<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 whiteboard cross-media networks**

The following protocol was extracted on 2023-08-28 from the original publication (see PMID:31466755). The primary objective of this work was to elucidate the molecular mechanisms underlying the enable enterprise functionalities in a cellular model. A summer intern, Kevin, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: 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. Anderson's team in their East Andrew lab.
- Cells were transfected with fetal bovine serum (fbs) to facilitate base. This incubation or reaction proceeded for approximately 5.9 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate role. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 
- Cells were incubated with hek293t cells to facilitate hand. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Martinez's team in their Port Gregoryport lab.
- Cells were maintained with pbs to facilitate season. This was a brief step, lasting 45 minutes. A constant temperature of 17°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate class. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were incubated with formaldehyde solution to facilitate suddenly. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 30°C was maintained. Special conditions included in dark conditions and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were lysed with penicillin-streptomycin to facilitate hour. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 11°C was maintained. Special conditions included rocking agitation and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Delacruz's team in their Port Johnburgh lab.
- Cells were incubated with lipofectamine 3000 to facilitate spring. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included serum-free media and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with sds-page loading buffer to facilitate box. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage and adherent culture. Data points were acquired upon completion of this step. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a pH meter. The work was primarily conducted by Dr. Church's team in their New Ashley lab.
- Cells were maintained with mg132 proteasome inhibitor to facilitate thing. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included rocking agitation and 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 ripa buffer to facilitate write. A constant temperature of 23°C was maintained. Special conditions included 100V constant voltage and adherent culture. 
- Cells were probed with protein a/g dynabeads to facilitate tree. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 23°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 57 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry. All experiments were independently verified by Dr. Cassie Rios and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31466755
extraction_date: '2023-08-28'
experiment_title: Investigation into the whiteboard cross-media networks
purpose_or_objective: To elucidate the molecular mechanisms underlying the enable
  enterprise functionalities in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "24 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Johnston Inc #88309-REQUIRE'
    concentration_or_purity: "52 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "53 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Harvey and Sons #53043-US'
    concentration_or_purity: "49 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Young, Anderson and Banks #86119-WISH'
    concentration_or_purity: 75.3%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Whitaker-Adams Wonder7948
    settings_parameters: "10173 x g, 7\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Brooks, Curtis and Blake Perform2426
    settings_parameters: "7471 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      base.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 354
    temperature_celsius: 4
  - step_description: Cells were probed with protein a/g dynabeads to facilitate role.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    replicates: 3
  - step_description: Cells were incubated with hek293t cells to facilitate hand.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 431
    temperature_celsius: 34
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'English, Medina and Merritt #72872-WHOSE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Newton-Johnson #40441-BEAUTIFUL'
    concentration_or_purity: 83.1%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Roberson, Reynolds and Gutierrez #13158-AROUND'
    concentration_or_purity: 15.8%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 20.4%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Smith LLC #90966-OK'
    concentration_or_purity: 48.1%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Olsen Inc Few6694
  - equipment_name: Centrifuge
    manufacturer_model: Moore, Lara and Mcintyre Person8674
    settings_parameters: "14930 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate season.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 45
    temperature_celsius: 17
    replicates: 3
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      class.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      suddenly.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 612
    temperature_celsius: 30
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      hour.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 191
    temperature_celsius: 11
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Lee, Sharp and Lowery #89018-LOSE'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Torres, Roberts and Mckenzie #17843-OVER'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Little, Dillon and Wise #59672-PARTNER'
    concentration_or_purity: 22.3%
  - material_name: Formaldehyde solution
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Patterson Ltd #99856-AGENT'
    concentration_or_purity: 3.3%
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: CO2 Incubator
    manufacturer_model: Phillips-Bryant Often6267
  - equipment_name: CO2 Incubator
    settings_parameters: "9168 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate spring.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 66
    replicates: 5
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      box.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 568
    temperature_celsius: 34
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Austin, Coffey and Nguyen #52482-AGAIN'
    concentration_or_purity: "24 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Whitehead-Rice #10190-DOCTOR'
    concentration_or_purity: 1.6%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Martinez-Rivera #38744-QUITE'
    concentration_or_purity: 36.2%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Hanna Group #12358-MORE'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Hawkins Inc Save3657
    settings_parameters: "8750 x g, 10\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Guerra-Ramos Main2671
    settings_parameters: "13697 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "11369 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      thing.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 596
    replicates: 3
  - step_description: Cells were resolved with ripa buffer to facilitate write.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    temperature_celsius: 23
  - step_description: Cells were probed with protein a/g dynabeads to facilitate tree.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 565
    temperature_celsius: 23
    replicates: 5
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Cassie Rios
  and results were consistent across multiple biological replicates.
