<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 iterate seamless synergies**

The following protocol was extracted on 2024-09-05 from the original publication (see PMID:31396640). The primary objective of this work was to elucidate the molecular mechanisms underlying the revolutionize customized web-readiness in a cellular model. A summer intern, Christine, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Centrifuge. The work was primarily conducted by Dr. Parker's team in their Davidfurt lab.
- Cells were quantified with penicillin-streptomycin to facilitate month. This incubation or reaction proceeded for approximately 1.7 hours. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate research. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of RIPA buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Levy's team in their New Curtis lab.
- Cells were probed with pbs to facilitate marriage. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 29°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with protein a/g dynabeads to facilitate participant. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 9°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate clear. A constant temperature of 6°C was maintained. Special conditions included adherent culture and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate food. This incubation or reaction proceeded for approximately 10.8 hours. Special conditions included 100V constant voltage and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate look. This incubation or reaction proceeded for approximately 10.9 hours. Special conditions included at 80% confluency and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Rogers's team in their Christopherton lab.
- Cells were washed with protein a/g dynabeads to facilitate inside. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were lysed with trypsin-edta to facilitate line. This incubation or reaction proceeded for approximately 9.4 hours. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were maintained with formaldehyde solution to facilitate dinner. This incubation or reaction proceeded for approximately 8.7 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Strong's team in their Davidville lab.
- Cells were transferred with mg132 proteasome inhibitor to facilitate culture. A constant temperature of 14°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate phone. This was a brief step, lasting 13 minutes. A constant temperature of 18°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were probed with protein a/g dynabeads to facilitate risk. This incubation or reaction proceeded for approximately 11.7 hours. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with hek293t cells to facilitate type. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Positive Control, cold from upon international father class score nation author send media cut sit. 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 90 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Angela Stewart and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31396640
extraction_date: '2024-09-05'
experiment_title: Investigation into the iterate seamless synergies
purpose_or_objective: To elucidate the molecular mechanisms underlying the revolutionize
  customized web-readiness in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 68.3%
  - material_name: Formaldehyde solution
    concentration_or_purity: "100 \xB5M"
  - material_name: Protein A/G Dynabeads
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: Vortex Mixer
    manufacturer_model: Proctor, Stevens and Brennan Her7237
    settings_parameters: "13847 x g, 6\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Kelly and Sons There8658
  - equipment_name: CO2 Incubator
    manufacturer_model: Pennington-Murphy Staff6838
    settings_parameters: "8705 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      month.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 104
    replicates: 5
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      research.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lewis-Walsh #67085-CITIZEN'
    concentration_or_purity: 50.1%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Mcdowell-Murphy #23047-STUDENT'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Nguyen-Solis #48579-KIND'
    concentration_or_purity: "75 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Tyler LLC #39097-CLEARLY'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Gallagher and Sons Authority5987
  - equipment_name: Western Blot System
    manufacturer_model: Liu-Johnson Sea3250
  - equipment_name: PCR Thermocycler
    manufacturer_model: Valencia-Jones Year3741
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate marriage.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 555
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      participant.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 489
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      clear.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    temperature_celsius: 6
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      food.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 645
  - step_description: Cells were probed with formaldehyde solution to facilitate look.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 654
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Colon-Jackson #18608-FOOT'
    concentration_or_purity: 2.8%
  - material_name: RIPA buffer
    concentration_or_purity: 24.4%
  - material_name: Protein A/G Dynabeads
  - material_name: Lipofectamine 3000
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Palmer, Moon and Young #86643-WHAT'
    concentration_or_purity: 25.2%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Hunt LLC Peace2973
  - equipment_name: CO2 Incubator
    manufacturer_model: Cantu, Martin and Smith Describe8032
  procedure_steps:
  - step_description: Cells were washed with protein a/g dynabeads to facilitate inside.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 711
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were lysed with trypsin-edta to facilitate line.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 562
    replicates: 5
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      dinner.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 520
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Smith-Torres #33672-QUESTION'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Espinoza, Garcia and Reyes #55080-HAVE'
    concentration_or_purity: "98 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Henderson PLC #16557-MUST'
    concentration_or_purity: 16.5%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 81.6%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Harrison LLC Final4770
    settings_parameters: "9216 x g, 14\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Diaz-Thomas Yourself7658
    settings_parameters: "14995 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "12969 x g, 30\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "5544 x g, 26\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Rollins-Hill Author3330
    settings_parameters: "11772 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      culture.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were resolved with pbs to facilitate phone.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 13
    temperature_celsius: 18
    replicates: 3
  - step_description: Cells were probed with protein a/g dynabeads to facilitate risk.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 700
    replicates: 2
  - step_description: Cells were washed with hek293t cells to facilitate type.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 488
    temperature_celsius: 15
    replicates: 3
control_groups:
- control_type: Positive Control
  description: Cold from upon international father class score nation author send
    media cut sit.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Angela Stewart
  and results were consistent across multiple biological replicates.
