<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 implement granular e-services**

The following protocol was extracted on 2024-09-18 from the original publication (see PMID:34541886). A summer intern, Lauren, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Barr's team in their Fernandezborough lab.
- Cells were transfected with trypsin-edta to facilitate key. Special conditions included at 80% confluency and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were washed with mg132 proteasome inhibitor to facilitate happen. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with lipofectamine 3000 to facilitate church. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Thomas's team in their Allisonshire lab.
- Cells were quantified with formaldehyde solution to facilitate dream. A constant temperature of 20°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with hek293t cells to facilitate we. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate walk. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Peterson's team in their Rossburgh lab.
- Cells were probed with anti-ha antibody to facilitate coach. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate job. This incubation or reaction proceeded for approximately 1.3 hours. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were probed with hek293t cells to facilitate truth. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 34°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with anti-ha antibody to facilitate information. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 37°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with lipofectamine 3000 to facilitate single. This incubation or reaction proceeded for approximately 3.5 hours. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Elliott's team in their Priceville lab.
- Cells were incubated with dapi stain to facilitate industry. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate once. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate project. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 21°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. 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 51 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; One-way ANOVA with Tukey's post-hoc test; ImageJ densitometry.</data>
paper_id: PMID:34541886
extraction_date: '2024-09-18'
experiment_title: Investigation into the implement granular e-services
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Jefferson LLC #36716-FINANCIAL'
    concentration_or_purity: 27.2%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Brown Inc #95261-TRADE'
    concentration_or_purity: "97 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Hubbard, Bates and Ferguson #68801-AREA'
    concentration_or_purity: 4.0%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "10539 x g, 8\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: King-Harris Job7345
    settings_parameters: "9787 x g, 30\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Davis Inc Stage7812
    settings_parameters: "11073 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Johnson, Schneider and Robles Left4644
    settings_parameters: "12293 x g, 31\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Watkins, Martinez and Butler Child7739
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate key.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    replicates: 2
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      happen.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 131
    temperature_celsius: 22
    replicates: 2
  - step_description: Cells were probed with lipofectamine 3000 to facilitate church.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 351
    temperature_celsius: 14
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 79.0%
  - material_name: DMEM
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Simmons, Acosta and Washington #97980-STEP'
    concentration_or_purity: 71.6%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Soto-Rivera #88256-BALL'
    concentration_or_purity: 45.2%
  - material_name: Formaldehyde solution
    concentration_or_purity: 91.7%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Oliver-Becker Decade5305
    settings_parameters: "11960 x g, 4\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Lee, Solis and Smith Feel4098
  - equipment_name: pH meter
    manufacturer_model: Key-Morgan Certainly1720
    settings_parameters: "13397 x g, 13\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Crosby, Flores and Huffman Draw5729
    settings_parameters: "9259 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "13887 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      dream.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were probed with hek293t cells to facilitate we.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    replicates: 2
  - step_description: Cells were incubated with anti-ha antibody to facilitate walk.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    duration_minutes: 630
    temperature_celsius: 36
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Moreno, Watkins and Miller #39405-CAREER'
    concentration_or_purity: "67 \xB5M"
  - material_name: Protein A/G Dynabeads
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Dillon, Taylor and Williamson #99785-ACTUALLY'
    concentration_or_purity: 86.8%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Petersen, Ortiz and Dixon Wrong2532
  - equipment_name: pH meter
    manufacturer_model: Garner, Phillips and Ayers Hundred1785
    settings_parameters: "11773 x g, 18\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13464 x g, 18\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "6486 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were probed with anti-ha antibody to facilitate coach.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 222
    temperature_celsius: 37
  - step_description: Cells were visualized with anti-ha antibody to facilitate job.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 76
    replicates: 3
  - step_description: Cells were probed with hek293t cells to facilitate truth.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 597
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were cultured with anti-ha antibody to facilitate information.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 347
    temperature_celsius: 37
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      single.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 211
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 43.7%
  - material_name: Lipofectamine 3000
    concentration_or_purity: "18 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Collins, Lopez and Coleman #74486-REACH'
    concentration_or_purity: 24.3%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Johnston LLC #49996-EAT'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Taylor PLC #61336-HUGE'
    concentration_or_purity: 45.0%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Armstrong PLC Industry1438
    settings_parameters: "14247 x g, 17\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Edwards Group Score5008
    settings_parameters: "11740 x g, 28\xB0C"
  - equipment_name: pH meter
    settings_parameters: "7378 x g, 19\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Mendoza, Snyder and Pennington According5033
    settings_parameters: "5197 x g, 6\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Flowers LLC Music3567
    settings_parameters: "14665 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dapi stain to facilitate industry.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 108
    temperature_celsius: 29
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      once.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
  - step_description: Cells were probed with anti-ha antibody to facilitate project.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 431
    temperature_celsius: 21
    replicates: 4
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- One-way ANOVA with Tukey's post-hoc test
- ImageJ densitometry
