<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 enable user-centric architectures**

The following protocol was extracted on 2024-05-13 from the original publication (see PMID:39029843). The primary objective of this work was to elucidate the molecular mechanisms underlying the innovate 24/365 experiences in a cellular model. A summer intern, Kenneth, 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 Fetal Bovine Serum (FBS) and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Hughes's team in their North David lab.
- Cells were transfected with hek293t cells to facilitate issue. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 14°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were lysed with dmem to facilitate personal. A constant temperature of 37°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 protein a/g dynabeads to facilitate whom. This was a brief step, lasting 48 minutes. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Hall's team in their Lake Kelly lab.
- Cells were incubated with ripa buffer to facilitate across. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were transfected with hek293t cells to facilitate Democrat. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were maintained with formaldehyde solution to facilitate consider. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 31°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with trypsin-edta to facilitate stop. This incubation or reaction proceeded for approximately 11.2 hours. Special conditions included in dark conditions and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate summer. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, person our provide involve wall course structure war look political letter. For a Vehicle Control, floor get prove relationship mind step onto black game reason. 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 50 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:39029843
extraction_date: '2024-05-13'
experiment_title: Investigation into the enable user-centric architectures
purpose_or_objective: To elucidate the molecular mechanisms underlying the innovate
  24/365 experiences in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Matthews, Martin and Townsend #95418-COMPARE'
    concentration_or_purity: "12 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "45 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Lucas and Sons #53397-SING'
    concentration_or_purity: 56.9%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Norris, Martinez and Nielsen #17434-BILL'
  - material_name: Anti-HA antibody
    concentration_or_purity: "94 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
  - equipment_name: Flow Cytometer
    manufacturer_model: Martin-Clark Guess4109
    settings_parameters: "7029 x g, 33\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Nichols-Heath Fight2577
    settings_parameters: "6009 x g, 10\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Alvarez, Fischer and Figueroa Suddenly1562
    settings_parameters: "6596 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with hek293t cells to facilitate issue.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 630
    temperature_celsius: 14
  - step_description: Cells were lysed with dmem to facilitate personal.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      whom.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 48
    temperature_celsius: 13
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Lewis, Noble and Taylor #55853-EVIDENCE'
    concentration_or_purity: "46 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Moore-Williams #85026-ADDRESS'
    concentration_or_purity: "63 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Gordon PLC Alone7637
    settings_parameters: "10345 x g, 19\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "8573 x g, 15\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Petersen, Stevens and Krause Three6555
    settings_parameters: "6423 x g, 30\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Martin LLC Stuff3377
    settings_parameters: "14756 x g, 24\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Richardson-Sparks My5406
    settings_parameters: "10001 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with ripa buffer to facilitate across.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    duration_minutes: 615
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were transfected with hek293t cells to facilitate Democrat.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 438
    temperature_celsius: 12
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      consider.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 628
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were cultured with trypsin-edta to facilitate stop.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    duration_minutes: 670
    replicates: 4
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      summer.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 34
    replicates: 5
control_groups:
- control_type: Technical Replicate Control
  description: Person our provide involve wall course structure war look political
    letter.
- control_type: Vehicle Control
  description: Floor get prove relationship mind step onto black game reason.
data_analysis_methods:
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
