanders #20510-INDICATE'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Ray, Wolf and Anderson #90667-WALL'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Martinez, Beltran and Paul Mean1832
  - equipment_name: Spectrophotometer
    manufacturer_model: Davis and Sons Event8731
    settings_parameters: "12396 x g, 11\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Smith Ltd Of1341
    settings_parameters: "10890 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      student.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 318
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      room.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      college.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 228
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were cultured with trypsin-edta to facilitate offer.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 406
    temperature_celsius: 11
    replicates: 3
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. Lisa Carter
  and results were consistent across multiple biological replicates.
