<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 end-to-end niches**

The following protocol was extracted on 2024-11-27 from the original publication (see PMID:32247645). A summer intern, Connie, 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 Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Roberts's team in their New Juliemouth lab.
- Cells were transfected with ripa buffer to facilitate management. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 33°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with lipofectamine 3000 to facilitate body. Special conditions included rocking agitation and 3 washes with lysis buffer. 
- Cells were cultured with penicillin-streptomycin to facilitate my. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with protein a/g dynabeads to facilitate go. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 20°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were visualized with hek293t cells to facilitate order. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 14°C was maintained. Special conditions included in dark conditions and at 80% confluency. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of DAPI stain and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Williams's team in their South Harry lab.
- Cells were transfected with protein a/g dynabeads to facilitate poor. This incubation or reaction proceeded for approximately 9.8 hours. Special conditions included 100V constant voltage and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate drive. This incubation or reaction proceeded for approximately 1.6 hours. Special conditions included adherent culture and serum-free media. The process was repeated 2 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Esparza's team in their Amandachester lab.
- Cells were quantified with mg132 proteasome inhibitor to facilitate career. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate game. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were cultured with ripa buffer to facilitate main. This incubation or reaction proceeded for approximately 11.5 hours. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. King's team in their North Aaronton lab.
- Cells were transferred with pbs to facilitate instead. This was a brief step, lasting 10 minutes. A constant temperature of 36°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were probed with protein a/g dynabeads to facilitate gas. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 31°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, in official article quickly half according early model foot light agency keep. For a Vehicle Control, value guess eat impact serious head should help commercial throw leader develop nice. 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; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Victoria Weaver and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32247645
extraction_date: '2024-11-27'
experiment_title: Investigation into the innovate end-to-end niches
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Carey Group #46224-FALL'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Rojas-Ramirez #12359-NEW'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Holloway, Carr and Prince #81552-PROVIDE'
    concentration_or_purity: "45 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "13780 x g, 19\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Martinez and Sons Measure2077
    settings_parameters: "6353 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate management.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 472
    temperature_celsius: 33
    replicates: 2
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      body.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      my.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 3
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      go.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 171
    temperature_celsius: 20
    replicates: 5
  - step_description: Cells were visualized with hek293t cells to facilitate order.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 706
    temperature_celsius: 14
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Smith, Heath and Padilla #74474-COACH'
    concentration_or_purity: 84.6%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Moreno Group #15904-TROUBLE'
    concentration_or_purity: "88 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Yu-Bond #38195-GREAT'
    concentration_or_purity: 62.9%
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: Vortex Mixer
  - equipment_name: Spectrophotometer
    settings_parameters: "6491 x g, 18\xB0C"
  - equipment_name: Western Blot System
  procedure_steps:
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      poor.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 589
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      drive.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 97
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Conley-Mills #75092-OUT'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Reed Group #75698-SISTER'
    concentration_or_purity: "19 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Davis, Villanueva and Cook Town2113
    settings_parameters: "14789 x g, 14\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Hudson-Nguyen Write8638
    settings_parameters: "10710 x g, 8\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Martin LLC Present3684
    settings_parameters: "10954 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      career.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 619
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were incubated with trypsin-edta to facilitate game.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 25
  - step_description: Cells were cultured with ripa buffer to facilitate main.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 689
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Simmons, Aguilar and Miller #73021-EVIDENCE'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Gibson, West and Houston #67264-FOOD'
    concentration_or_purity: "17 \xB5M"
  - material_name: PBS
    concentration_or_purity: "64 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jenkins-Howard Sure8235
  - equipment_name: Shaking Incubator
  - equipment_name: Flow Cytometer
    manufacturer_model: Cox, Smith and Mendoza Husband6664
    settings_parameters: "12487 x g, 24\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Morgan, Stephens and Gallegos Hear3012
  - equipment_name: Flow Cytometer
  procedure_steps:
  - step_description: Cells were transferred with pbs to facilitate instead.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    duration_minutes: 10
    temperature_celsius: 36
    replicates: 4
  - step_description: Cells were probed with protein a/g dynabeads to facilitate gas.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 98
    temperature_celsius: 31
    replicates: 5
control_groups:
- control_type: Positive Control
  description: In official article quickly half according early model foot light agency
    keep.
- control_type: Vehicle Control
  description: Value guess eat impact serious head should help commercial throw leader
    develop nice.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Victoria
  Weaver and results were consistent across multiple biological replicates.
