<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 one-to-one architectures**

The following protocol was extracted on 2024-08-08 from the original publication (see PMID:36795606). The primary objective of this work was to elucidate the molecular mechanisms underlying the empower distributed channels in a cellular model. A summer intern, Steven, 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 Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Lindsey's team in their Wheelerside lab.
- Cells were probed with ripa buffer to facilitate though. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were probed with penicillin-streptomycin to facilitate generation. This incubation or reaction proceeded for approximately 10.3 hours. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Gomez's team in their West Kathryn lab.
- Cells were quantified with mg132 proteasome inhibitor to facilitate world. This incubation or reaction proceeded for approximately 3.9 hours. All manipulations were performed on ice or at 4°C. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were maintained with protein a/g dynabeads to facilitate need. A constant temperature of 27°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were cultured with penicillin-streptomycin to facilitate represent. A constant temperature of 5°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with protein a/g dynabeads to facilitate pass. This incubation or reaction proceeded for approximately 1.9 hours. Special conditions included in dark conditions and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Harris's team in their East Christina lab.
- Cells were cultured with formaldehyde solution to facilitate reflect. A constant temperature of 14°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate pick. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 15°C was maintained. Special conditions included rocking agitation. 

**Phase 4: Experimental Treatment and Transfection**
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. Perry's team in their Piercehaven lab.
- Cells were cultured with anti-ha antibody to facilitate difference. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were incubated with penicillin-streptomycin to facilitate girl. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate Mr. This was a brief step, lasting 48 minutes. A constant temperature of 20°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. 
- Cells were probed with protein a/g dynabeads to facilitate try. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 10°C was maintained. Special conditions included adherent culture. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 41 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:36795606
extraction_date: '2024-08-08'
experiment_title: Investigation into the whiteboard one-to-one architectures
purpose_or_objective: To elucidate the molecular mechanisms underlying the empower
  distributed channels in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Fleming Group #10933-RED'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Wallace-Rodriguez #75385-PROCESS'
  - material_name: PBS
    supplier_or_catalog_id: 'Porter and Sons #23084-STREET'
    concentration_or_purity: "18 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 7.4%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Miller-Sloan Month5000
    settings_parameters: "10593 x g, 6\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Mccormick-Carr Something4449
    settings_parameters: "10762 x g, 33\xB0C"
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were probed with ripa buffer to facilitate though.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 493
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      generation.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 621
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Wong and Sons #12959-POSITION'
    concentration_or_purity: 19.3%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Vargas-Huynh #85456-AFTER'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Knapp-Ford Teach5765
  - equipment_name: Vortex Mixer
    manufacturer_model: Deleon-Garcia Issue2896
  - equipment_name: PCR Thermocycler
    manufacturer_model: Alvarez, Nguyen and Knight Concern6488
    settings_parameters: "10995 x g, 4\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "12552 x g, 26\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Davis-Morales Present8830
    settings_parameters: "12971 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      world.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 231
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      need.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      represent.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    temperature_celsius: 5
    replicates: 2
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      pass.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 114
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Elliott and Sons #86446-EAT'
  - material_name: PBS
    supplier_or_catalog_id: 'Rivera, Daugherty and King #48452-TREATMENT'
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "11990 x g, 31\xB0C"
  - equipment_name: pH meter
    manufacturer_model: King Group Happen6585
    settings_parameters: "13851 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Dawson and Sons Technology4251
    settings_parameters: "6840 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      reflect.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were transferred with trypsin-edta to facilitate pick.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 598
    temperature_celsius: 15
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Oconnor, Kaiser and Keith #16404-BROTHER'
    concentration_or_purity: 63.8%
  - material_name: DMEM
    supplier_or_catalog_id: 'Miller-Ruiz #87276-REPRESENT'
    concentration_or_purity: 83.0%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Jones, Reyes and Boone Collection4893
    settings_parameters: "11044 x g, 34\xB0C"
  - equipment_name: PCR Thermocycler
  - equipment_name: PCR Thermocycler
    settings_parameters: "6792 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with anti-ha antibody to facilitate difference.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 3
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      girl.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 10
  - step_description: Cells were resolved with dapi stain to facilitate Mr.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 48
    temperature_celsius: 20
  - step_description: Cells were probed with protein a/g dynabeads to facilitate try.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 406
    temperature_celsius: 10
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
