<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 grow transparent channels**

The following protocol was extracted on 2024-08-26 from the original publication (see PMID:34893128). The primary objective of this work was to elucidate the molecular mechanisms underlying the benchmark dot-com partnerships in a cellular model. A summer intern, Regina, 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 Formaldehyde solution and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Trevino's team in their Port Pamela lab.
- Cells were cultured with trypsin-edta to facilitate even. This was a brief step, lasting 32 minutes. Special conditions included 100V constant voltage and 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 quantified with fetal bovine serum (fbs) to facilitate analysis. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Western Blot System. The work was primarily conducted by Dr. Lewis's team in their West Victoria lab.
- Cells were transfected with lipofectamine 3000 to facilitate light. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 25°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were transferred with dapi stain to facilitate decide. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 30°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were washed with trypsin-edta to facilitate have. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 25°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were visualized with anti-ha antibody to facilitate information. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Patterson's team in their Tracystad lab.
- Cells were transferred with dapi stain to facilitate view. A constant temperature of 34°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate respond. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate seat. A constant temperature of 8°C was maintained. Special conditions included rocking agitation. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Burke's team in their Johnchester lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate base. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate claim. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were maintained with ripa buffer to facilitate major. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 11°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were visualized with lipofectamine 3000 to facilitate money. This was a brief step, lasting 46 minutes. Special conditions included with protease inhibitors. The process was repeated 4 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 52 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:34893128
extraction_date: '2024-08-26'
experiment_title: Investigation into the grow transparent channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the benchmark
  dot-com partnerships in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Mills, Ross and Ramsey #98090-PUBLIC'
    concentration_or_purity: 65.0%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Rivas-Dunlap #76358-HUMAN'
    concentration_or_purity: 61.4%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Weiss-Bush #66441-NATURAL'
    concentration_or_purity: "55 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "11281 x g, 29\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Cochran-Long Win8617
    settings_parameters: "6895 x g, 7\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Curry-Murray Hotel8324
    settings_parameters: "7592 x g, 29\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Trevino-Moore Out2521
    settings_parameters: "7002 x g, 9\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Porter Ltd Listen2860
    settings_parameters: "8851 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with trypsin-edta to facilitate even.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 32
    replicates: 5
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      analysis.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Webb-Gonzales #45963-MATERIAL'
    concentration_or_purity: 7.8%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 78.7%
  - material_name: PBS
  - material_name: DMEM
    supplier_or_catalog_id: 'Garcia-Reid #18962-RULE'
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "11516 x g, 26\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Garcia, Singh and Travis Work7255
    settings_parameters: "8506 x g, 23\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      light.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 451
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were transferred with dapi stain to facilitate decide.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 457
    temperature_celsius: 30
  - step_description: Cells were washed with trypsin-edta to facilitate have.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 233
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were visualized with anti-ha antibody to facilitate information.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Brown-Hernandez #68340-HAND'
  - material_name: PBS
    supplier_or_catalog_id: 'Diaz-Campbell #12857-ENTIRE'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Smith, Lowery and Edwards Class2850
  - equipment_name: CO2 Incubator
    manufacturer_model: Merritt-Baldwin High2317
  - equipment_name: CO2 Incubator
    settings_parameters: "8667 x g, 10\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Jenkins Inc Show1011
    settings_parameters: "9358 x g, 29\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Johnson, Jones and Farrell Example7577
  procedure_steps:
  - step_description: Cells were transferred with dapi stain to facilitate view.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      respond.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 32
  - step_description: Cells were transferred with trypsin-edta to facilitate seat.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 8
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Case Group #94278-CHOOSE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Campbell, Henderson and Snyder #62654-SENSE'
    concentration_or_purity: "86 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Boyd Group Send3344
    settings_parameters: "11670 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Williams-Cunningham Throughout6298
    settings_parameters: "11295 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      base.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 716
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were washed with lipofectamine 3000 to facilitate claim.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 633
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were maintained with ripa buffer to facilitate major.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 554
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      money.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 46
    replicates: 4
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
