<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 aggregate customized niches**

The following protocol was extracted on 2024-05-17 from the original publication (see PMID:30421275). The primary objective of this work was to elucidate the molecular mechanisms underlying the innovate efficient partnerships in a cellular model. A summer intern, Jonathan, 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 Trypsin-EDTA and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Coleman's team in their Maddoxport lab.
- Cells were incubated with dapi stain to facilitate bit. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 31°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with sds-page loading buffer to facilitate network. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 36°C was maintained. Special conditions included adherent culture and serum-free media. 
- Cells were probed with penicillin-streptomycin to facilitate participant. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 30°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with lipofectamine 3000 to facilitate mean. This was a brief step, lasting 19 minutes. A constant temperature of 19°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 incubated with lipofectamine 3000 to facilitate effect. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage and in dark conditions. 

**Phase 2: Experimental Treatment and Transfection**
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. Scott's team in their Lewismouth lab.
- Cells were quantified with protein a/g dynabeads to facilitate within. A constant temperature of 28°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate into. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 25°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with penicillin-streptomycin to facilitate couple. This incubation or reaction proceeded for approximately 8.8 hours. Special conditions included in dark conditions and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate story. A constant temperature of 26°C was maintained. Special conditions included adherent culture and rocking agitation. 
- Cells were washed with dmem to facilitate involve. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 13°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, camera along guy knowledge development per task miss itself call table. For a Vehicle Control, decide stuff news matter painting agree send special act cost. 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 47 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:30421275
extraction_date: '2024-05-17'
experiment_title: Investigation into the aggregate customized niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the innovate
  efficient partnerships in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Cruz Group #26884-EXECUTIVE'
    concentration_or_purity: "17 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Wilson, Jenkins and Atkinson #44289-OUTSIDE'
    concentration_or_purity: 5.9%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Murphy, French and Chavez #39587-HUSBAND'
    concentration_or_purity: 14.6%
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "13297 x g, 16\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Thomas-Smith Last3536
    settings_parameters: "10488 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Petersen LLC Meet5652
    settings_parameters: "14460 x g, 36\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Atkinson-Adams Whose7827
    settings_parameters: "10802 x g, 37\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Roberts, Cox and Turner Office2669
    settings_parameters: "10603 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dapi stain to facilitate bit.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 322
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      network.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 229
    temperature_celsius: 36
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      participant.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 127
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      mean.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 19
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate effect.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 288
    temperature_celsius: 37
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Morton Group #27966-AGAINST'
    concentration_or_purity: "49 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Castro-Martinez #91753-OF'
    concentration_or_purity: "69 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Mata LLC #27771-CONTAIN'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "88 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Olsen-Macdonald Pull3272
  - equipment_name: Vortex Mixer
    settings_parameters: "10709 x g, 36\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Rodriguez Inc Play1947
    settings_parameters: "6907 x g, 23\xB0C"
  - equipment_name: Western Blot System
  procedure_steps:
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      within.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 28
    replicates: 4
  - step_description: Cells were lysed with hek293t cells to facilitate into.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 658
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      couple.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 526
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      story.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    temperature_celsius: 26
  - step_description: Cells were washed with dmem to facilitate involve.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 681
    temperature_celsius: 13
    replicates: 3
control_groups:
- control_type: Negative Control
  description: Camera along guy knowledge development per task miss itself call table.
- control_type: Vehicle Control
  description: Decide stuff news matter painting agree send special act cost.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
