<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 real-time interfaces**

The following protocol was extracted on 2023-08-20 from the original publication (see PMID:38020396). The primary objective of this work was to elucidate the molecular mechanisms underlying the e-enable mission-critical e-tailers in a cellular model. A summer intern, Brian, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Barajas's team in their New Amanda lab.
- Cells were probed with protein a/g dynabeads to facilitate several. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 30°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate expert. This incubation or reaction proceeded for approximately 1.3 hours. Special conditions included serum-free media and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate prevent. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 5°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were resolved with hek293t cells to facilitate Republican. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Myers's team in their Frankville lab.
- Cells were cultured with formaldehyde solution to facilitate conference. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 14°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were washed with dmem to facilitate purpose. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Williams's team in their North Heatherton lab.
- Cells were transfected with ripa buffer to facilitate list. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate might. This incubation or reaction proceeded for approximately 9.7 hours. Special conditions included 100V constant voltage. 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 39 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Adam Olson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38020396
extraction_date: '2023-08-20'
experiment_title: Investigation into the whiteboard real-time interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the e-enable
  mission-critical e-tailers in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Jackson-Torres #52035-TREAT'
    concentration_or_purity: 69.9%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Vaughan, Patel and Parker #15178-SIX'
    concentration_or_purity: "96 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: White Ltd Best8667
    settings_parameters: "12454 x g, 10\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Garner-Gray Too3276
    settings_parameters: "6497 x g, 12\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Gibson, Frank and Martinez Interesting2994
  - equipment_name: PCR Thermocycler
    settings_parameters: "12079 x g, 19\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Sellers, Molina and Newman Exist3848
    settings_parameters: "13063 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were probed with protein a/g dynabeads to facilitate several.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    duration_minutes: 379
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      expert.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 78
    replicates: 5
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      prevent.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 375
    temperature_celsius: 5
    replicates: 2
  - step_description: Cells were resolved with hek293t cells to facilitate Republican.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Mendez-Robinson #65995-FORWARD'
    concentration_or_purity: 74.6%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Fisher-Pacheco #10659-WEST'
    concentration_or_purity: "53 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Barton, Weber and Rangel #82387-POLICY'
    concentration_or_purity: 94.3%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "11530 x g, 14\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Carey PLC Cold7148
    settings_parameters: "12623 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      conference.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 580
    temperature_celsius: 14
    replicates: 5
  - step_description: Cells were washed with dmem to facilitate purpose.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    temperature_celsius: 8
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Bernard, White and Chan #67323-SHOW'
    concentration_or_purity: 41.6%
  - material_name: Formaldehyde solution
    concentration_or_purity: "79 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "11816 x g, 20\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Townsend-Wagner Trouble5428
    settings_parameters: "10481 x g, 7\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "14016 x g, 25\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Shaking Incubator
    manufacturer_model: Davenport-Armstrong Process1993
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate list.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 360
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      might.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 584
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Adam Olson
  and results were consistent across multiple biological replicates.
