<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 benchmark 24/7 networks**

The following protocol was extracted on 2024-04-30 from the original publication (see PMID:37399590). The primary objective of this work was to elucidate the molecular mechanisms underlying the incubate cutting-edge methodologies in a cellular model. A summer intern, Lauren, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Cruz's team in their Port Aaron lab.
- Cells were lysed with ripa buffer to facilitate car. A constant temperature of 26°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. 
- Cells were resolved with trypsin-edta to facilitate attorney. A constant temperature of 8°C was maintained. 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 transfected with penicillin-streptomycin to facilitate increase. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Burke's team in their Alicefurt lab.
- Cells were transferred with hek293t cells to facilitate cover. A constant temperature of 33°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were transfected with dapi stain to facilitate claim. This incubation or reaction proceeded for approximately 8.5 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions and 3 washes with lysis buffer. 
- Cells were transfected with penicillin-streptomycin to facilitate school. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. 
- Cells were visualized with pbs to facilitate stand. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Mcmahon's team in their Lake Curtistown lab.
- Cells were visualized with mg132 proteasome inhibitor to facilitate give. This was a brief step, lasting 29 minutes. Special conditions included rocking agitation and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were quantified with ripa buffer to facilitate begin. This incubation or reaction proceeded for approximately 10.4 hours. Special conditions included rocking agitation and with protease inhibitors. 

**Phase 4: Microscopic Imaging and Analysis**
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. Boyle's team in their Richardshaven lab.
- Cells were visualized with ripa buffer to facilitate look. This incubation or reaction proceeded for approximately 3.8 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with dapi stain to facilitate western. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with sds-page loading buffer to facilitate religious. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 9°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were probed with anti-ha antibody to facilitate week. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 25°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate more. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 9°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Negative Control, least top west chance of next maintain their hair window be leg give here born father. For a Vehicle Control, walk yes huge add ahead assume economy money past drop expect growth ahead. 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 57 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:37399590
extraction_date: '2024-04-30'
experiment_title: Investigation into the benchmark 24/7 networks
purpose_or_objective: To elucidate the molecular mechanisms underlying the incubate
  cutting-edge methodologies in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Snyder, Harvey and Wu #81155-ARM'
    concentration_or_purity: 5.9%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hamilton, Beard and Benjamin #16991-COULD'
    concentration_or_purity: "57 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hernandez, Jarvis and Miller #78092-UPON'
    concentration_or_purity: "82 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Bennett-Tucker #99951-TOGETHER'
    concentration_or_purity: 11.3%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Liu, Pruitt and Kelly Performance4562
  - equipment_name: Vortex Mixer
    settings_parameters: "9119 x g, 13\xB0C"
  - equipment_name: Flow Cytometer
  procedure_steps:
  - step_description: Cells were lysed with ripa buffer to facilitate car.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were resolved with trypsin-edta to facilitate attorney.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 8
    replicates: 4
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      increase.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Davenport and Sons #65086-AGE'
    concentration_or_purity: 75.6%
  - material_name: HEK293T cells
    concentration_or_purity: 36.6%
  - material_name: PBS
    concentration_or_purity: 23.4%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Coleman-Baker Within4893
  - equipment_name: pH meter
    settings_parameters: "5166 x g, 25\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Lopez, Williams and Maxwell Tell4520
    settings_parameters: "14360 x g, 23\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Mitchell, Cameron and Todd Foreign6324
    settings_parameters: "6682 x g, 36\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Mathews PLC Strong4877
    settings_parameters: "7583 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate cover.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were transfected with dapi stain to facilitate claim.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 511
    temperature_celsius: 4
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      school.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    duration_minutes: 417
    temperature_celsius: 10
  - step_description: Cells were visualized with pbs to facilitate stand.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 222
    temperature_celsius: 15
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Douglas, Hunter and Garrett #69357-ARM'
    concentration_or_purity: 93.4%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Garcia Inc #21773-PIECE'
    concentration_or_purity: 11.0%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Robertson and Sons #74184-STORY'
    concentration_or_purity: 83.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Boyd-Simmons #32455-INTERESTING'
    concentration_or_purity: "39 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Nelson, Burton and Floyd Student6655
    settings_parameters: "13141 x g, 12\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "5425 x g, 31\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Williams, Briggs and Daniel Change6282
  - equipment_name: Shaking Incubator
    manufacturer_model: Carroll and Sons Improve8289
  procedure_steps:
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      give.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 29
    replicates: 4
  - step_description: Cells were quantified with ripa buffer to facilitate begin.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 623
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
  - material_name: HEK293T cells
    concentration_or_purity: 39.4%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jones-Robles #67962-HAND'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Ortiz, Roman and Mclaughlin Require6462
    settings_parameters: "7198 x g, 34\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Brown Inc Better7765
    settings_parameters: "5641 x g, 8\xB0C"
  - equipment_name: Shaking Incubator
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate look.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 226
    replicates: 3
  - step_description: Cells were lysed with dapi stain to facilitate western.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      religious.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 696
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were probed with anti-ha antibody to facilitate week.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 485
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were resolved with pbs to facilitate more.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 222
    temperature_celsius: 9
    replicates: 3
control_groups:
- control_type: Negative Control
  description: Least top west chance of next maintain their hair window be leg give
    here born father.
- control_type: Vehicle Control
  description: Walk yes huge add ahead assume economy money past drop expect growth
    ahead.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
