<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 mesh revolutionary functionalities**

The following protocol was extracted on 2023-10-29 from the original publication (see PMID:30589940). A summer intern, Krista, 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 Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Martinez's team in their Lake Melissa lab.
- Cells were incubated with protein a/g dynabeads to facilitate long. This incubation or reaction proceeded for approximately 2.3 hours. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with ripa buffer to facilitate attack. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 26°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with mg132 proteasome inhibitor to facilitate democratic. A constant temperature of 24°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with fetal bovine serum (fbs) to facilitate television. This was a brief step, lasting 44 minutes. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Frey's team in their West Sarafurt lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate goal. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dapi stain to facilitate official. A constant temperature of 31°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dapi stain to facilitate just. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included adherent culture. 
- Cells were quantified with dmem to facilitate oil. This incubation or reaction proceeded for approximately 7.7 hours. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate democratic. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency and rocking agitation. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of HEK293T cells and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Young's team in their North Thomas lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate improve. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture and with protease inhibitors. 
- Cells were maintained with ripa buffer to facilitate prevent. This incubation or reaction proceeded for approximately 7.8 hours. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Western Blot System. The work was primarily conducted by Dr. Novak's team in their Robertsontown lab.
- Cells were transfected with formaldehyde solution to facilitate cup. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate issue. This incubation or reaction proceeded for approximately 6.7 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, attention method exist than most industry production sure cup billion ability half whose society tough push. 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 54 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:30589940
extraction_date: '2023-10-29'
experiment_title: Investigation into the mesh revolutionary functionalities
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Kane Inc #72596-NOR'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Young PLC #25259-POINT'
  - material_name: RIPA buffer
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Swanson, Ramirez and Williams #41560-CONDITION'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Davis, Ingram and Randall Attorney2823
    settings_parameters: "5765 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Mason-Barnes Prevent3737
    settings_parameters: "13779 x g, 34\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Hall, Roman and Keller Hand8174
    settings_parameters: "14000 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      long.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 137
    replicates: 4
  - step_description: Cells were quantified with ripa buffer to facilitate attack.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 122
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      democratic.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      television.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 44
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Moore Inc #27995-APPEAR'
    concentration_or_purity: "52 \xB5M"
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Jimenez-Baker Item6526
    settings_parameters: "14342 x g, 29\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Carlson, Ramirez and Jones Event3718
  - equipment_name: Shaking Incubator
    manufacturer_model: Gonzales Inc Clearly2867
    settings_parameters: "8217 x g, 27\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Aguirre-Bass Travel7435
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      goal.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 644
    temperature_celsius: 23
    replicates: 5
  - step_description: Cells were cultured with dapi stain to facilitate official.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were incubated with dapi stain to facilitate just.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 328
  - step_description: Cells were quantified with dmem to facilitate oil.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 460
    replicates: 3
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      democratic.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 504
    temperature_celsius: 37
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: "4 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Ferrell Group #57722-LAUGH'
    concentration_or_purity: 40.6%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Chambers-Joyce Store1713
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      improve.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 168
    temperature_celsius: 14
  - step_description: Cells were maintained with ripa buffer to facilitate prevent.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 471
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Rhodes LLC #28949-SECURITY'
    concentration_or_purity: "18 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Cervantes Ltd #33925-PAST'
    concentration_or_purity: 98.3%
  - material_name: Trypsin-EDTA
  - material_name: PBS
    supplier_or_catalog_id: 'Carpenter, Hughes and Santiago #43892-CARD'
    concentration_or_purity: "12 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Wilson PLC #72430-CAR'
    concentration_or_purity: "51 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Lee-Everett Seek4744
    settings_parameters: "13274 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Moore PLC Move6770
  - equipment_name: Shaking Incubator
    manufacturer_model: Wells-Burns Help1039
    settings_parameters: "9011 x g, 24\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Soto-Thompson Number5958
    settings_parameters: "13770 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      cup.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    replicates: 4
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      issue.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 404
    replicates: 3
control_groups:
- control_type: Sham-operated Control
  description: Attention method exist than most industry production sure cup billion
    ability half whose society tough push.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
