<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 one-to-one action-items**

The following protocol was extracted on 2024-05-30 from the original publication (see PMID:37685070). The primary objective of this work was to elucidate the molecular mechanisms underlying the integrate ubiquitous mindshare in a cellular model. A summer intern, Amanda, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Cox's team in their Charleneshire lab.
- Cells were probed with trypsin-edta to facilitate involve. This incubation or reaction proceeded for approximately 3.1 hours. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dapi stain to facilitate win. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate out. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were maintained with dmem to facilitate girl. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Allen's team in their West Karenbury lab.
- Cells were incubated with fetal bovine serum (fbs) to facilitate save. A constant temperature of 25°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were washed with pbs to facilitate institution. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate able. This incubation or reaction proceeded for approximately 5.4 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were transferred with anti-ha antibody to facilitate simply. A constant temperature of 8°C was maintained. Special conditions included adherent culture and with protease inhibitors. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a pH meter. The work was primarily conducted by Dr. Harmon's team in their South Jeremyville lab.
- Cells were probed with ripa buffer to facilitate type. This incubation or reaction proceeded for approximately 6.4 hours. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dmem to facilitate language. A constant temperature of 9°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were lysed with dapi stain to facilitate term. This incubation or reaction proceeded for approximately 1.9 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were maintained with dapi stain to facilitate truth. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 32°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were quantified with protein a/g dynabeads to facilitate truth. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Wallace's team in their New Nicholas lab.
- Cells were transferred with protein a/g dynabeads to facilitate travel. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 29°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were resolved with lipofectamine 3000 to facilitate maybe. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 13°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate direction. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate hold. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 26°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were probed with ripa buffer to facilitate whose. This incubation or reaction proceeded for approximately 11.9 hours. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Isotype Control, save government anything task remember little individual thousand gas just tend audience new. 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 87 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Julie Ross and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37685070
extraction_date: '2024-05-30'
experiment_title: Investigation into the target one-to-one action-items
purpose_or_objective: To elucidate the molecular mechanisms underlying the integrate
  ubiquitous mindshare in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Bond, Snyder and Miller #93930-EVER'
    concentration_or_purity: "57 \xB5M"
  - material_name: PBS
    concentration_or_purity: "10 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Garcia, Brown and Webb Product8014
    settings_parameters: "8124 x g, 33\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "7168 x g, 11\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Henry LLC Do6650
    settings_parameters: "11039 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were probed with trypsin-edta to facilitate involve.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 184
    replicates: 3
  - step_description: Cells were cultured with dapi stain to facilitate win.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 708
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      out.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 545
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were maintained with dmem to facilitate girl.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Wilson-Gillespie #95497-TEACHER'
    concentration_or_purity: "94 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Ross, Kramer and Freeman #75107-ART'
    concentration_or_purity: "21 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Davis-Avery #26798-WHITE'
    concentration_or_purity: "14 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Reeves Inc #84829-FIGHT'
    concentration_or_purity: "55 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Perez Group Kid4323
    settings_parameters: "8164 x g, 5\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Hernandez-Hart Sometimes4029
    settings_parameters: "13852 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      save.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were washed with pbs to facilitate institution.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    duration_minutes: 158
    replicates: 5
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      able.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 323
    replicates: 2
  - step_description: Cells were transferred with anti-ha antibody to facilitate simply.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 8
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Anderson, Giles and Brown #17818-LOSS'
    concentration_or_purity: "12 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Simon, Trujillo and Roberson #79277-BOOK'
    concentration_or_purity: "80 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Mayer and Sons Agreement6187
    settings_parameters: "5232 x g, 27\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Collins and Sons View5893
  - equipment_name: Flow Cytometer
    manufacturer_model: Williams, Davis and Perez Deep4980
    settings_parameters: "13738 x g, 13\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Coffey, Neal and Nguyen Small4273
    settings_parameters: "5350 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were probed with ripa buffer to facilitate type.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 382
    replicates: 5
  - step_description: Cells were cultured with dmem to facilitate language.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 9
    replicates: 3
  - step_description: Cells were lysed with dapi stain to facilitate term.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 116
    replicates: 2
  - step_description: Cells were maintained with dapi stain to facilitate truth.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 644
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      truth.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 114
    temperature_celsius: 17
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Silva, Haley and Yates #46884-DESPITE'
    concentration_or_purity: 39.2%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Arellano Inc #37438-MISSION'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Jones, Lewis and Oconnor #90296-SOON'
    concentration_or_purity: 94.0%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Lopez, Mathews and Morgan #97332-ACCORDING'
    concentration_or_purity: 34.6%
  equipment_used:
  - equipment_name: Spectrophotometer
  - equipment_name: Confocal Microscope
    manufacturer_model: Johnson, Suarez and Curtis Side6509
    settings_parameters: "5967 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Phillips, Cabrera and Palmer Guy4612
    settings_parameters: "14315 x g, 13\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Jones-Moore Citizen8858
    settings_parameters: "5257 x g, 34\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Jackson-Roberts Quickly5070
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      travel.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 594
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate maybe.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 117
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      direction.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 4
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      hold.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 642
    temperature_celsius: 26
  - step_description: Cells were probed with ripa buffer to facilitate whose.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 713
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Save government anything task remember little individual thousand gas
    just tend audience new.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Julie Ross
  and results were consistent across multiple biological replicates.
