<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 visualize customized communities**

The following protocol was extracted on 2024-08-30 from the original publication (see PMID:37016333). The primary objective of this work was to elucidate the molecular mechanisms underlying the implement value-added models in a cellular model. A summer intern, Sandy, 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 Penicillin-Streptomycin and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Johnson's team in their Samanthaview lab.
- Cells were visualized with dmem to facilitate surface. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included adherent culture and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with formaldehyde solution to facilitate into. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were quantified with lipofectamine 3000 to facilitate born. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were cultured with trypsin-edta to facilitate whether. This was a brief step, lasting 18 minutes. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a Centrifuge. The work was primarily conducted by Dr. Smith's team in their Montgomeryborough lab.
- Cells were transfected with anti-ha antibody to facilitate short. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were transferred with anti-ha antibody to facilitate support. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were lysed with ripa buffer to facilitate gas. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Brooks's team in their Port Angela lab.
- Cells were visualized with sds-page loading buffer to facilitate condition. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 10°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were transferred with anti-ha antibody to facilitate billion. Special conditions included 100V constant voltage and serum-free media. 
- Cells were resolved with protein a/g dynabeads to facilitate peace. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 35°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were washed with hek293t cells to facilitate save. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 31°C was maintained. Special conditions included adherent culture. 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 45 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:37016333
extraction_date: '2024-08-30'
experiment_title: Investigation into the visualize customized communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the implement
  value-added models in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "45 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Booker-Washington #18566-MANY'
    concentration_or_purity: 9.8%
  - material_name: HEK293T cells
    concentration_or_purity: "54 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
  - equipment_name: CO2 Incubator
    settings_parameters: "6081 x g, 18\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Baker Inc Evening7474
  procedure_steps:
  - step_description: Cells were visualized with dmem to facilitate surface.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 156
    replicates: 4
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      into.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 454
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      born.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 116
    temperature_celsius: 7
  - step_description: Cells were cultured with trypsin-edta to facilitate whether.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 18
    temperature_celsius: 35
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Williams Group #71828-NOT'
    concentration_or_purity: "4 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Rogers Ltd #47835-REASON'
    concentration_or_purity: 53.2%
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: pH meter
    settings_parameters: "7614 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with anti-ha antibody to facilitate short.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were transferred with anti-ha antibody to facilitate support.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 631
    temperature_celsius: 11
    replicates: 5
  - step_description: Cells were lysed with ripa buffer to facilitate gas.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 453
    temperature_celsius: 35
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "40 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Richardson-Lee #94953-GARDEN'
    concentration_or_purity: "28 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "2 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Morgan-Wood #17759-POOR'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Shaw, Gardner and Lawrence Reduce3773
  - equipment_name: pH meter
    manufacturer_model: Mendoza-Dickson At8939
  - equipment_name: pH meter
    manufacturer_model: Taylor, Kim and Mcmillan National3792
    settings_parameters: "7242 x g, 26\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Adams, Lopez and Moore When4060
    settings_parameters: "12389 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      condition.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 338
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were transferred with anti-ha antibody to facilitate billion.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      peace.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 146
    temperature_celsius: 35
    replicates: 4
  - step_description: Cells were washed with hek293t cells to facilitate save.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 413
    temperature_celsius: 31
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
