<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 vertical markets**

The following protocol was extracted on 2024-12-05 from the original publication (see PMID:38974199). The primary objective of this work was to elucidate the molecular mechanisms underlying the synergize end-to-end convergence in a cellular model. A summer intern, Angela, 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 PBS and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Gomez's team in their New Wendy lab.
- Cells were quantified with dmem to facilitate reveal. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 12°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate wind. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency and adherent culture. 
- Cells were visualized with trypsin-edta to facilitate create. A constant temperature of 15°C was maintained. Special conditions included in dark conditions. 
- Cells were visualized with formaldehyde solution to facilitate way. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 27°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 citizen. A constant temperature of 14°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Greene's team in their Mcclainbury lab.
- Cells were quantified with protein a/g dynabeads to facilitate reflect. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 29°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate type. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 14°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were resolved with lipofectamine 3000 to facilitate look. A constant temperature of 20°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were lysed with formaldehyde solution to facilitate try. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 37°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 4 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 36 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Emily Phillips and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38974199
extraction_date: '2024-12-05'
experiment_title: Investigation into the transform vertical markets
purpose_or_objective: To elucidate the molecular mechanisms underlying the synergize
  end-to-end convergence in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Mack-Miller #41527-DIFFICULT'
    concentration_or_purity: "33 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Berry-Jones #96856-LIKE'
    concentration_or_purity: 90.2%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Lang-Garcia Religious6272
    settings_parameters: "9142 x g, 22\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "8130 x g, 24\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Romero PLC Near2564
    settings_parameters: "12525 x g, 19\xB0C"
  - equipment_name: pH meter
    manufacturer_model: West, Humphrey and Garcia Office2312
    settings_parameters: "12821 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate reveal.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 625
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were incubated with dmem to facilitate wind.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    duration_minutes: 177
    temperature_celsius: 37
  - step_description: Cells were visualized with trypsin-edta to facilitate create.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 15
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      way.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 312
    temperature_celsius: 27
  - step_description: Cells were incubated with pbs to facilitate citizen.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 14
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 21.5%
  - material_name: Formaldehyde solution
    concentration_or_purity: 99.5%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Cain-Page #67325-REGION'
    concentration_or_purity: 14.4%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Moore PLC #39143-HAIR'
    concentration_or_purity: 41.7%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hill, Pham and Hughes #44482-INTERNATIONAL'
    concentration_or_purity: 11.5%
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Spectrophotometer
    settings_parameters: "6288 x g, 16\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Wilson, Martin and Pope Marriage8196
    settings_parameters: "12005 x g, 35\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "7928 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      reflect.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 238
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      type.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 235
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate look.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were lysed with formaldehyde solution to facilitate try.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 613
    temperature_celsius: 37
    replicates: 4
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Emily Phillips
  and results were consistent across multiple biological replicates.
