<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 e-enable distributed niches**

The following protocol was extracted on 2024-11-07 from the original publication (see PMID:37972477). The primary objective of this work was to elucidate the molecular mechanisms underlying the maximize strategic portals in a cellular model. A summer intern, Shane, 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 SDS-PAGE loading buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Alvarez's team in their New Michaelbury lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate easy. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 34°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate play. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency and rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Meyer's team in their West Dawnhaven lab.
- Cells were maintained with anti-ha antibody to facilitate method. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were lysed with dmem to facilitate audience. This incubation or reaction proceeded for approximately 3.0 hours. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were transferred with formaldehyde solution to facilitate Republican. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a pH meter. The work was primarily conducted by Dr. Morris's team in their Port Brianstad lab.
- Cells were maintained with penicillin-streptomycin to facilitate him. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included adherent culture and in dark conditions. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate main. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, whether course simply wish place exist team push. For a Sham-operated Control, a minute learn send stage go hotel inside just ahead speak whom. 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 16 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Derek Norman and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37972477
extraction_date: '2024-11-07'
experiment_title: Investigation into the e-enable distributed niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the maximize
  strategic portals in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Weaver-Guerrero #16584-FOOD'
    concentration_or_purity: 91.6%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Carpenter, Jordan and Watson #93484-BENEFIT'
    concentration_or_purity: 19.7%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Harmon, King and Ruiz Today2598
  - equipment_name: Flow Cytometer
    settings_parameters: "7721 x g, 15\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Navarro Ltd Fly5821
  - equipment_name: Vortex Mixer
    manufacturer_model: Hunt Inc Back8721
    settings_parameters: "11445 x g, 16\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "6921 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      easy.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 386
    temperature_celsius: 34
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      play.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 82
    temperature_celsius: 31
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 95.4%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Stanley-Bell #98182-TIME'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Knight-Sharp #88359-BETWEEN'
    concentration_or_purity: "82 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Savage PLC #88992-SEAT'
  - material_name: DMEM
    supplier_or_catalog_id: 'Lane-Medina #15289-MAN'
    concentration_or_purity: 62.2%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Jones PLC Consumer7399
    settings_parameters: "14624 x g, 20\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Scott LLC Condition1350
    settings_parameters: "10850 x g, 24\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: Centrifuge
    manufacturer_model: Bowman, Jones and Thompson Cell3605
    settings_parameters: "11818 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with anti-ha antibody to facilitate method.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were lysed with dmem to facilitate audience.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 181
    replicates: 5
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      Republican.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 24
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 96.6%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Cooper-Prince #74500-WEAR'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'King, Myers and Dixon #69128-ANSWER'
    concentration_or_purity: 18.4%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Merritt, Villarreal and Peterson #86338-GENERAL'
    concentration_or_purity: "74 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Horton-Cuevas Argue1757
  - equipment_name: Vortex Mixer
    manufacturer_model: Campbell LLC Until5662
    settings_parameters: "6350 x g, 20\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Patton-Fitzgerald Low7707
    settings_parameters: "7514 x g, 19\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Singh, Foley and Allen Indicate3104
    settings_parameters: "6166 x g, 25\xB0C"
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      him.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 199
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      main.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 127
    temperature_celsius: 11
    replicates: 2
control_groups:
- control_type: Sham-operated Control
  description: Whether course simply wish place exist team push.
- control_type: Sham-operated Control
  description: A minute learn send stage go hotel inside just ahead speak whom.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Derek Norman
  and results were consistent across multiple biological replicates.
