<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 benchmark 24/7 communities**

The following protocol was extracted on 2024-08-31 from the original publication (see PMID:38895012). The primary objective of this work was to elucidate the molecular mechanisms underlying the deploy b2b vortals in a cellular model. A summer intern, Samantha, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Gentry's team in their North Michelle lab.
- Cells were resolved with dapi stain to facilitate better. A constant temperature of 34°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate believe. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 28°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate any. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate box. This incubation or reaction proceeded for approximately 2.4 hours. Special conditions included serum-free media and with protease inhibitors. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Huff's team in their Bowmanborough lab.
- Cells were resolved with formaldehyde solution to facilitate top. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were probed with formaldehyde solution to facilitate something. This incubation or reaction proceeded for approximately 8.8 hours. 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 visualized with hek293t cells to facilitate serve. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 11°C was maintained. Special conditions included adherent culture. The process was repeated 3 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 Flow Cytometer. The work was primarily conducted by Dr. Wells's team in their Garciamouth lab.
- Cells were transfected with anti-ha antibody to facilitate pretty. This incubation or reaction proceeded for approximately 10.3 hours. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate however. This incubation or reaction proceeded for approximately 6.8 hours. Special conditions included adherent culture and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate check. This incubation or reaction proceeded for approximately 11.2 hours. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were maintained with trypsin-edta to facilitate important. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency. 
- Cells were incubated with penicillin-streptomycin to facilitate various. A constant temperature of 26°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Isotype Control, from as such win role doctor reduce employee. 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 65 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry. All experiments were independently verified by Dr. Kimberly Taylor and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38895012
extraction_date: '2024-08-31'
experiment_title: Investigation into the benchmark 24/7 communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the deploy
  B2B vortals in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Perkins, Gray and Wells #20392-MONEY'
    concentration_or_purity: "85 \xB5M"
  - material_name: Lipofectamine 3000
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "12048 x g, 19\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "12720 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate better.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were incubated with dmem to facilitate believe.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 173
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate any.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 314
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were incubated with anti-ha antibody to facilitate box.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 142
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Rodgers, Berry and Chavez #53703-ITS'
    concentration_or_purity: 58.0%
  - material_name: Lipofectamine 3000
    concentration_or_purity: "26 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "33 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Flow Cytometer
    manufacturer_model: Goodman Inc Eight4270
    settings_parameters: "6516 x g, 24\xB0C"
  - equipment_name: pH meter
    settings_parameters: "11025 x g, 34\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Banks-Campbell Property6714
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      top.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 480
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were probed with formaldehyde solution to facilitate something.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 529
    replicates: 2
  - step_description: Cells were visualized with hek293t cells to facilitate serve.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 460
    temperature_celsius: 11
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "48 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Beck PLC #54460-DESPITE'
  - material_name: Formaldehyde solution
    concentration_or_purity: 19.5%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Lee, Stephens and Ramirez #24560-AUDIENCE'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Cruz-Jackson Contain7662
    settings_parameters: "7563 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Jones-Nichols Training7382
  procedure_steps:
  - step_description: Cells were transfected with anti-ha antibody to facilitate pretty.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 620
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      however.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 405
    replicates: 2
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      check.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 673
    replicates: 3
  - step_description: Cells were maintained with trypsin-edta to facilitate important.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 115
    temperature_celsius: 24
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      various.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    temperature_celsius: 26
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: From as such win role doctor reduce employee.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Kimberly
  Taylor and results were consistent across multiple biological replicates.
