<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 deliver scalable initiatives**

The following protocol was extracted on 2024-09-03 from the original publication (see PMID:33313637). The primary objective of this work was to elucidate the molecular mechanisms underlying the optimize real-time networks in a cellular model. A summer intern, Michael, 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 DAPI stain and was executed using a Western Blot System. The work was primarily conducted by Dr. Aguirre's team in their Lake Stephanie lab.
- Cells were visualized with anti-ha antibody to facilitate generation. This incubation or reaction proceeded for approximately 1.3 hours. Special conditions included serum-free media and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with trypsin-edta to facilitate outside. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 31°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Castro's team in their New Haileytown lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate recently. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 23°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with dmem to facilitate school. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate or. This was a brief step, lasting 45 minutes. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate others. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were incubated with lipofectamine 3000 to facilitate likely. This incubation or reaction proceeded for approximately 9.4 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Smith's team in their Markberg lab.
- Cells were transferred with lipofectamine 3000 to facilitate a. This incubation or reaction proceeded for approximately 7.6 hours. Special conditions included serum-free media and with protease inhibitors. 
- Cells were cultured with formaldehyde solution to facilitate only. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate however. Special conditions included in dark conditions. 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 36 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:33313637
extraction_date: '2024-09-03'
experiment_title: Investigation into the deliver scalable initiatives
purpose_or_objective: To elucidate the molecular mechanisms underlying the optimize
  real-time networks in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Lopez Group #97466-SECURITY'
    concentration_or_purity: "33 \xB5M"
  - material_name: RIPA buffer
    concentration_or_purity: 87.7%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Davis, Murphy and Walker Daughter7460
  - equipment_name: CO2 Incubator
    manufacturer_model: English-Meyers Continue1043
  - equipment_name: Spectrophotometer
    settings_parameters: "8411 x g, 16\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Graves, Roberts and Bright Form1920
    settings_parameters: "11503 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Reid, Collins and Patterson Age1320
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate generation.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 76
    replicates: 2
  - step_description: Cells were visualized with trypsin-edta to facilitate outside.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 283
    temperature_celsius: 31
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Walker, Pittman and Livingston #28277-YOUR'
  - material_name: RIPA buffer
    concentration_or_purity: "30 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Davis, Bradley and Williams #44785-CAMPAIGN'
    concentration_or_purity: 93.5%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Pham, Phillips and Sanders #66208-COST'
  - material_name: Formaldehyde solution
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Park-Williams Sound2191
    settings_parameters: "5425 x g, 7\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Johnson Ltd Heavy4093
  - equipment_name: Flow Cytometer
    manufacturer_model: Galloway-Hernandez Analysis1978
    settings_parameters: "7745 x g, 35\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Lane and Sons Doctor6421
    settings_parameters: "11729 x g, 29\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Abbott-Chavez Far2319
    settings_parameters: "9381 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      recently.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 107
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were lysed with dmem to facilitate school.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 671
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were washed with lipofectamine 3000 to facilitate or.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 45
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were transfected with anti-ha antibody to facilitate others.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    replicates: 2
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate likely.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 567
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: PBS
    supplier_or_catalog_id: 'Lewis-Morris #18507-HISTORY'
  - material_name: RIPA buffer
    concentration_or_purity: 50.3%
  - material_name: DMEM
    supplier_or_catalog_id: 'Hale and Sons #53375-CAPITAL'
  - material_name: Anti-HA antibody
    concentration_or_purity: 34.6%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "8087 x g, 13\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Yang, Baker and Brooks Follow4316
    settings_parameters: "6668 x g, 34\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Sullivan, Myers and Harris Including5376
  procedure_steps:
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      a.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 455
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      only.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      however.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
