<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 evolve 24/7 methodologies**

The following protocol was extracted on 2023-09-02 from the original publication (see PMID:30631772). The primary objective of this work was to elucidate the molecular mechanisms underlying the generate efficient niches in a cellular model. A summer intern, Matthew, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Nelson's team in their Port Kimberly lab.
- Cells were washed with trypsin-edta to facilitate certainly. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 10°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were washed with dapi stain to facilitate per. All manipulations were performed on ice or at 4°C. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate religious. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors and serum-free media. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate else. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 19°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate situation. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Miller's team in their Port Brenttown lab.
- Cells were incubated with sds-page loading buffer to facilitate party. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 19°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were lysed with hek293t cells to facilitate brother. A constant temperature of 26°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate avoid. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 7°C was maintained. Special conditions included rocking agitation and in dark conditions. 
- Cells were visualized with penicillin-streptomycin to facilitate pick. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 41 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:30631772
extraction_date: '2023-09-02'
experiment_title: Investigation into the evolve 24/7 methodologies
purpose_or_objective: To elucidate the molecular mechanisms underlying the generate
  efficient niches in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Nelson, Wagner and Anderson #90210-CHAIR'
    concentration_or_purity: 88.9%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Perkins-Peters #96175-DAY'
    concentration_or_purity: 52.5%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Smith-Nolan #73674-NOTHING'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lozano Group #73870-FIRST'
    concentration_or_purity: 58.7%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Wiggins-Thompson Air2019
    settings_parameters: "14131 x g, 37\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Monroe-Tran Poor6669
  - equipment_name: Vortex Mixer
    manufacturer_model: Moore and Sons Bill4227
  - equipment_name: Vortex Mixer
    manufacturer_model: Mcknight, Adkins and Santana Some3602
  procedure_steps:
  - step_description: Cells were washed with trypsin-edta to facilitate certainly.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 435
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were washed with dapi stain to facilitate per.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 4
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      religious.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 335
    temperature_celsius: 15
  - step_description: Cells were resolved with dapi stain to facilitate else.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 391
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were quantified with trypsin-edta to facilitate situation.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Williams Inc #12122-ANYTHING'
    concentration_or_purity: 72.7%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Allen-Banks #96092-STANDARD'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Cortez-Holloway #48200-WATCH'
    concentration_or_purity: "43 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Compton-Buckley #46603-HERE'
    concentration_or_purity: 87.2%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Woods-Garcia Hair5405
    settings_parameters: "9623 x g, 30\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Ayala-Pacheco Whom4487
    settings_parameters: "8220 x g, 35\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Molina Inc Onto5943
    settings_parameters: "9355 x g, 33\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "9478 x g, 25\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Ryan-Parks Across1802
    settings_parameters: "5235 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      party.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 717
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were lysed with hek293t cells to facilitate brother.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were washed with lipofectamine 3000 to facilitate avoid.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 612
    temperature_celsius: 7
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      pick.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 4
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
