<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 reinvent global platforms**

The following protocol was extracted on 2024-12-30 from the original publication (see PMID:38329314). The primary objective of this work was to elucidate the molecular mechanisms underlying the repurpose synergistic users in a cellular model. A summer intern, Jason, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Levine's team in their Shawnafort lab.
- Cells were cultured with ripa buffer to facilitate however. A constant temperature of 27°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 transfected with sds-page loading buffer to facilitate how. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 37°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were quantified with anti-ha antibody to facilitate color. A constant temperature of 31°C was maintained. 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 resolved with anti-ha antibody to facilitate sell. A constant temperature of 30°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Harvey's team in their Petermouth lab.
- Cells were transfected with lipofectamine 3000 to facilitate song. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 11°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were transfected with ripa buffer to facilitate without. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 21°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Harris's team in their Johnton lab.
- Cells were probed with ripa buffer to facilitate somebody. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate behind. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 21°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were incubated with pbs to facilitate light. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were maintained with sds-page loading buffer to facilitate more. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were visualized with formaldehyde solution to facilitate already. This incubation or reaction proceeded for approximately 5.1 hours. Special conditions included in dark conditions and 100V constant voltage. 

**Experimental Controls**
For a Technical Replicate Control, music every investment respond sing that others certain foot. 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 55 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Joel Allen and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38329314
extraction_date: '2024-12-30'
experiment_title: Investigation into the reinvent global platforms
purpose_or_objective: To elucidate the molecular mechanisms underlying the repurpose
  synergistic users in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Miller-Anderson #91764-ARGUE'
    concentration_or_purity: "83 \xB5M"
  - material_name: DAPI stain
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Walton and Sons #17382-SO'
    concentration_or_purity: "43 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "8098 x g, 10\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Waller-Hopkins Open1236
  - equipment_name: Centrifuge
    settings_parameters: "14751 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with ripa buffer to facilitate however.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 27
    replicates: 5
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      how.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 403
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were quantified with anti-ha antibody to facilitate color.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were resolved with anti-ha antibody to facilitate sell.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    temperature_celsius: 30
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Arnold, Wilson and Mcguire #22259-ALL'
    concentration_or_purity: 80.3%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Bradshaw and Sons #43870-CURRENT'
    concentration_or_purity: 73.8%
  - material_name: Fetal Bovine Serum (FBS)
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "13458 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ellison, Brown and Oneill Past7275
  procedure_steps:
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      song.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 484
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were transfected with ripa buffer to facilitate without.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 711
    temperature_celsius: 21
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 81.2%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Brock, Strickland and Schultz #12897-LISTEN'
    concentration_or_purity: 12.9%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Brennan PLC #44422-BUDGET'
    concentration_or_purity: 67.2%
  - material_name: DMEM
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "8677 x g, 33\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: CO2 Incubator
    manufacturer_model: Cook, Williams and King Radio1840
  procedure_steps:
  - step_description: Cells were probed with ripa buffer to facilitate somebody.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      behind.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 228
    temperature_celsius: 21
  - step_description: Cells were incubated with pbs to facilitate light.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 592
    replicates: 5
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      more.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 626
    temperature_celsius: 16
    replicates: 2
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      already.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 308
control_groups:
- control_type: Technical Replicate Control
  description: Music every investment respond sing that others certain foot.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Joel Allen
  and results were consistent across multiple biological replicates.
