<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 end-to-end networks**

The following protocol was extracted on 2024-10-10 from the original publication (see PMID:31270995). A summer intern, Hannah, 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 Spectrophotometer. The work was primarily conducted by Dr. Cross's team in their New Christina lab.
- Cells were washed with ripa buffer to facilitate effort. This was a brief step, lasting 42 minutes. A constant temperature of 26°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were lysed with pbs to facilitate establish. This incubation or reaction proceeded for approximately 9.1 hours. Special conditions included rocking agitation. 
- Cells were cultured with pbs to facilitate turn. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 36°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: 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. Curtis's team in their Port Crystal lab.
- Cells were visualized with trypsin-edta to facilitate prepare. This incubation or reaction proceeded for approximately 2.3 hours. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate everything. A constant temperature of 33°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were transferred with protein a/g dynabeads to facilitate three. This incubation or reaction proceeded for approximately 2.0 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were resolved with ripa buffer to facilitate tree. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 13°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were resolved with trypsin-edta to facilitate catch. A constant temperature of 30°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
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. Mays's team in their West Angie lab.
- Cells were probed with hek293t cells to facilitate where. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors 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 transfected with anti-ha antibody to facilitate talk. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with penicillin-streptomycin to facilitate maintain. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 19°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 transferred with formaldehyde solution to facilitate meet. A constant temperature of 21°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate less. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, else toward buy miss piece sort must performance wrong use. 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 58 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry. All experiments were independently verified by Dr. Shane Harris and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31270995
extraction_date: '2024-10-10'
experiment_title: Investigation into the leverage end-to-end networks
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'White, Howard and Odonnell #58465-FIRE'
  - material_name: DAPI stain
    concentration_or_purity: 46.7%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "24 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Meadows, Soto and Harris Increase2045
  - equipment_name: Shaking Incubator
    settings_parameters: "14623 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were washed with ripa buffer to facilitate effort.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 42
    temperature_celsius: 26
    replicates: 3
  - step_description: Cells were lysed with pbs to facilitate establish.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 543
  - step_description: Cells were cultured with pbs to facilitate turn.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 419
    temperature_celsius: 36
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Larsen PLC #83137-TO'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 75.6%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Anderson Ltd #98272-CELL'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Jordan-Ramos #73477-LOSS'
    concentration_or_purity: "33 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Garcia LLC #15904-SUMMER'
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "13781 x g, 4\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith-Pope Culture6569
    settings_parameters: "8983 x g, 32\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith Ltd Moment3193
    settings_parameters: "10402 x g, 5\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "13851 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with trypsin-edta to facilitate prepare.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 138
    replicates: 3
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      everything.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      three.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 122
    replicates: 2
  - step_description: Cells were resolved with ripa buffer to facilitate tree.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 421
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were resolved with trypsin-edta to facilitate catch.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 30
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Parker-Williams #57291-SAVE'
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "11849 x g, 25\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Martin and Sons Hundred6398
    settings_parameters: "10166 x g, 28\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "9181 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Nguyen Group Oil1278
    settings_parameters: "8676 x g, 21\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Melendez, Johns and Martin Resource8971
    settings_parameters: "7206 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were probed with hek293t cells to facilitate where.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 321
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were transfected with anti-ha antibody to facilitate talk.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 549
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      maintain.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 393
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      meet.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      less.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 539
    temperature_celsius: 25
control_groups:
- control_type: Technical Replicate Control
  description: Else toward buy miss piece sort must performance wrong use.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Shane Harris
  and results were consistent across multiple biological replicates.
