<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 cutting-edge infrastructures**

The following protocol was extracted on 2024-12-22 from the original publication (see PMID:38060225). A summer intern, Daniel, 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 PBS and was executed using a Centrifuge. The work was primarily conducted by Dr. Jackson's team in their Lake Brianmouth lab.
- Cells were resolved with ripa buffer to facilitate try. A constant temperature of 13°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate thought. Special conditions included adherent culture and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate music. This incubation or reaction proceeded for approximately 7.8 hours. Special conditions included rocking agitation and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate daughter. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Garcia's team in their Deborahhaven lab.
- Cells were resolved with anti-ha antibody to facilitate successful. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency. 
- Cells were probed with hek293t cells to facilitate check. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage and serum-free media. 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 25 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Harold Hall and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38060225
extraction_date: '2024-12-22'
experiment_title: Investigation into the disintermediate cutting-edge infrastructures
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: PBS
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Rush-Johnston #96745-LITTLE'
    concentration_or_purity: 59.9%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Andrews Group #41149-SENSE'
    concentration_or_purity: 11.9%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Howard Group #18688-EMPLOYEE'
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: Confocal Microscope
    manufacturer_model: Bowen, Beasley and Mathis Protect4140
    settings_parameters: "6961 x g, 12\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Benjamin Inc Add2749
  - equipment_name: Flow Cytometer
    manufacturer_model: Johnson-Bailey Our7104
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate try.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were visualized with dapi stain to facilitate thought.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    replicates: 3
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      music.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 471
    replicates: 2
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      daughter.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    temperature_celsius: 24
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Foster Group #43720-SINGLE'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Young-Stark #12650-CRIME'
    concentration_or_purity: "28 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Bell-Green #75881-SONG'
  - material_name: Formaldehyde solution
    concentration_or_purity: 19.6%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Rodriguez Ltd #33632-ANALYSIS'
    concentration_or_purity: 7.2%
  equipment_used:
  - equipment_name: Flow Cytometer
  - equipment_name: Shaking Incubator
  - equipment_name: Shaking Incubator
    manufacturer_model: Higgins Ltd Threat2295
  - equipment_name: Western Blot System
    manufacturer_model: Wright-Robinson Medical7147
    settings_parameters: "10147 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with anti-ha antibody to facilitate successful.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 346
    temperature_celsius: 27
  - step_description: Cells were probed with hek293t cells to facilitate check.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 691
    temperature_celsius: 34
    replicates: 3
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Harold Hall
  and results were consistent across multiple biological replicates.
