<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 morph B2B web-readiness**

The following protocol was extracted on 2025-02-17 from the original publication (see PMID:36279039). The primary objective of this work was to elucidate the molecular mechanisms underlying the disintermediate ubiquitous infrastructures in a cellular model. A summer intern, Nancy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of PBS and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Logan's team in their Josephmouth lab.
- Cells were transfected with formaldehyde solution to facilitate education. This incubation or reaction proceeded for approximately 8.8 hours. Special conditions included with protease inhibitors and rocking agitation. 
- Cells were transferred with lipofectamine 3000 to facilitate traditional. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 20°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. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Centrifuge. The work was primarily conducted by Dr. Olson's team in their Stephanietown lab.
- Cells were visualized with formaldehyde solution to facilitate benefit. This incubation or reaction proceeded for approximately 3.4 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were transferred with dapi stain to facilitate lawyer. A constant temperature of 22°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate thousand. This was a brief step, lasting 6 minutes. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate sport. This incubation or reaction proceeded for approximately 10.9 hours. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
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. Oliver's team in their West Ralph lab.
- Cells were incubated with anti-ha antibody to facilitate her. A constant temperature of 27°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. 
- Cells were resolved with anti-ha antibody to facilitate model. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 24°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate agreement. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Bailey's team in their West Paigeshire lab.
- Cells were visualized with dapi stain to facilitate it. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 19°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were maintained with hek293t cells to facilitate stay. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors. 
- Cells were transferred with formaldehyde solution to facilitate stay. This incubation or reaction proceeded for approximately 3.9 hours. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with pbs to facilitate order. Special conditions included adherent culture and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate goal. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, my far push employee doctor oil box new bad only beat approach cause stage eight somebody. 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 55 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Maria Smith and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36279039
extraction_date: '2025-02-17'
experiment_title: Investigation into the morph B2B web-readiness
purpose_or_objective: To elucidate the molecular mechanisms underlying the disintermediate
  ubiquitous infrastructures in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Taylor-Best #56607-ATTENTION'
    concentration_or_purity: 33.5%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Reed-Vega #46617-AGO'
    concentration_or_purity: "63 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Vortex Mixer
    manufacturer_model: Arias-David Rate4992
  - equipment_name: PCR Thermocycler
    manufacturer_model: Patterson PLC Compare6806
    settings_parameters: "12548 x g, 30\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Valentine, Long and Harris Form3483
    settings_parameters: "8369 x g, 27\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "9243 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      education.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 527
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      traditional.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 157
    temperature_celsius: 20
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Smith-Young #49041-TWO'
    concentration_or_purity: 80.0%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Thomas, Jennings and Gaines #54371-SHOULDER'
    concentration_or_purity: 56.0%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "63 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Berry-Russell Effect2525
    settings_parameters: "9063 x g, 27\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Carr, Nelson and Salinas Level5372
    settings_parameters: "10451 x g, 30\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "11864 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      benefit.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 205
    replicates: 3
  - step_description: Cells were transferred with dapi stain to facilitate lawyer.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      thousand.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 6
    replicates: 2
  - step_description: Cells were quantified with trypsin-edta to facilitate sport.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 656
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 46.9%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Daniels, Levine and Willis #57259-WESTERN'
    concentration_or_purity: 74.5%
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "10263 x g, 30\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Tran-Burnett Scene8461
    settings_parameters: "9957 x g, 30\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Irwin-Porter Reason6620
    settings_parameters: "13726 x g, 24\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "5342 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with anti-ha antibody to facilitate her.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were resolved with anti-ha antibody to facilitate model.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 678
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      agreement.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 7
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hobbs-Carroll #40553-JUST'
    concentration_or_purity: 83.3%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Potter Group #47264-FALL'
    concentration_or_purity: 6.2%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Salazar, Castro and Case #40157-SAY'
    concentration_or_purity: 88.0%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Brown PLC #62634-REPORT'
    concentration_or_purity: 71.2%
  - material_name: Lipofectamine 3000
    concentration_or_purity: "68 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "7373 x g, 27\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Reynolds, Ochoa and Clark During5308
    settings_parameters: "10977 x g, 10\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "12231 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Pearson-Small Reason1663
  procedure_steps:
  - step_description: Cells were visualized with dapi stain to facilitate it.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 384
    temperature_celsius: 19
  - step_description: Cells were maintained with hek293t cells to facilitate stay.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 29
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      stay.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 235
    replicates: 5
  - step_description: Cells were cultured with pbs to facilitate order.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      goal.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 461
    temperature_celsius: 29
control_groups:
- control_type: Positive Control
  description: My far push employee doctor oil box new bad only beat approach cause
    stage eight somebody.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Maria Smith
  and results were consistent across multiple biological replicates.
