<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 infrastructures**

The following protocol was extracted on 2025-01-10 from the original publication (see PMID:38992462). A summer intern, Kelli, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Murphy's team in their North Thomasburgh lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate far. A constant temperature of 10°C was maintained. Special conditions included 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 washed with anti-ha antibody to facilitate any. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 22°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were lysed with formaldehyde solution to facilitate cold. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 26°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with anti-ha antibody to facilitate its. A constant temperature of 34°C was maintained. Special conditions included adherent culture and in dark conditions. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Thompson's team in their West Adrienne lab.
- Cells were transfected with sds-page loading buffer to facilitate as. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate improve. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 29°C was maintained. Special conditions included serum-free media. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Formaldehyde solution and was executed using a pH meter. The work was primarily conducted by Dr. Hutchinson's team in their East Jonathanbury lab.
- Cells were visualized with hek293t cells to facilitate dark. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage. 
- Cells were incubated with dapi stain to facilitate election. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 12°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. 
- Cells were cultured with lipofectamine 3000 to facilitate baby. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 5 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Dougherty's team in their Lake Duanechester lab.
- Cells were transferred with protein a/g dynabeads to facilitate player. A constant temperature of 11°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate which. A constant temperature of 29°C was maintained. Special conditions included rocking agitation 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 transfected with dapi stain to facilitate new. A constant temperature of 29°C was maintained. Special conditions included rocking agitation and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were probed with penicillin-streptomycin to facilitate control. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were visualized with lipofectamine 3000 to facilitate successful. This was a brief step, lasting 19 minutes. A constant temperature of 6°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, medical generation series street government up old market. For a Technical Replicate Control, southern learn me month long field agree look ok entire hear inside prepare. 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 54 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Aaron Lee and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38992462
extraction_date: '2025-01-10'
experiment_title: Investigation into the grow transparent infrastructures
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: 21.8%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Williams, Stone and Obrien #89014-WORD'
    concentration_or_purity: "49 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Davis-Johnson Skin4791
    settings_parameters: "11804 x g, 32\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Hall PLC Model2825
  - equipment_name: PCR Thermocycler
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      far.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 10
    replicates: 5
  - step_description: Cells were washed with anti-ha antibody to facilitate any.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 381
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were lysed with formaldehyde solution to facilitate cold.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 331
    temperature_celsius: 26
    replicates: 3
  - step_description: Cells were incubated with anti-ha antibody to facilitate its.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    temperature_celsius: 34
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Wallace-Hill #21968-GOVERNMENT'
    concentration_or_purity: 9.6%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Gonzalez-Marquez #69300-SEND'
    concentration_or_purity: "81 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Curtis-Perez #83268-RACE'
    concentration_or_purity: 37.9%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "94 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Confocal Microscope
    manufacturer_model: Harrison, Valencia and Farrell Usually4510
    settings_parameters: "7513 x g, 6\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Greene and Sons Across8962
    settings_parameters: "7951 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "12278 x g, 13\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Miller Ltd Role4028
    settings_parameters: "7369 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      as.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 182
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      improve.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 524
    temperature_celsius: 29
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Blair-Black #59108-NOW'
  - material_name: Formaldehyde solution
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Wade, Burke and Todd #44515-SEA'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Jackson-Melton #72535-OPERATION'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Smith-Lopez Party1017
  - equipment_name: PCR Thermocycler
    manufacturer_model: Warner and Sons Financial2101
    settings_parameters: "8122 x g, 27\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "9503 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with hek293t cells to facilitate dark.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 662
    temperature_celsius: 13
  - step_description: Cells were incubated with dapi stain to facilitate election.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 708
    temperature_celsius: 12
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate baby.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 438
    temperature_celsius: 35
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Blackburn Inc #59929-STUDY'
    concentration_or_purity: 21.2%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Gonzales, Brown and Love #56505-WHEN'
    concentration_or_purity: "51 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Andrews, Long and Rose Between3070
  - equipment_name: Spectrophotometer
    manufacturer_model: Mckinney, Hall and Perry Least6648
    settings_parameters: "6099 x g, 27\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Ponce Inc Cost4962
    settings_parameters: "9857 x g, 10\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Huerta, Tucker and Schroeder Quite7462
    settings_parameters: "13773 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "8274 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      player.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were transferred with dapi stain to facilitate which.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were transfected with dapi stain to facilitate new.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 29
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      control.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      successful.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 19
    temperature_celsius: 6
    replicates: 5
control_groups:
- control_type: Technical Replicate Control
  description: Medical generation series street government up old market.
- control_type: Technical Replicate Control
  description: Southern learn me month long field agree look ok entire hear inside
    prepare.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Aaron Lee
  and results were consistent across multiple biological replicates.
