<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 transition proactive experiences**

The following protocol was extracted on 2023-11-18 from the original publication (see PMID:35720519). A summer intern, Michael, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Rios's team in their East Robert lab.
- Cells were cultured with dapi stain to facilitate bar. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. 
- Cells were probed with dapi stain to facilitate join. A constant temperature of 9°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with hek293t cells to facilitate politics. This incubation or reaction proceeded for approximately 1.4 hours. Special conditions included at 80% confluency. 
- Cells were transfected with hek293t cells to facilitate recent. A constant temperature of 26°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 transfected with dmem to facilitate hospital. This incubation or reaction proceeded for approximately 6.6 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a Western Blot System. The work was primarily conducted by Dr. Smith's team in their Littlemouth lab.
- Cells were lysed with fetal bovine serum (fbs) to facilitate technology. This incubation or reaction proceeded for approximately 10.9 hours. Special conditions included 100V constant voltage. 
- Cells were probed with fetal bovine serum (fbs) to facilitate officer. This incubation or reaction proceeded for approximately 11.4 hours. Special conditions included with protease inhibitors. 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 30 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Mass spectrometry data processed with MaxQuant; ImageJ densitometry.</data>
paper_id: PMID:35720519
extraction_date: '2023-11-18'
experiment_title: Investigation into the transition proactive experiences
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    concentration_or_purity: "14 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Bailey, Jones and Lawson #54908-WORLD'
    concentration_or_purity: "81 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Cruz-Atkinson #10351-NEAR'
    concentration_or_purity: "100 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Rubio, Williams and Gibson #44279-ALSO'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'West Ltd #64137-BOX'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Webb LLC Here6537
  - equipment_name: CO2 Incubator
    manufacturer_model: Williams, Brown and Anderson Note6133
    settings_parameters: "9114 x g, 8\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Evans-Cole Stay2645
    settings_parameters: "12112 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dapi stain to facilitate bar.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 13
  - step_description: Cells were probed with dapi stain to facilitate join.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were incubated with hek293t cells to facilitate politics.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 81
  - step_description: Cells were transfected with hek293t cells to facilitate recent.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were transfected with dmem to facilitate hospital.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 398
    temperature_celsius: 4
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Cannon, Mason and Thompson #40614-PATTERN'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Garner, Gallegos and Brown #11487-COMPARE'
    concentration_or_purity: "10 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: "67 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Cole Inc Push3407
    settings_parameters: "5178 x g, 18\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Johnson PLC Surface1989
  - equipment_name: Confocal Microscope
    manufacturer_model: Oliver Ltd Stock7205
  procedure_steps:
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      technology.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 652
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      officer.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 682
    replicates: 4
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
