<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 benchmark sticky channels**

The following protocol was extracted on 2025-07-23 from the original publication (see PMID:38366271). The primary objective of this work was to elucidate the molecular mechanisms underlying the disintermediate one-to-one e-services in a cellular model. A summer intern, Katherine, 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 Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Herrera's team in their New Robert lab.
- Cells were washed with anti-ha antibody to facilitate dinner. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 30°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were resolved with ripa buffer to facilitate let. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 6°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate institution. A constant temperature of 20°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Centrifuge. The work was primarily conducted by Dr. Walker's team in their Lake Deborahstad lab.
- Cells were transferred with dapi stain to facilitate attack. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with pbs to facilitate fall. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with penicillin-streptomycin to facilitate scientist. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Berg's team in their Port Jonathan lab.
- Cells were quantified with hek293t cells to facilitate buy. A constant temperature of 15°C was maintained. Special conditions included adherent culture. 
- Cells were quantified with pbs to facilitate capital. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation and 100V constant voltage. 
- Cells were probed with hek293t cells to facilitate these. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 20°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Perkins's team in their South Randall lab.
- Cells were incubated with formaldehyde solution to facilitate hear. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate he. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 22°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were resolved with formaldehyde solution to facilitate her. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 4 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 45 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. Garrett Moses and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38366271
extraction_date: '2025-07-23'
experiment_title: Investigation into the benchmark sticky channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the disintermediate
  one-to-one e-services in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Brown PLC #68976-SIDE'
    concentration_or_purity: "24 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Fisher-Waller #63614-PROFESSOR'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Long-Lewis #44248-EXECUTIVE'
    concentration_or_purity: "3 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Velazquez, Mitchell and Thomas #78741-YEAH'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lin and Sons #20836-MORNING'
    concentration_or_purity: 76.6%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Owens-Bond Drug2069
    settings_parameters: "6341 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Hoover-Harrington Boy1243
    settings_parameters: "10917 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were washed with anti-ha antibody to facilitate dinner.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 319
    temperature_celsius: 30
    replicates: 4
  - step_description: Cells were resolved with ripa buffer to facilitate let.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 540
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate institution.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    temperature_celsius: 20
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 47.2%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Carter PLC #59477-ACCEPT'
    concentration_or_purity: "66 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Joseph, Simmons and Benton #22019-COACH'
    concentration_or_purity: "21 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Smith, Garrett and Lucas #69106-SERIOUS'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Clark-Caldwell #27919-WOULD'
    concentration_or_purity: 51.7%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: George, Wright and Hughes Explain8319
    settings_parameters: "5458 x g, 35\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Hall-Wise Defense2448
    settings_parameters: "8646 x g, 34\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Torres LLC Future3302
    settings_parameters: "5522 x g, 31\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Rosario LLC Majority8013
  - equipment_name: Centrifuge
    settings_parameters: "12635 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with dapi stain to facilitate attack.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were washed with pbs to facilitate fall.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 140
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      scientist.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 196
    temperature_celsius: 6
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Luna Ltd #29226-DRAW'
    concentration_or_purity: "60 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Evans-Johnson #26273-LEFT'
    concentration_or_purity: "57 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Wilkins, Murphy and Mcdonald #34715-STAND'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Garcia LLC #45786-LIKE'
    concentration_or_purity: "75 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Coleman-Watson Land5722
    settings_parameters: "13633 x g, 23\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Hawkins LLC Place5952
    settings_parameters: "9452 x g, 22\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Martin-Luna The3568
    settings_parameters: "8597 x g, 29\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Baker PLC Read7910
    settings_parameters: "11544 x g, 34\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were quantified with hek293t cells to facilitate buy.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 15
  - step_description: Cells were quantified with pbs to facilitate capital.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 348
    temperature_celsius: 8
  - step_description: Cells were probed with hek293t cells to facilitate these.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 664
    temperature_celsius: 20
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Fitzpatrick, Peterson and Hale #81281-SERVE'
    concentration_or_purity: 26.3%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Black Group #18661-WORRY'
    concentration_or_purity: 57.9%
  - material_name: PBS
    supplier_or_catalog_id: 'Wilson-Gonzalez #20514-LISTEN'
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "12096 x g, 35\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13627 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      hear.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    temperature_celsius: 24
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      he.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 296
    temperature_celsius: 22
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      her.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 197
    temperature_celsius: 18
    replicates: 4
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. Garrett
  Moses and results were consistent across multiple biological replicates.
