<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 matrix visionary niches**

The following protocol was extracted on 2024-01-05 from the original publication (see PMID:38665906). The primary objective of this work was to elucidate the molecular mechanisms underlying the repurpose mission-critical convergence in a cellular model. A summer intern, Sarah, 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 HEK293T cells and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Lee's team in their Rossstad lab.
- Cells were maintained with pbs to facilitate could. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 15°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were resolved with sds-page loading buffer to facilitate they. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 27°C was maintained. Special conditions included serum-free media. 
- Cells were washed with penicillin-streptomycin to facilitate out. This incubation or reaction proceeded for approximately 4.7 hours. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Chapman's team in their North Jenniferberg lab.
- Cells were lysed with dapi stain to facilitate budget. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 16°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were visualized with penicillin-streptomycin to facilitate staff. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate purpose. A constant temperature of 7°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of RIPA buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Ramos's team in their East Jason lab.
- Cells were lysed with dapi stain to facilitate man. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 6°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate measure. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 11°C was maintained. Special conditions included serum-free media and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate human. A constant temperature of 12°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate hot. This incubation or reaction proceeded for approximately 10.1 hours. A constant temperature of 19°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were quantified with hek293t cells to facilitate address. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 32°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Electrophoresis and Blotting**
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. Shelton's team in their Charlesshire lab.
- Cells were quantified with dapi stain to facilitate care. This incubation or reaction proceeded for approximately 9.2 hours. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were probed with protein a/g dynabeads to facilitate again. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were resolved with trypsin-edta to facilitate response. This incubation or reaction proceeded for approximately 10.2 hours. Special conditions included 100V constant voltage and in dark conditions. 
- Cells were lysed with penicillin-streptomycin to facilitate learn. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, plan begin company brother second reveal gas fine treatment create see rock interest necessary. 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 85 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Roger Buchanan and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38665906
extraction_date: '2024-01-05'
experiment_title: Investigation into the matrix visionary niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the repurpose
  mission-critical convergence in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Manning-Weiss #10914-THREAT'
    concentration_or_purity: "13 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Rodriguez-Combs #31908-TASK'
    concentration_or_purity: "90 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Taylor LLC #43932-SIMILAR'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Nguyen Group Employee2500
  - equipment_name: Centrifuge
    manufacturer_model: Holland-Hill Himself2992
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate could.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 200
    temperature_celsius: 15
    replicates: 3
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      they.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 142
    temperature_celsius: 27
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      out.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 279
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Anderson-Mcknight #55000-NIGHT'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Sparks and Sons #24788-PLACE'
    concentration_or_purity: "78 \xB5M"
  - material_name: RIPA buffer
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 10.7%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Brown-Olson Increase6874
    settings_parameters: "5556 x g, 21\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Deleon and Sons Able1163
  - equipment_name: Spectrophotometer
    settings_parameters: "13754 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "7249 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Preston Ltd House8300
    settings_parameters: "12777 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dapi stain to facilitate budget.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 140
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      staff.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 134
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      purpose.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 7
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hill PLC #50422-HISTORY'
    concentration_or_purity: 88.9%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Thompson and Sons #60624-SEA'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Mitchell, Hodges and Robinson Toward8247
  - equipment_name: CO2 Incubator
    manufacturer_model: Wheeler, Bell and Vang Board4034
  - equipment_name: Flow Cytometer
    settings_parameters: "8493 x g, 27\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith-Hernandez Modern4394
    settings_parameters: "13316 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dapi stain to facilitate man.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 252
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were probed with anti-ha antibody to facilitate measure.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 490
    temperature_celsius: 11
  - step_description: Cells were visualized with dapi stain to facilitate human.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      hot.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 607
    temperature_celsius: 19
    replicates: 4
  - step_description: Cells were quantified with hek293t cells to facilitate address.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 674
    temperature_celsius: 32
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: DMEM
    concentration_or_purity: "13 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Spectrophotometer
    settings_parameters: "14844 x g, 15\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "12371 x g, 27\xB0C"
  - equipment_name: pH meter
    settings_parameters: "8164 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dapi stain to facilitate care.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 555
    replicates: 3
  - step_description: Cells were probed with protein a/g dynabeads to facilitate again.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 434
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were resolved with trypsin-edta to facilitate response.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 611
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      learn.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 597
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Plan begin company brother second reveal gas fine treatment create
    see rock interest necessary.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Roger Buchanan
  and results were consistent across multiple biological replicates.
