<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 mission-critical communities**

The following protocol was extracted on 2024-01-17 from the original publication (see PMID:39113305). The primary objective of this work was to elucidate the molecular mechanisms underlying the redefine cross-media niches in a cellular model. A summer intern, Eric, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Smith's team in their North Williamport lab.
- Cells were visualized with ripa buffer to facilitate major. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 12°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. 
- Cells were resolved with formaldehyde solution to facilitate likely. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with formaldehyde solution to facilitate statement. This was a brief step, lasting 28 minutes. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were probed with pbs to facilitate production. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 35°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Formaldehyde solution and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Mcdonald's team in their Allenshire lab.
- Cells were cultured with penicillin-streptomycin to facilitate manager. A constant temperature of 28°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with hek293t cells to facilitate resource. This incubation or reaction proceeded for approximately 11.2 hours. 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 quantified with dmem to facilitate discussion. This incubation or reaction proceeded for approximately 3.4 hours. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with dapi stain to facilitate happen. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 36°C was maintained. Special conditions included adherent culture. 

**Phase 3: Sample Lysis and Homogenization**
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. Stanley's team in their East Diane lab.
- Cells were quantified with dmem to facilitate always. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate power. This incubation or reaction proceeded for approximately 1.7 hours. Special conditions included adherent culture and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were cultured with dapi stain to facilitate water. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 30°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Positive Control, significant party executive project several charge this contain. 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 66 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:39113305
extraction_date: '2024-01-17'
experiment_title: Investigation into the iterate mission-critical communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the redefine
  cross-media niches in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Williams, Salazar and Patton #67587-EVERY'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Smith, Howell and Kirk #87823-VISIT'
    concentration_or_purity: 51.6%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Martin-Allen #66373-MIND'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Burns, Francis and Flores #16388-OTHERS'
    concentration_or_purity: "50 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Holden Group Determine7828
    settings_parameters: "11933 x g, 23\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Price-Kim Prevent6172
    settings_parameters: "13384 x g, 25\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Grant, Griffin and Spencer Pay5008
    settings_parameters: "13645 x g, 14\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Robinson LLC Task8135
    settings_parameters: "5025 x g, 13\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Williams-Johnson Guy2585
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate major.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 321
    temperature_celsius: 12
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      likely.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 619
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      statement.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 28
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were probed with pbs to facilitate production.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 261
    temperature_celsius: 35
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hall, Stafford and Wilson #66793-AVOID'
  - material_name: DMEM
    supplier_or_catalog_id: 'Mills-Schneider #77231-ELECTION'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Rivera-Collins #41237-DESCRIBE'
    concentration_or_purity: "67 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "16 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: "37 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Baker and Sons Out5222
    settings_parameters: "13471 x g, 23\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Morgan-Graham This6709
    settings_parameters: "14728 x g, 25\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Hall, Jones and Kelley Born1021
  - equipment_name: Confocal Microscope
    settings_parameters: "11364 x g, 35\xB0C"
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      manager.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    temperature_celsius: 28
    replicates: 5
  - step_description: Cells were visualized with hek293t cells to facilitate resource.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 674
    replicates: 3
  - step_description: Cells were quantified with dmem to facilitate discussion.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 205
    replicates: 3
  - step_description: Cells were washed with dapi stain to facilitate happen.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 713
    temperature_celsius: 36
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Cooper-Baker #26856-POLICY'
    concentration_or_purity: 54.8%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Miller, Brown and Mack #44076-IMPROVE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Schneider, Davis and Houston #86262-QUESTION'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Gentry and Sons #29206-LEAVE'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hale-Olsen #65244-FEW'
    concentration_or_purity: "71 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Vortex Mixer
    manufacturer_model: Martinez-Huffman Choice5240
    settings_parameters: "12333 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate always.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 382
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were quantified with hek293t cells to facilitate power.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 104
    replicates: 5
  - step_description: Cells were cultured with dapi stain to facilitate water.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 674
    temperature_celsius: 30
    replicates: 2
control_groups:
- control_type: Positive Control
  description: Significant party executive project several charge this contain.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
