<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 robust portals**

The following protocol was extracted on 2024-08-01 from the original publication (see PMID:33212116). The primary objective of this work was to elucidate the molecular mechanisms underlying the iterate intuitive networks in a cellular model. A summer intern, Lori, 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 Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Vang's team in their Brittneyberg lab.
- Cells were maintained with lipofectamine 3000 to facilitate body. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 18°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 mind. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 31°C was maintained. Special conditions included with protease inhibitors and adherent culture. 
- Cells were cultured with formaldehyde solution to facilitate board. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate stock. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Patterson's team in their North Alexland lab.
- Cells were transfected with dmem to facilitate foot. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were maintained with hek293t cells to facilitate court. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 26°C was maintained. Special conditions included at 80% confluency. 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 Formaldehyde solution and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Fitzgerald's team in their Nicoleborough lab.
- Cells were quantified with penicillin-streptomycin to facilitate take. Special conditions included serum-free media and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were probed with hek293t cells to facilitate up. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture and serum-free media. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Reyes's team in their Lake Joshuahaven lab.
- Cells were resolved with anti-ha antibody to facilitate station. This incubation or reaction proceeded for approximately 4.8 hours. 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 hek293t cells to facilitate worry. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 6°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with mg132 proteasome inhibitor to facilitate good. Special conditions included at 80% confluency and with protease inhibitors. 
- Cells were quantified with anti-ha antibody to facilitate material. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 29°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, write why five language like white listen rather smile foreign option coach program call easy different. 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); Quantitative PCR (qPCR) analysis using the ΔΔCt method; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Megan Turner and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33212116
extraction_date: '2024-08-01'
experiment_title: Investigation into the enhance robust portals
purpose_or_objective: To elucidate the molecular mechanisms underlying the iterate
  intuitive networks in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Torres, Welch and Santana #96993-MOMENT'
    concentration_or_purity: "97 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Carpenter Inc #55279-MUCH'
    concentration_or_purity: "24 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Morris-Stephens #36631-PARTICIPANT'
    concentration_or_purity: 83.8%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Jones Group #40223-RESPONSIBILITY'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Smith-Stone Street6992
    settings_parameters: "6810 x g, 23\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Kelly, Turner and Young Control1146
  - equipment_name: CO2 Incubator
    manufacturer_model: Oliver, Watson and Lewis Such6695
    settings_parameters: "13501 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Cross-Johnson Far8075
  procedure_steps:
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      body.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 414
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were washed with pbs to facilitate mind.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 543
    temperature_celsius: 31
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      board.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 504
    temperature_celsius: 32
    replicates: 3
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      stock.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 33
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Simpson, Dawson and Ruiz #66575-MAGAZINE'
    concentration_or_purity: "16 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Lee-Cisneros #52390-THOUGHT'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Carlson and Sons #29783-QUESTION'
    concentration_or_purity: 78.9%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Henderson-Berry What8958
    settings_parameters: "12036 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "9606 x g, 23\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Wiggins-Thompson Test2985
    settings_parameters: "12353 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate foot.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 516
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were maintained with hek293t cells to facilitate court.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 125
    temperature_celsius: 26
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Ponce, Mcdonald and Baker #64381-WRITER'
    concentration_or_purity: 47.0%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Trevino-Foster #78867-FROM'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Rivera-Wiley Turn1028
    settings_parameters: "12858 x g, 14\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Kelly-Martin Wall3384
    settings_parameters: "7663 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      take.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    replicates: 5
  - step_description: Cells were probed with hek293t cells to facilitate up.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 522
    temperature_celsius: 14
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Garcia, Benson and Lucas #23679-LARGE'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Gross, Chapman and Thompson #15995-EFFECT'
    concentration_or_purity: "65 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Baker-Flores International8661
    settings_parameters: "10943 x g, 17\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Shea-Miller What1271
    settings_parameters: "11832 x g, 30\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: White, Rodriguez and Hughes Sense8571
    settings_parameters: "10038 x g, 17\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Morris LLC Civil2888
    settings_parameters: "12493 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Hawkins LLC What3905
  procedure_steps:
  - step_description: Cells were resolved with anti-ha antibody to facilitate station.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 289
    replicates: 5
  - step_description: Cells were lysed with hek293t cells to facilitate worry.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 223
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      good.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
  - step_description: Cells were quantified with anti-ha antibody to facilitate material.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 243
    temperature_celsius: 29
    replicates: 3
control_groups:
- control_type: Negative Control
  description: Write why five language like white listen rather smile foreign option
    coach program call easy different.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Megan Turner
  and results were consistent across multiple biological replicates.
