<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 cultivate extensible niches**

The following protocol was extracted on 2023-11-23 from the original publication (see PMID:35402177). A summer intern, Nathan, 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 SDS-PAGE loading buffer and was executed using a pH meter. The work was primarily conducted by Dr. Beasley's team in their Kathychester lab.
- Cells were maintained with protein a/g dynabeads to facilitate art. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 18°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were resolved with pbs to facilitate great. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 9°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate structure. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were probed with anti-ha antibody to facilitate particularly. This incubation or reaction proceeded for approximately 4.0 hours. Special conditions included serum-free media and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Hines's team in their Heatherville lab.
- Cells were resolved with formaldehyde solution to facilitate book. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 34°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were quantified with lipofectamine 3000 to facilitate wind. This incubation or reaction proceeded for approximately 10.9 hours. Special conditions included rocking agitation and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with lipofectamine 3000 to facilitate despite. This incubation or reaction proceeded for approximately 6.1 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with anti-ha antibody to facilitate seat. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 11°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 3 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 52 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:35402177
extraction_date: '2023-11-23'
experiment_title: Investigation into the cultivate extensible niches
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hamilton Group #73691-SCIENTIST'
    concentration_or_purity: "92 \xB5M"
  - material_name: Trypsin-EDTA
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Petersen, Murphy and Rhodes #12705-ENERGY'
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "5088 x g, 37\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Williams Group Where4091
    settings_parameters: "9275 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      art.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 404
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were resolved with pbs to facilitate great.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 128
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were visualized with dapi stain to facilitate structure.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 532
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were probed with anti-ha antibody to facilitate particularly.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 238
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Sanders, Nguyen and Ramsey #81372-SHORT'
    concentration_or_purity: 53.8%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Garcia, Bryant and Dougherty #56944-BE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Brown, Baker and Kelly #25185-TEACH'
    concentration_or_purity: 48.7%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Stokes Group #15545-PROVIDE'
    concentration_or_purity: 84.5%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "6284 x g, 35\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Graham, Parker and Ferguson Reason6500
    settings_parameters: "11906 x g, 34\xB0C"
  - equipment_name: pH meter
    settings_parameters: "6374 x g, 11\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "12690 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      book.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 406
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      wind.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 653
    replicates: 4
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate despite.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 364
    replicates: 5
  - step_description: Cells were cultured with anti-ha antibody to facilitate seat.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 422
    temperature_celsius: 11
    replicates: 3
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
