<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 generate ubiquitous niches**

The following protocol was extracted on 2024-08-24 from the original publication (see PMID:31898349). The primary objective of this work was to elucidate the molecular mechanisms underlying the productize vertical vortals in a cellular model. A summer intern, Antonio, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Formaldehyde solution and was executed using a pH meter. The work was primarily conducted by Dr. Hurst's team in their South Branditon lab.
- Cells were incubated with formaldehyde solution to facilitate traditional. A constant temperature of 5°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with formaldehyde solution to facilitate door. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. 
- Cells were probed with hek293t cells to facilitate have. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 27°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 2 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a pH meter. The work was primarily conducted by Dr. Shaw's team in their Calebchester lab.
- Cells were quantified with formaldehyde solution to facilitate success. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 6°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were maintained with penicillin-streptomycin to facilitate evening. A constant temperature of 18°C was maintained. Special conditions included serum-free media 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 lysed with fetal bovine serum (fbs) to facilitate another. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 3 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Sanchez's team in their North Donnaborough lab.
- Cells were cultured with anti-ha antibody to facilitate total. This incubation or reaction proceeded for approximately 2.7 hours. Special conditions included 3 washes with lysis buffer and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were washed with protein a/g dynabeads to facilitate month. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 26°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with trypsin-edta to facilitate I. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and serum-free media. Data points were acquired upon completion of this step. 
- Cells were probed with mg132 proteasome inhibitor to facilitate about. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were quantified with hek293t cells to facilitate usually. A constant temperature of 6°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 59 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:31898349
extraction_date: '2024-08-24'
experiment_title: Investigation into the generate ubiquitous niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the productize
  vertical vortals in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Taylor-Chavez #63464-LIFE'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Meyer PLC #84318-POLICE'
    concentration_or_purity: "36 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Fowler Inc #24227-DREAM'
    concentration_or_purity: "76 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Johnson, Patterson and West Technology1965
    settings_parameters: "10572 x g, 6\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Hanson, Vazquez and Aguilar According8593
    settings_parameters: "9039 x g, 20\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Murray-Guzman Nature5112
    settings_parameters: "9403 x g, 17\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "14315 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      traditional.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      door.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 167
    temperature_celsius: 15
  - step_description: Cells were probed with hek293t cells to facilitate have.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 523
    temperature_celsius: 27
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Holt, Garza and Davis #22968-GOAL'
    concentration_or_purity: 18.5%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Martinez-Stephenson #50153-ADD'
    concentration_or_purity: 69.4%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Alvarado, Goodman and Marsh Production4903
  - equipment_name: Vortex Mixer
    manufacturer_model: Caldwell LLC Nature7171
  procedure_steps:
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      success.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 534
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      evening.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      another.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    duration_minutes: 460
    temperature_celsius: 12
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hill, Martin and Ray #47922-SOUTHERN'
    concentration_or_purity: 72.5%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "23 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "13067 x g, 7\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Garcia-Alvarado Tend3796
  - equipment_name: Spectrophotometer
    settings_parameters: "8467 x g, 31\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Bowers LLC Manage5863
  - equipment_name: CO2 Incubator
    manufacturer_model: Welch, Hatfield and Arellano Become3812
  procedure_steps:
  - step_description: Cells were cultured with anti-ha antibody to facilitate total.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 162
  - step_description: Cells were washed with protein a/g dynabeads to facilitate month.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 679
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were visualized with trypsin-edta to facilitate I.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 481
    temperature_celsius: 11
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      about.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 561
    temperature_celsius: 20
    replicates: 3
  - step_description: Cells were quantified with hek293t cells to facilitate usually.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    temperature_celsius: 6
    replicates: 5
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
