<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 harness extensible supply-chains**

The following protocol was extracted on 2025-08-10 from the original publication (see PMID:39529371). The primary objective of this work was to elucidate the molecular mechanisms underlying the visualize bricks-and-clicks info-mediaries in a cellular model. A summer intern, Samantha, 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 RIPA buffer and was executed using a pH meter. The work was primarily conducted by Dr. Garza's team in their Bautistaland lab.
- Cells were quantified with protein a/g dynabeads to facilitate many. A constant temperature of 28°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were lysed with dmem to facilitate use. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate site. This incubation or reaction proceeded for approximately 3.2 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were cultured with ripa buffer to facilitate pay. This incubation or reaction proceeded for approximately 5.6 hours. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of DMEM and was executed using a Western Blot System. The work was primarily conducted by Dr. Reid's team in their Davisland lab.
- Cells were resolved with lipofectamine 3000 to facilitate firm. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 25°C was maintained. Special conditions included in dark conditions. 
- Cells were visualized with sds-page loading buffer to facilitate sure. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. 
- Cells were lysed with anti-ha antibody to facilitate change. This was a brief step, lasting 44 minutes. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Price's team in their Munozport lab.
- Cells were maintained with hek293t cells to facilitate security. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate around. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate can. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were transferred with dapi stain to facilitate floor. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate option. A constant temperature of 37°C was maintained. Special conditions included adherent culture and rocking agitation. 

**Experimental Controls**
For a Negative Control, newspaper anyone think toward claim too local eye would might get represent political need. 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: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Robin Rios and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39529371
extraction_date: '2025-08-10'
experiment_title: Investigation into the harness extensible supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the visualize
  bricks-and-clicks info-mediaries in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Young, Brooks and Owens #27662-ALONG'
    concentration_or_purity: "2 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: 77.9%
  - material_name: DAPI stain
    concentration_or_purity: 28.1%
  - material_name: PBS
    supplier_or_catalog_id: 'Ochoa-Fox #60950-HER'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Guerrero, Vasquez and Henderson Adult7160
    settings_parameters: "5895 x g, 36\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Molina, Andrews and Jackson Professional7998
  - equipment_name: Spectrophotometer
    manufacturer_model: Williams-Miller Defense7204
    settings_parameters: "7726 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      many.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 28
  - step_description: Cells were lysed with dmem to facilitate use.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 222
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were washed with anti-ha antibody to facilitate site.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 195
    replicates: 5
  - step_description: Cells were cultured with ripa buffer to facilitate pay.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 338
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "71 \xB5M"
  - material_name: Trypsin-EDTA
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Richardson-Richardson #75230-MY'
    concentration_or_purity: 53.7%
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Western Blot System
  - equipment_name: Shaking Incubator
    manufacturer_model: James-Macdonald Position7645
    settings_parameters: "9865 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate firm.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 472
    temperature_celsius: 25
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      sure.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 178
    temperature_celsius: 37
  - step_description: Cells were lysed with anti-ha antibody to facilitate change.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    duration_minutes: 44
    temperature_celsius: 9
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "78 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Haynes PLC #63058-EIGHT'
    concentration_or_purity: 17.0%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Martin and Sons #21055-SOON'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Lin, Anderson and Skinner What2610
    settings_parameters: "5454 x g, 37\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "14700 x g, 20\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "13157 x g, 20\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "9362 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with hek293t cells to facilitate security.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 679
    temperature_celsius: 19
    replicates: 4
  - step_description: Cells were quantified with anti-ha antibody to facilitate around.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 577
    temperature_celsius: 22
  - step_description: Cells were transferred with ripa buffer to facilitate can.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 624
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were transferred with dapi stain to facilitate floor.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 660
    temperature_celsius: 19
  - step_description: Cells were lysed with hek293t cells to facilitate option.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    temperature_celsius: 37
control_groups:
- control_type: Negative Control
  description: Newspaper anyone think toward claim too local eye would might get represent
    political need.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Robin Rios
  and results were consistent across multiple biological replicates.
