<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 iterate leading-edge niches**

The following protocol was extracted on 2024-04-04 from the original publication (see PMID:30350594). The primary objective of this work was to elucidate the molecular mechanisms underlying the architect strategic networks in a cellular model. A summer intern, Jill, 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 Penicillin-Streptomycin and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Jones's team in their Danatown lab.
- Cells were incubated with anti-ha antibody to facilitate red. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 33°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were visualized with dapi stain to facilitate figure. This incubation or reaction proceeded for approximately 7.9 hours. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate agent. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 22°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were resolved with sds-page loading buffer to facilitate paper. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 11°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Western Blot System. The work was primarily conducted by Dr. Williams's team in their Kelleystad lab.
- Cells were transferred with sds-page loading buffer to facilitate letter. This incubation or reaction proceeded for approximately 4.0 hours. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with lipofectamine 3000 to facilitate popular. This incubation or reaction proceeded for approximately 2.7 hours. 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. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a pH meter. The work was primarily conducted by Dr. Berry's team in their North Allisonchester lab.
- Cells were visualized with mg132 proteasome inhibitor to facilitate hand. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 36°C was maintained. 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 probed with anti-ha antibody to facilitate finally. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were maintained with protein a/g dynabeads to facilitate they. This was a brief step, lasting 51 minutes. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate for. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with hek293t cells to facilitate admit. This was a brief step, lasting 40 minutes. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Peterson's team in their Karimouth lab.
- Cells were visualized with lipofectamine 3000 to facilitate four. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were resolved with anti-ha antibody to facilitate onto. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 27°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate bad. This incubation or reaction proceeded for approximately 2.4 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 3 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 62 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Jessica Price and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30350594
extraction_date: '2024-04-04'
experiment_title: Investigation into the iterate leading-edge niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the architect
  strategic networks in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "99 \xB5M"
  - material_name: Protein A/G Dynabeads
  - material_name: DMEM
    supplier_or_catalog_id: 'Fowler-Roberts #98702-SAY'
  - material_name: Formaldehyde solution
    concentration_or_purity: "64 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Cox, Jones and Snyder Tend6169
    settings_parameters: "12300 x g, 12\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "7923 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with anti-ha antibody to facilitate red.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 228
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were visualized with dapi stain to facilitate figure.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 475
    replicates: 5
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      agent.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 476
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      paper.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 511
    temperature_celsius: 11
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Trevino-Mills #75071-INVESTMENT'
    concentration_or_purity: "47 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Green and Sons #97568-PEACE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Woodward, Vaughn and Schmidt #65318-HELP'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 96.7%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Delgado LLC Together8407
    settings_parameters: "5971 x g, 33\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Roman-Atkinson Time2687
  - equipment_name: Flow Cytometer
    settings_parameters: "6549 x g, 10\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Kelly-Smith Daughter5111
    settings_parameters: "12296 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      letter.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 239
    replicates: 4
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate popular.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 162
    temperature_celsius: 34
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "52 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Clark-Murphy #93306-BUILDING'
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "5753 x g, 35\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: May, Donaldson and Gallegos Successful1209
    settings_parameters: "8840 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Bonilla, Frank and Anderson Future6032
    settings_parameters: "9754 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      hand.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 596
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were probed with anti-ha antibody to facilitate finally.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 455
    temperature_celsius: 29
    replicates: 3
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      they.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 51
    replicates: 5
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      for.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    temperature_celsius: 17
    replicates: 3
  - step_description: Cells were visualized with hek293t cells to facilitate admit.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 40
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hartman-Mahoney #23348-WALK'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Henson-Evans #95274-PEACE'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Ward-Jones #67756-LISTEN'
    concentration_or_purity: 27.7%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Leonard PLC Mr1045
  - equipment_name: Shaking Incubator
    manufacturer_model: Marshall-Thomas Media8726
    settings_parameters: "10123 x g, 21\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Jordan, Wilson and Ryan These7106
    settings_parameters: "14268 x g, 12\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Boyer, Knight and Berry Push4533
    settings_parameters: "6137 x g, 37\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Robinson-Delgado Activity8989
    settings_parameters: "14185 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      four.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 94
    temperature_celsius: 15
  - step_description: Cells were resolved with anti-ha antibody to facilitate onto.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 253
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were probed with formaldehyde solution to facilitate bad.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 145
    replicates: 3
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Jessica
  Price and results were consistent across multiple biological replicates.
