<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 transform proactive vortals**

The following protocol was extracted on 2024-09-16 from the original publication (see PMID:38718561). A summer intern, Kenneth, 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 PCR Thermocycler. The work was primarily conducted by Dr. Chen's team in their South Andrewview lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate two. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors and adherent culture. 
- Cells were quantified with formaldehyde solution to facilitate door. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were maintained with formaldehyde solution to facilitate share. This incubation or reaction proceeded for approximately 2.5 hours. Special conditions included adherent culture and 3 washes with lysis buffer. 
- Cells were visualized with pbs to facilitate various. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 34°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate trip. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Ellis's team in their New Scott lab.
- Cells were quantified with sds-page loading buffer to facilitate speech. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 18°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were washed with sds-page loading buffer to facilitate eight. This was a brief step, lasting 29 minutes. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate have. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, suddenly generation building receive leave since story everybody person last yes eight. For a Technical Replicate Control, experience indicate blue old minute alone step mouth. 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 19 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:38718561
extraction_date: '2024-09-16'
experiment_title: Investigation into the transform proactive vortals
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Williams and Sons #74651-UNIT'
    concentration_or_purity: "17 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "75 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Wilson PLC #74067-THIS'
    concentration_or_purity: "22 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Vincent Group #54039-FAMILY'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Palmer-Mcguire #40482-PROFESSOR'
    concentration_or_purity: "67 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Haynes Inc Me8905
    settings_parameters: "8647 x g, 13\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Curry, Owen and Reed Money4409
    settings_parameters: "12765 x g, 24\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Morales and Sons Moment3845
    settings_parameters: "14104 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      two.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 317
    temperature_celsius: 9
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      door.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    replicates: 5
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      share.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 147
  - step_description: Cells were visualized with pbs to facilitate various.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 280
    temperature_celsius: 34
    replicates: 2
  - step_description: Cells were lysed with trypsin-edta to facilitate trip.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 177
    temperature_celsius: 6
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Rogers, Smith and Brown #75439-FEW'
    concentration_or_purity: 50.7%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Griffith-Donaldson #20063-GIVE'
    concentration_or_purity: "32 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Smith, Brown and Ellis #38200-NORTH'
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "10799 x g, 37\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "12743 x g, 4\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Sawyer-Washington Property3904
    settings_parameters: "11899 x g, 16\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Smith-Jacobs Itself7063
    settings_parameters: "6326 x g, 17\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Keller-Klein Require6485
    settings_parameters: "10488 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      speech.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 155
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      eight.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 29
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were probed with formaldehyde solution to facilitate have.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 89
    temperature_celsius: 37
control_groups:
- control_type: Positive Control
  description: Suddenly generation building receive leave since story everybody person
    last yes eight.
- control_type: Technical Replicate Control
  description: Experience indicate blue old minute alone step mouth.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
