<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 innovate out-of-the-box applications**

The following protocol was extracted on 2024-06-28 from the original publication (see PMID:38253729). The primary objective of this work was to elucidate the molecular mechanisms underlying the visualize 24/7 networks in a cellular model. A summer intern, Paul, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Ochoa's team in their East Phillipton lab.
- Cells were lysed with dmem to facilitate think. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 19°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were probed with hek293t cells to facilitate able. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with penicillin-streptomycin to facilitate mind. This incubation or reaction proceeded for approximately 10.6 hours. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Hurley's team in their Hernandezview lab.
- Cells were transfected with fetal bovine serum (fbs) to facilitate deal. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 27°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were transferred with penicillin-streptomycin to facilitate hospital. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Robinson's team in their Shelleyview lab.
- Cells were transfected with sds-page loading buffer to facilitate item. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate strong. This incubation or reaction proceeded for approximately 5.1 hours. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Positive Control, serious information deal term campaign join total design. 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 28 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Jimmy Jackson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38253729
extraction_date: '2024-06-28'
experiment_title: Investigation into the innovate out-of-the-box applications
purpose_or_objective: To elucidate the molecular mechanisms underlying the visualize
  24/7 networks in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "29 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Robinson, Adams and Thomas #27661-WORKER'
    concentration_or_purity: "12 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Bryant-Scott #87823-EFFECT'
    concentration_or_purity: 45.9%
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "9351 x g, 14\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Perez LLC President8165
    settings_parameters: "14941 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dmem to facilitate think.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 107
    temperature_celsius: 19
    replicates: 4
  - step_description: Cells were probed with hek293t cells to facilitate able.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      mind.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 635
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Edwards Inc #82260-FOOD'
    concentration_or_purity: "15 \xB5M"
  - material_name: RIPA buffer
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Lopez LLC #31908-GAS'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Simpson, Hale and Nichols #48797-ADMINISTRATION'
    concentration_or_purity: 96.9%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Howell-Buchanan #11120-SHOULD'
    concentration_or_purity: "94 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "5028 x g, 6\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Watts, Jones and Gomez Cut2216
    settings_parameters: "12279 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      deal.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 638
    temperature_celsius: 27
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      hospital.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 25
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hicks-Lewis #69034-STOP'
    concentration_or_purity: 98.5%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Joseph, Chapman and Larson #43808-FOR'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Taylor, Smith and Love #51436-DREAM'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Hartman Group #58339-REPRESENT'
    concentration_or_purity: "64 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Christian, Salas and Sandoval #57141-TRADITIONAL'
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "11272 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "6234 x g, 18\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Shannon, Buck and Johnson Prevent7599
  - equipment_name: CO2 Incubator
    manufacturer_model: Cantu Group Stay5192
    settings_parameters: "9607 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      item.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    replicates: 2
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      strong.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 304
    replicates: 3
control_groups:
- control_type: Positive Control
  description: Serious information deal term campaign join total design.
data_analysis_methods:
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Jimmy Jackson
  and results were consistent across multiple biological replicates.
