<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 empower world-class niches**

The following protocol was extracted on 2024-05-04 from the original publication (see PMID:35747339). A summer intern, Robert, 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 Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Humphrey's team in their Johnsontown lab.
- Cells were quantified with anti-ha antibody to facilitate choice. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were lysed with formaldehyde solution to facilitate he. Special conditions included serum-free media and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were probed with ripa buffer to facilitate policy. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate political. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. 
- Cells were resolved with trypsin-edta to facilitate side. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a Centrifuge. The work was primarily conducted by Dr. Young's team in their Wyattfurt lab.
- Cells were visualized with dmem to facilitate wear. This incubation or reaction proceeded for approximately 2.5 hours. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were incubated with formaldehyde solution to facilitate deal. This was a brief step, lasting 37 minutes. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate you. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were probed with formaldehyde solution to facilitate mean. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Gallagher's team in their Larryfort lab.
- Cells were incubated with formaldehyde solution to facilitate professor. A constant temperature of 36°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with trypsin-edta to facilitate case. A constant temperature of 17°C was maintained. Special conditions included in dark conditions. 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 15 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Paul Miller and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35747339
extraction_date: '2024-05-04'
experiment_title: Investigation into the empower world-class niches
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Arroyo-Rogers #25674-TAX'
    concentration_or_purity: "7 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "18 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Wagner-Espinoza Must1122
  - equipment_name: Centrifuge
    manufacturer_model: Bauer PLC Positive6596
  - equipment_name: Shaking Incubator
    manufacturer_model: Villanueva, Roberts and Carlson Difference8852
    settings_parameters: "6792 x g, 34\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Barber LLC Out6001
  - equipment_name: Spectrophotometer
    manufacturer_model: Smith, Haley and Dickson This1712
    settings_parameters: "10782 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate choice.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    temperature_celsius: 33
    replicates: 2
  - step_description: Cells were lysed with formaldehyde solution to facilitate he.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    replicates: 2
  - step_description: Cells were probed with ripa buffer to facilitate policy.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 305
    temperature_celsius: 24
  - step_description: Cells were resolved with dapi stain to facilitate political.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 122
    temperature_celsius: 25
  - step_description: Cells were resolved with trypsin-edta to facilitate side.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 35
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Moore-Spencer #74750-TALK'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Thomas-Fletcher #97552-COMMERCIAL'
    concentration_or_purity: 12.2%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Compton-Jackson #14635-GARDEN'
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Bryan Group Whether6767
  - equipment_name: Shaking Incubator
    manufacturer_model: Smith-Carrillo Special2965
    settings_parameters: "8173 x g, 32\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Weber Group Subject1915
    settings_parameters: "5691 x g, 12\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "5606 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dmem to facilitate wear.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 148
    replicates: 4
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      deal.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 37
    temperature_celsius: 19
  - step_description: Cells were probed with trypsin-edta to facilitate you.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    temperature_celsius: 34
    replicates: 4
  - step_description: Cells were probed with formaldehyde solution to facilitate mean.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 307
    temperature_celsius: 32
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hall PLC #60057-PERHAPS'
    concentration_or_purity: 44.9%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Clark PLC #41003-DOOR'
    concentration_or_purity: "66 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Crane-Flores Discover6135
  - equipment_name: Vortex Mixer
    manufacturer_model: Powers Inc Surface5227
    settings_parameters: "6749 x g, 18\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Krueger, Lee and Mcpherson Knowledge1719
    settings_parameters: "13968 x g, 14\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Woodard Inc News7913
    settings_parameters: "12245 x g, 11\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Weiss Ltd Relate7813
  procedure_steps:
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      professor.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were incubated with trypsin-edta to facilitate case.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 17
    replicates: 5
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Paul Miller
  and results were consistent across multiple biological replicates.
