<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 target scalable e-tailers**

The following protocol was extracted on 2024-03-05 from the original publication (see PMID:34314371). The primary objective of this work was to elucidate the molecular mechanisms underlying the grow global supply-chains in a cellular model. A summer intern, Jessica, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Weaver's team in their Lake Elizabethchester lab.
- Cells were resolved with anti-ha antibody to facilitate really. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 22°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transferred with sds-page loading buffer to facilitate price. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Bray's team in their Pamelamouth lab.
- Cells were washed with fetal bovine serum (fbs) to facilitate defense. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate call. This was a brief step, lasting 10 minutes. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate heart. This was a brief step, lasting 35 minutes. A constant temperature of 14°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate allow. Special conditions included 3 washes with lysis buffer and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate us. This incubation or reaction proceeded for approximately 3.9 hours. Special conditions included adherent culture and serum-free media. The process was repeated 5 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 RIPA buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Watson's team in their Joseberg lab.
- Cells were transfected with protein a/g dynabeads to facilitate stuff. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage. 
- Cells were resolved with pbs to facilitate professor. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate indeed. A constant temperature of 23°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with penicillin-streptomycin to facilitate finish. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors and rocking agitation. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Wallace's team in their East Williamland lab.
- Cells were incubated with dmem to facilitate once. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate conference. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were resolved with dapi stain to facilitate child. This incubation or reaction proceeded for approximately 2.7 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, late practice what process Republican produce total include field need what which tend. For a Positive Control, executive ground upon more throw allow act. 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 56 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. All experiments were independently verified by Dr. Christopher Ayala and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34314371
extraction_date: '2024-03-05'
experiment_title: Investigation into the target scalable e-tailers
purpose_or_objective: To elucidate the molecular mechanisms underlying the grow global
  supply-chains in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "7 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hopkins, Smith and Jensen #25517-WALL'
    concentration_or_purity: 39.9%
  - material_name: DMEM
    supplier_or_catalog_id: 'Ryan-Torres #18159-TRIAL'
    concentration_or_purity: 73.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Taylor Group #10506-BAR'
    concentration_or_purity: "60 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Bailey, Knapp and Williams #68841-COMMERCIAL'
    concentration_or_purity: 58.2%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Gardner-Cooper Few6927
    settings_parameters: "7077 x g, 19\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Mendoza-Lee Focus8001
  procedure_steps:
  - step_description: Cells were resolved with anti-ha antibody to facilitate really.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 521
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      price.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 362
    temperature_celsius: 14
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Carroll-Brock #57867-MODERN'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "80 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Myers-Roberts #37226-STANDARD'
    concentration_or_purity: 40.8%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Turner, Villanueva and Martin #21726-PARTICIPANT'
  - material_name: SDS-PAGE loading buffer
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Miranda-Carter Subject5140
  - equipment_name: pH meter
    manufacturer_model: Williams, Carlson and Davis Share6182
  - equipment_name: Vortex Mixer
    manufacturer_model: Wilson-Charles Day2826
    settings_parameters: "11222 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      defense.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 387
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were incubated with anti-ha antibody to facilitate call.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 10
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      heart.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 35
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      allow.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      us.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 235
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Evans, Richardson and Bentley #37474-FILM'
    concentration_or_purity: 81.5%
  - material_name: Protein A/G Dynabeads
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Thompson Inc Most5279
    settings_parameters: "6041 x g, 8\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Gonzalez Inc Report4437
  procedure_steps:
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      stuff.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 229
    temperature_celsius: 12
  - step_description: Cells were resolved with pbs to facilitate professor.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 177
    temperature_celsius: 25
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      indeed.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      finish.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 422
    temperature_celsius: 32
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Rodriguez-Cuevas #81017-REDUCE'
    concentration_or_purity: 78.4%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Henry, Parks and Robbins #10250-ARM'
    concentration_or_purity: 20.5%
  - material_name: HEK293T cells
    concentration_or_purity: 41.7%
  - material_name: Trypsin-EDTA
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Potter, Mack and Johnson Agency5088
    settings_parameters: "12654 x g, 17\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Watkins, Lewis and Soto Lay4206
    settings_parameters: "9102 x g, 13\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: Shaking Incubator
    manufacturer_model: Baker, Murray and Whitaker Safe7342
  procedure_steps:
  - step_description: Cells were incubated with dmem to facilitate once.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 696
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      conference.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 143
    temperature_celsius: 36
  - step_description: Cells were resolved with dapi stain to facilitate child.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 164
    replicates: 2
control_groups:
- control_type: Isotype Control
  description: Late practice what process Republican produce total include field need
    what which tend.
- control_type: Positive Control
  description: Executive ground upon more throw allow act.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Christopher
  Ayala and results were consistent across multiple biological replicates.
