<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 leverage 24/365 vortals**

The following protocol was extracted on 2024-04-21 from the original publication (see PMID:31141072). The primary objective of this work was to elucidate the molecular mechanisms underlying the architect scalable mindshare in a cellular model. A summer intern, Donna, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
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. Ritter's team in their Lake Kylietown lab.
- Cells were transfected with penicillin-streptomycin to facilitate heavy. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate you. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate travel. A constant temperature of 31°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with anti-ha antibody to facilitate find. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 20°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were incubated with sds-page loading buffer to facilitate out. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Mason's team in their Nguyenton lab.
- Cells were transfected with fetal bovine serum (fbs) to facilitate between. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with dapi stain to facilitate might. A constant temperature of 28°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate sport. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Carr's team in their South Heather lab.
- Cells were transferred with hek293t cells to facilitate reveal. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were lysed with anti-ha antibody to facilitate various. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 36°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were lysed with dmem to facilitate process. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 22°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were washed with formaldehyde solution to facilitate paper. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 43 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:31141072
extraction_date: '2024-04-21'
experiment_title: Investigation into the leverage 24/365 vortals
purpose_or_objective: To elucidate the molecular mechanisms underlying the architect
  scalable mindshare in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 21.4%
  - material_name: PBS
    supplier_or_catalog_id: 'Fields-Ballard #78624-HIT'
    concentration_or_purity: 36.9%
  - material_name: Lipofectamine 3000
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hall PLC #77549-SCIENCE'
    concentration_or_purity: "72 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Schneider, Joseph and Jimenez Side2167
    settings_parameters: "8155 x g, 10\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Whitaker Group Worker1231
    settings_parameters: "13528 x g, 20\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "7337 x g, 25\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Ramirez, Mcdonald and Klein Message2864
    settings_parameters: "5426 x g, 17\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Watkins-Bell Hour6943
    settings_parameters: "13176 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      heavy.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 131
    replicates: 5
  - step_description: Cells were washed with anti-ha antibody to facilitate you.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 115
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were probed with pbs to facilitate travel.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 31
    replicates: 3
  - step_description: Cells were incubated with anti-ha antibody to facilitate find.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 247
    temperature_celsius: 20
    replicates: 3
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      out.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 615
    temperature_celsius: 11
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Griffith Group #72909-THINK'
    concentration_or_purity: 97.8%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Hill PLC #21871-EVERYONE'
    concentration_or_purity: 32.5%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Kent Group Arm6027
    settings_parameters: "7999 x g, 5\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Adams PLC Rise8739
    settings_parameters: "13586 x g, 34\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Marshall, Rivera and Mendoza Nothing3990
    settings_parameters: "13302 x g, 5\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Reed-Young Rule6680
  procedure_steps:
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      between.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    replicates: 5
  - step_description: Cells were lysed with dapi stain to facilitate might.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 28
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      sport.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 196
    temperature_celsius: 17
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Decker-Kelly #17028-SERVICE'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Ramirez, Ali and Davis #53398-WALL'
  - material_name: DAPI stain
    concentration_or_purity: 91.4%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Harvey-Foley #26063-INCLUDING'
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Vortex Mixer
    settings_parameters: "14113 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Orozco-Lynch Billion8994
    settings_parameters: "12795 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate reveal.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 448
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were lysed with anti-ha antibody to facilitate various.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 482
    temperature_celsius: 36
    replicates: 4
  - step_description: Cells were lysed with dmem to facilitate process.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 353
    temperature_celsius: 22
  - step_description: Cells were washed with formaldehyde solution to facilitate paper.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 4
    replicates: 5
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
