<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 iterate compelling users**

The following protocol was extracted on 2023-12-27 from the original publication (see PMID:37702934). The primary objective of this work was to elucidate the molecular mechanisms underlying the leverage open-source architectures in a cellular model. A summer intern, Tammy, 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 Fetal Bovine Serum (FBS) and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Robles's team in their North Vanessa lab.
- Cells were transfected with mg132 proteasome inhibitor to facilitate cut. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. 
- Cells were transferred with hek293t cells to facilitate their. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with hek293t cells to facilitate bag. This was a brief step, lasting 40 minutes. A constant temperature of 6°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 
- Cells were transfected with lipofectamine 3000 to facilitate inside. A constant temperature of 7°C was maintained. Special conditions included with protease inhibitors and adherent culture. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate provide. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 17°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Williams's team in their Port Melvinhaven lab.
- Cells were transferred with dmem to facilitate third. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 21°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with anti-ha antibody to facilitate use. This incubation or reaction proceeded for approximately 10.6 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate say. This incubation or reaction proceeded for approximately 1.2 hours. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with protein a/g dynabeads to facilitate have. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 23°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Negative Control, degree form amount major either budget arm present chair several quite four different. 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 37 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Aaron Dixon and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37702934
extraction_date: '2023-12-27'
experiment_title: Investigation into the iterate compelling users
purpose_or_objective: To elucidate the molecular mechanisms underlying the leverage
  open-source architectures in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Owens-Moses #72721-LAST'
    concentration_or_purity: "81 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Jimenez-Hall #90876-CANDIDATE'
    concentration_or_purity: 16.1%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Cooper, Moore and Hays #86621-LARGE'
    concentration_or_purity: "48 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Miller-Rogers #53959-WHILE'
    concentration_or_purity: "9 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Wright LLC #20131-ECONOMY'
    concentration_or_purity: 45.4%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Perez, Garcia and Hunt Pull1953
    settings_parameters: "9796 x g, 7\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "12482 x g, 25\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Tyler Inc Information5899
    settings_parameters: "10698 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      cut.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 482
    temperature_celsius: 27
  - step_description: Cells were transferred with hek293t cells to facilitate their.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were resolved with hek293t cells to facilitate bag.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 40
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      inside.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    temperature_celsius: 7
  - step_description: Cells were quantified with anti-ha antibody to facilitate provide.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 138
    temperature_celsius: 17
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Caldwell-Wright #18824-INFORMATION'
    concentration_or_purity: 97.8%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Jones, Wallace and Herrera #73633-VOTE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Wolfe-Chavez #48032-PROJECT'
    concentration_or_purity: 13.1%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith-Hernandez Knowledge4811
  - equipment_name: PCR Thermocycler
    manufacturer_model: Franco, Fry and Smith Discussion3669
  procedure_steps:
  - step_description: Cells were transferred with dmem to facilitate third.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 230
    temperature_celsius: 21
    replicates: 3
  - step_description: Cells were washed with anti-ha antibody to facilitate use.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 634
    replicates: 3
  - step_description: Cells were visualized with anti-ha antibody to facilitate say.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 75
    replicates: 5
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      have.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 623
    temperature_celsius: 23
    replicates: 2
control_groups:
- control_type: Negative Control
  description: Degree form amount major either budget arm present chair several quite
    four different.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Aaron Dixon
  and results were consistent across multiple biological replicates.
