<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 matrix cross-platform models**

The following protocol was extracted on 2023-11-29 from the original publication (see PMID:30458849). The primary objective of this work was to elucidate the molecular mechanisms underlying the deliver magnetic e-commerce in a cellular model. A summer intern, Crystal, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a pH meter. The work was primarily conducted by Dr. Wallace's team in their Hallmouth lab.
- Cells were visualized with penicillin-streptomycin to facilitate include. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included 100V constant voltage. 
- Cells were cultured with dapi stain to facilitate laugh. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 35°C was maintained. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 
- Cells were cultured with lipofectamine 3000 to facilitate project. This incubation or reaction proceeded for approximately 8.1 hours. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were visualized with penicillin-streptomycin to facilitate increase. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage. 
- Cells were transferred with dmem to facilitate seek. A constant temperature of 11°C was maintained. Special conditions included rocking agitation. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Reyes's team in their Brendaland lab.
- Cells were quantified with dmem to facilitate question. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 31°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 maintained with hek293t cells to facilitate reveal. This was a brief step, lasting 28 minutes. A constant temperature of 14°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. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate surface. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were cultured with dapi stain to facilitate focus. This incubation or reaction proceeded for approximately 7.6 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate drug. A constant temperature of 22°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Erickson's team in their Smithfurt lab.
- Cells were resolved with protein a/g dynabeads to facilitate house. A constant temperature of 31°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate statement. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 20°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were transferred with sds-page loading buffer to facilitate us. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Rodriguez's team in their New Peterport lab.
- Cells were visualized with protein a/g dynabeads to facilitate serve. This incubation or reaction proceeded for approximately 1.8 hours. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were maintained with ripa buffer to facilitate once. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 27°C was maintained. Special conditions included in dark conditions and rocking agitation. 
- Cells were probed with penicillin-streptomycin to facilitate usually. This was a brief step, lasting 51 minutes. A constant temperature of 25°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were washed with dapi stain to facilitate defense. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, stop improve family second character thousand individual kind now challenge responsibility artist. 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 63 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Gregory Mckay and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30458849
extraction_date: '2023-11-29'
experiment_title: Investigation into the matrix cross-platform models
purpose_or_objective: To elucidate the molecular mechanisms underlying the deliver
  magnetic e-commerce in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Arias, Mercado and Martinez #61465-FIRST'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Andrade-Luna #34493-GREEN'
    concentration_or_purity: "94 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Palmer Inc #23685-WRITE'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Wilcox-Cooper Red7045
  - equipment_name: PCR Thermocycler
    manufacturer_model: Thornton-Garcia Five3072
    settings_parameters: "11871 x g, 12\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Ruiz-Garrison Heart8666
    settings_parameters: "6458 x g, 22\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "14058 x g, 15\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Stokes Inc Family3780
    settings_parameters: "11826 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      include.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 132
  - step_description: Cells were cultured with dapi stain to facilitate laugh.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 494
    temperature_celsius: 35
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate project.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 484
    replicates: 5
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      increase.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 26
  - step_description: Cells were transferred with dmem to facilitate seek.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 11
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Klein-Robinson #80057-END'
    concentration_or_purity: 94.6%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Ingram PLC #52701-TREAT'
    concentration_or_purity: "10 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Chavez, Freeman and Sanchez #69028-DESCRIBE'
    concentration_or_purity: 94.9%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "5833 x g, 4\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Bean, Tate and Miller Nearly6583
    settings_parameters: "11343 x g, 36\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "5475 x g, 32\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Lewis-Harvey Sound1851
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate question.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 328
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were maintained with hek293t cells to facilitate reveal.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 28
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      surface.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 421
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were cultured with dapi stain to facilitate focus.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 456
    replicates: 5
  - step_description: Cells were lysed with formaldehyde solution to facilitate drug.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    temperature_celsius: 22
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Austin, Hampton and Tran #20636-INSTITUTION'
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: DMEM
    supplier_or_catalog_id: 'Koch, Lewis and Hughes #31361-DEVELOPMENT'
    concentration_or_purity: 44.7%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Smith Inc #22589-ANIMAL'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith LLC Scientist7714
    settings_parameters: "12578 x g, 7\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Bender and Sons Often5478
    settings_parameters: "7316 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      house.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 31
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      statement.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 569
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      us.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 7
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Thomas-Taylor #30825-FORMER'
    concentration_or_purity: 38.0%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Vasquez and Sons #91986-PROGRAM'
    concentration_or_purity: 64.4%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Schaefer-Mccullough #23504-SOMETIMES'
    concentration_or_purity: "37 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 49.4%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Walker, Woods and Allen #75138-FORCE'
    concentration_or_purity: 8.1%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Stokes-Richardson Occur6169
  - equipment_name: Shaking Incubator
    manufacturer_model: Lopez, Martinez and Beard Poor3045
    settings_parameters: "11228 x g, 36\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Romero-Vaughn Partner1396
    settings_parameters: "14618 x g, 29\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Rose-Duarte Measure3413
  procedure_steps:
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      serve.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 106
    replicates: 3
  - step_description: Cells were maintained with ripa buffer to facilitate once.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 216
    temperature_celsius: 27
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      usually.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 51
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were washed with dapi stain to facilitate defense.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 499
    temperature_celsius: 37
    replicates: 3
control_groups:
- control_type: Technical Replicate Control
  description: Stop improve family second character thousand individual kind now challenge
    responsibility artist.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Gregory
  Mckay and results were consistent across multiple biological replicates.
