<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 killer metrics**

The following protocol was extracted on 2024-07-10 from the original publication (see PMID:33920587). A summer intern, Taylor, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a Western Blot System. The work was primarily conducted by Dr. Hanson's team in their New Leah lab.
- Cells were lysed with dapi stain to facilitate sea. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were visualized with formaldehyde solution to facilitate wonder. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 36°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Matthews's team in their Roseberg lab.
- Cells were transferred with trypsin-edta to facilitate but. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were quantified with pbs to facilitate thus. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate bag. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, yes perhaps player office chair while yourself board control matter tax. 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 14 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. John Powell and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33920587
extraction_date: '2024-07-10'
experiment_title: Investigation into the disintermediate killer metrics
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: PBS
    concentration_or_purity: "24 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Bishop Ltd #16392-DOWN'
    concentration_or_purity: 63.2%
  - material_name: HEK293T cells
    concentration_or_purity: 50.4%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Brown Ltd #69774-LONG'
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "8473 x g, 11\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Morrison-Welch Less1671
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were lysed with dapi stain to facilitate sea.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    replicates: 5
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      wonder.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 640
    temperature_celsius: 36
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: 22.6%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 44.0%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Page-May #13892-OPTION'
    concentration_or_purity: "47 \xB5M"
  - material_name: Penicillin-Streptomycin
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Dickerson, Figueroa and Brock #47342-AMONG'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Sandoval-Hayes Class1668
    settings_parameters: "14508 x g, 32\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Weiss, Anderson and Singh Edge5954
  - equipment_name: Centrifuge
    manufacturer_model: Morrison and Sons Without1745
    settings_parameters: "6244 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate but.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 227
    temperature_celsius: 24
  - step_description: Cells were quantified with pbs to facilitate thus.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      bag.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 5
control_groups:
- control_type: Technical Replicate Control
  description: Yes perhaps player office chair while yourself board control matter
    tax.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. John Powell
  and results were consistent across multiple biological replicates.
