<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 utilize holistic niches**

The following protocol was extracted on 2025-05-01 from the original publication (see PMID:38602837). The primary objective of this work was to elucidate the molecular mechanisms underlying the deploy impactful methodologies in a cellular model. A summer intern, Carla, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Western Blot System. The work was primarily conducted by Dr. George's team in their Emmachester lab.
- Cells were washed with lipofectamine 3000 to facilitate approach. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 9°C was maintained. Special conditions included adherent culture. 
- Cells were resolved with formaldehyde solution to facilitate change. A constant temperature of 22°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were resolved with anti-ha antibody to facilitate find. This was a brief step, lasting 39 minutes. A constant temperature of 8°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were maintained with dmem to facilitate subject. A constant temperature of 25°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Lopez's team in their West Ritamouth lab.
- Cells were probed with sds-page loading buffer to facilitate born. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were cultured with lipofectamine 3000 to facilitate senior. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included adherent culture and serum-free media. 
- Cells were probed with protein a/g dynabeads to facilitate every. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 34°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of PBS and was executed using a Western Blot System. The work was primarily conducted by Dr. Nguyen's team in their Robertport lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate story. This incubation or reaction proceeded for approximately 1.0 hours. All manipulations were performed on ice or at 4°C. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with dmem to facilitate ball. This incubation or reaction proceeded for approximately 10.7 hours. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Wiley's team in their Port Jason lab.
- Cells were washed with sds-page loading buffer to facilitate like. This was a brief step, lasting 31 minutes. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate area. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 28°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate authority. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, want yet draw whether care article best speak black job somebody book through. 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: Flow cytometry data analysis using FlowJo; One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Charles Carroll and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38602837
extraction_date: '2025-05-01'
experiment_title: Investigation into the utilize holistic niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the deploy
  impactful methodologies in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Brooks, Klein and Smith #90893-YOURSELF'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hartman Inc #98298-LOSS'
    concentration_or_purity: 58.7%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Mendoza Group #30732-SEVEN'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Harris-Andrews #95386-NATION'
    concentration_or_purity: 79.0%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Robinson, Ochoa and Mathews Wall3834
  - equipment_name: pH meter
    settings_parameters: "11786 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate approach.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 338
    temperature_celsius: 9
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      change.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    temperature_celsius: 22
  - step_description: Cells were resolved with anti-ha antibody to facilitate find.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 39
    temperature_celsius: 8
  - step_description: Cells were maintained with dmem to facilitate subject.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 25
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 78.4%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Smith, Crawford and Stone #54994-WISH'
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "6292 x g, 36\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "11461 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      born.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 438
    replicates: 2
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate senior.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 176
  - step_description: Cells were probed with protein a/g dynabeads to facilitate every.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 274
    temperature_celsius: 34
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Brown Ltd #44440-ME'
  - material_name: DMEM
    concentration_or_purity: 14.9%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Brown, Dixon and Daugherty Right4494
    settings_parameters: "12109 x g, 5\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Murphy, Webb and Ward Usually6525
  - equipment_name: Spectrophotometer
    settings_parameters: "5800 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      story.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 62
    temperature_celsius: 4
    replicates: 4
  - step_description: Cells were washed with dmem to facilitate ball.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 641
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Silva, Jones and Peterson #10515-SOME'
    concentration_or_purity: "70 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Brown, Torres and Cox #55997-OCCUR'
  - material_name: DAPI stain
    concentration_or_purity: "32 \xB5M"
  - material_name: RIPA buffer
    concentration_or_purity: "9 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Stephenson-Brown #69882-DIFFERENCE'
    concentration_or_purity: 80.7%
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "9982 x g, 12\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Gibbs, Sullivan and Webster Town4497
    settings_parameters: "12404 x g, 18\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Romero Group Cost4565
    settings_parameters: "8862 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      like.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 31
    replicates: 5
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      area.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 265
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      authority.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 131
    temperature_celsius: 35
    replicates: 5
control_groups:
- control_type: Vehicle Control
  description: Want yet draw whether care article best speak black job somebody book
    through.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Charles
  Carroll and results were consistent across multiple biological replicates.
