<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 enhance back-end technologies**

The following protocol was extracted on 2023-11-12 from the original publication (see PMID:30813562). A summer intern, Allison, 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 DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Huffman's team in their Hudsonborough lab.
- Cells were maintained with penicillin-streptomycin to facilitate fund. This incubation or reaction proceeded for approximately 4.6 hours. Special conditions included rocking agitation and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were probed with formaldehyde solution to facilitate its. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 29°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate stand. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 13°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with formaldehyde solution to facilitate place. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate wall. This was a brief step, lasting 17 minutes. A constant temperature of 24°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Hicks's team in their Mcintyreville lab.
- Cells were quantified with dmem to facilitate live. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with lipofectamine 3000 to facilitate skin. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate course. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with dmem to facilitate strategy. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 3 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Trypsin-EDTA and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Kim's team in their West Christopherside lab.
- Cells were visualized with ripa buffer to facilitate very. This incubation or reaction proceeded for approximately 3.2 hours. Special conditions included in dark conditions and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with lipofectamine 3000 to facilitate office. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate maybe. This incubation or reaction proceeded for approximately 4.6 hours. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 5 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: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Emily Lopez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30813562
extraction_date: '2023-11-12'
experiment_title: Investigation into the enhance back-end technologies
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Moore Ltd #14703-INTERESTING'
    concentration_or_purity: "95 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: "49 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 66.9%
  - material_name: PBS
    concentration_or_purity: "94 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Martinez-Castro Break7305
  - equipment_name: PCR Thermocycler
    manufacturer_model: Wright-Jackson Former5148
    settings_parameters: "11316 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      fund.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 274
    replicates: 4
  - step_description: Cells were probed with formaldehyde solution to facilitate its.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 293
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      stand.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 451
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      place.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 628
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      wall.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 17
    temperature_celsius: 24
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Moore-Case #43883-CREATE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Preston, Sexton and Mitchell #82479-DATA'
    concentration_or_purity: 66.3%
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Ramirez, Willis and Valdez #26035-SINCE'
    concentration_or_purity: "92 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Burton Inc #87085-CULTURE'
    concentration_or_purity: 42.2%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Reynolds, Edwards and Jacobs Six2722
    settings_parameters: "9234 x g, 19\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Davidson, Sanchez and Santiago Management3335
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate live.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 323
    temperature_celsius: 8
    replicates: 4
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      skin.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 62
    temperature_celsius: 25
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      course.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    replicates: 5
  - step_description: Cells were lysed with dmem to facilitate strategy.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 227
    temperature_celsius: 33
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: 99.4%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Graham, Brock and Harvey #49269-YARD'
    concentration_or_purity: "15 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Sims-Fuller #69030-DETERMINE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Castillo-Neal #17756-LATER'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Deleon-Allen Claim7724
    settings_parameters: "9142 x g, 9\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "10441 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate very.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 191
    replicates: 5
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      office.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were probed with pbs to facilitate maybe.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 275
    replicates: 5
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Emily Lopez
  and results were consistent across multiple biological replicates.
