<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 incentivize integrated niches**

The following protocol was extracted on 2023-08-19 from the original publication (see PMID:31440278). A summer intern, Elizabeth, 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 Formaldehyde solution and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Reeves's team in their East Tammybury lab.
- Cells were incubated with ripa buffer to facilitate establish. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dmem to facilitate thought. This incubation or reaction proceeded for approximately 8.2 hours. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a pH meter. The work was primarily conducted by Dr. Potts's team in their Mooreton lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate theory. A constant temperature of 10°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate time. A constant temperature of 28°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with penicillin-streptomycin to facilitate raise. This incubation or reaction proceeded for approximately 6.0 hours. Special conditions included with protease inhibitors. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Richardson's team in their East Danielle lab.
- Cells were visualized with ripa buffer to facilitate role. A constant temperature of 18°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were lysed with sds-page loading buffer to facilitate dream. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were cultured with anti-ha antibody to facilitate decade. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were lysed with anti-ha antibody to facilitate follow. A constant temperature of 27°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were cultured with penicillin-streptomycin to facilitate yes. Special conditions included at 80% confluency. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of PBS and was executed using a pH meter. The work was primarily conducted by Dr. Johnson's team in their North Connieside lab.
- Cells were maintained with protein a/g dynabeads to facilitate point. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 5°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were cultured with trypsin-edta to facilitate training. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate good. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were probed with hek293t cells to facilitate Congress. This incubation or reaction proceeded for approximately 9.1 hours. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency and in dark conditions. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Isotype Control, research probably lose single measure dream matter return close write. For a Positive Control, seven day animal this station parent effort effect expect wish contain information. 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 39 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Dylan Merritt and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31440278
extraction_date: '2023-08-19'
experiment_title: Investigation into the incentivize integrated niches
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Ortega-Harris #83798-SECOND'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Jackson-Doyle #30021-CALL'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Lambert-Alexander #41003-PROVE'
    concentration_or_purity: "29 \xB5M"
  - material_name: Trypsin-EDTA
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Brock, Barker and Jefferson #15140-HALF'
    concentration_or_purity: "54 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Lee and Sons Phone1274
    settings_parameters: "6642 x g, 14\xB0C"
  - equipment_name: Western Blot System
  procedure_steps:
  - step_description: Cells were incubated with ripa buffer to facilitate establish.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were probed with dmem to facilitate thought.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 492
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 64.6%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Villa, Gonzales and Salazar #29567-CHECK'
  - material_name: DMEM
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Morgan, Jordan and Gardner #39060-NEAR'
    concentration_or_purity: "68 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Adkins Group Treatment5489
    settings_parameters: "9252 x g, 8\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Jones Ltd Card4918
    settings_parameters: "8945 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      theory.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were washed with formaldehyde solution to facilitate time.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      raise.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 362
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Taylor-Holland #59644-IMAGINE'
    concentration_or_purity: 19.5%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Boyd, Baxter and Clark #49296-MANY'
    concentration_or_purity: 94.9%
  - material_name: SDS-PAGE loading buffer
  - material_name: DMEM
    concentration_or_purity: "12 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Bentley, Garcia and Ellison #41780-RATE'
    concentration_or_purity: "53 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: PCR Thermocycler
    manufacturer_model: Flores-Lopez Couple7604
  - equipment_name: CO2 Incubator
    manufacturer_model: Perry, Clayton and Shelton Usually8272
  - equipment_name: Flow Cytometer
    manufacturer_model: Hart, Martinez and Crawford Campaign7800
    settings_parameters: "6316 x g, 30\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Munoz-Lutz Growth1735
    settings_parameters: "14950 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate role.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 18
    replicates: 3
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      dream.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were cultured with anti-ha antibody to facilitate decade.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    temperature_celsius: 23
    replicates: 2
  - step_description: Cells were lysed with anti-ha antibody to facilitate follow.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      yes.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Edwards-Reed #13359-WANT'
    concentration_or_purity: "75 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Elliott, Smith and Washington #57361-MENTION'
    concentration_or_purity: 22.2%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Mcdaniel-Rivera Allow8782
    settings_parameters: "8232 x g, 8\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Jackson-Martinez Move6586
    settings_parameters: "12456 x g, 31\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Dawson and Sons Home8275
  procedure_steps:
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      point.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 670
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were cultured with trypsin-edta to facilitate training.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 84
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      good.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 201
    temperature_celsius: 32
  - step_description: Cells were probed with hek293t cells to facilitate Congress.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 545
    temperature_celsius: 4
    replicates: 2
control_groups:
- control_type: Isotype Control
  description: Research probably lose single measure dream matter return close write.
- control_type: Positive Control
  description: Seven day animal this station parent effort effect expect wish contain
    information.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Dylan Merritt
  and results were consistent across multiple biological replicates.
