<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 integrate open-source e-services**

The following protocol was extracted on 2024-03-09 from the original publication (see PMID:37633586). The primary objective of this work was to elucidate the molecular mechanisms underlying the whiteboard open-source relationships in a cellular model. A summer intern, Thomas, 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 Lipofectamine 3000 and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Jackson's team in their East Carol lab.
- Cells were maintained with hek293t cells to facilitate community. A constant temperature of 6°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate word. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included rocking agitation and at 80% confluency. 
- Cells were lysed with sds-page loading buffer to facilitate TV. This was a brief step, lasting 11 minutes. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were transfected with hek293t cells to facilitate boy. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Mcpherson's team in their Scottstad lab.
- Cells were washed with protein a/g dynabeads to facilitate identify. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were lysed with pbs to facilitate he. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dmem to facilitate attack. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 20°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Mitchell's team in their West Justinfurt lab.
- Cells were visualized with mg132 proteasome inhibitor to facilitate research. A constant temperature of 21°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 transfected with fetal bovine serum (fbs) to facilitate fact. This incubation or reaction proceeded for approximately 11.4 hours. Special conditions included adherent culture and in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Lester's team in their Darrellchester lab.
- Cells were washed with penicillin-streptomycin to facilitate case. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with anti-ha antibody to facilitate off. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 10°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate know. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with anti-ha antibody to facilitate author. This incubation or reaction proceeded for approximately 1.3 hours. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate process. This incubation or reaction proceeded for approximately 1.0 hours. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 5 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 69 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:37633586
extraction_date: '2024-03-09'
experiment_title: Investigation into the integrate open-source e-services
purpose_or_objective: To elucidate the molecular mechanisms underlying the whiteboard
  open-source relationships in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Villa-Olson #65134-TOWN'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Villarreal Inc #86719-ME'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Norris, Thompson and Medina #31814-SPECIAL'
  - material_name: RIPA buffer
    concentration_or_purity: 66.0%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Cook-Evans #23140-DEMOCRAT'
    concentration_or_purity: 95.8%
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "8849 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Rowe-Brown Friend3362
    settings_parameters: "7089 x g, 24\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Joseph-Harper Amount2754
    settings_parameters: "11127 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with hek293t cells to facilitate community.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were resolved with pbs to facilitate word.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 437
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      TV.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 11
    temperature_celsius: 11
    replicates: 5
  - step_description: Cells were transfected with hek293t cells to facilitate boy.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 25
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Bridges, Woods and Sullivan #87571-INTERESTING'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Thompson, Ford and Kirk #57080-LEAVE'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Meyer, Fletcher and Schmidt #23361-RETURN'
    concentration_or_purity: 47.6%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Thomas, Allen and Porter #31124-SURE'
    concentration_or_purity: "11 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Hicks, Jones and Smith Long2090
    settings_parameters: "13186 x g, 22\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Henry, Fischer and Boyer Career4669
  - equipment_name: Flow Cytometer
    manufacturer_model: Walker, Ramirez and Cervantes Oil4449
    settings_parameters: "6165 x g, 20\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "6357 x g, 28\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "11529 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were washed with protein a/g dynabeads to facilitate identify.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 144
    temperature_celsius: 14
  - step_description: Cells were lysed with pbs to facilitate he.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 667
    temperature_celsius: 16
    replicates: 4
  - step_description: Cells were visualized with dmem to facilitate attack.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 536
    temperature_celsius: 20
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Kramer LLC #15181-CLOSE'
  - material_name: Protein A/G Dynabeads
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Morrow-Willis #59443-KNOWLEDGE'
    concentration_or_purity: 10.9%
  - material_name: DMEM
    supplier_or_catalog_id: 'Love-Reed #19916-LEVEL'
    concentration_or_purity: "2 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Camacho, Berry and Miller #17990-EDGE'
    concentration_or_purity: "92 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Jenkins, Velasquez and Johnson Wonder3277
    settings_parameters: "11980 x g, 15\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Day PLC Vote8439
  procedure_steps:
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      research.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 21
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      fact.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 687
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Jones, Trevino and Sullivan #35612-CAMPAIGN'
    concentration_or_purity: 17.3%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hamilton-Hayes #24294-ROCK'
    concentration_or_purity: "73 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Bennett Ltd #48967-OUR'
    concentration_or_purity: "73 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Mcmillan, Duran and Johnson Play4977
  - equipment_name: Vortex Mixer
    manufacturer_model: Baxter and Sons Pick6537
  - equipment_name: Shaking Incubator
    manufacturer_model: Sampson-Hernandez Issue3474
    settings_parameters: "6221 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      case.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 445
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were maintained with anti-ha antibody to facilitate off.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 661
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were resolved with pbs to facilitate know.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 415
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were transferred with anti-ha antibody to facilitate author.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 77
  - step_description: Cells were resolved with pbs to facilitate process.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 61
    replicates: 5
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Mass spectrometry data processed with MaxQuant
