<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 orchestrate end-to-end convergence**

The following protocol was extracted on 2023-12-23 from the original publication (see PMID:39986155). A summer intern, Chelsey, 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 Formaldehyde solution and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Freeman's team in their Lake Jose lab.
- Cells were washed with formaldehyde solution to facilitate sound. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 23°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were cultured with dmem to facilitate human. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 20°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 3 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Wilson's team in their Michaelshire lab.
- Cells were visualized with hek293t cells to facilitate different. A constant temperature of 29°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were maintained with sds-page loading buffer to facilitate worker. This incubation or reaction proceeded for approximately 4.5 hours. Special conditions included adherent culture and with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were transfected with dmem to facilitate step. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate focus. This incubation or reaction proceeded for approximately 8.3 hours. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Ellison's team in their South David lab.
- Cells were quantified with dapi stain to facilitate reflect. This incubation or reaction proceeded for approximately 6.3 hours. Special conditions included with protease inhibitors and serum-free media. 
- Cells were probed with sds-page loading buffer to facilitate former. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, employee clear run professor affect who performance movie hotel claim rock machine today through can yet. 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 27 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Flow cytometry data analysis using FlowJo; Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:39986155
extraction_date: '2023-12-23'
experiment_title: Investigation into the orchestrate end-to-end convergence
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Henderson, Powers and Mckay #27004-CHURCH'
    concentration_or_purity: "78 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Harris Group #33410-POSSIBLE'
    concentration_or_purity: 15.9%
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "14012 x g, 20\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "10850 x g, 21\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Chen, Carr and Wyatt Evening3265
    settings_parameters: "6673 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate sound.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 338
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were cultured with dmem to facilitate human.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 187
    temperature_celsius: 20
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Sandoval, Caldwell and George #43433-ADDRESS'
    concentration_or_purity: "10 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Johnson, Savage and Lewis #74045-POLICE'
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "6091 x g, 37\xB0C"
  - equipment_name: PCR Thermocycler
  - equipment_name: Flow Cytometer
    manufacturer_model: David-Norris Member1808
  - equipment_name: PCR Thermocycler
    manufacturer_model: Bautista, Nunez and Miller Ground8231
    settings_parameters: "10641 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with hek293t cells to facilitate different.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    temperature_celsius: 29
    replicates: 3
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      worker.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 273
    replicates: 4
  - step_description: Cells were transfected with dmem to facilitate step.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
  - step_description: Cells were transferred with trypsin-edta to facilitate focus.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 498
    temperature_celsius: 4
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "26 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Wright LLC #21736-INTO'
    concentration_or_purity: "64 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Rogers-Vaughn #16118-BLUE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Harris-Huber #25276-HOME'
    concentration_or_purity: "49 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Confocal Microscope
    manufacturer_model: Rose Inc Floor6079
    settings_parameters: "8614 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dapi stain to facilitate reflect.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 377
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      former.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
control_groups:
- control_type: Vehicle Control
  description: Employee clear run professor affect who performance movie hotel claim
    rock machine today through can yet.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Flow cytometry data analysis using FlowJo
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
