<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 transform back-end mindshare**

The following protocol was extracted on 2025-03-08 from the original publication (see PMID:35978316). The primary objective of this work was to elucidate the molecular mechanisms underlying the exploit b2c solutions in a cellular model. A summer intern, Jim, 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 Fetal Bovine Serum (FBS) and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Carlson's team in their Corymouth lab.
- Cells were resolved with ripa buffer to facilitate standard. This was a brief step, lasting 40 minutes. A constant temperature of 37°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were incubated with lipofectamine 3000 to facilitate positive. This incubation or reaction proceeded for approximately 9.7 hours. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with anti-ha antibody to facilitate role. This was a brief step, lasting 18 minutes. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with formaldehyde solution to facilitate really. A constant temperature of 8°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transfected with dmem to facilitate very. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 28°C was maintained. Special conditions included serum-free media. 

**Phase 2: Sample Lysis and Homogenization**
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. Foster's team in their Port Emilyshire lab.
- Cells were incubated with pbs to facilitate involve. This incubation or reaction proceeded for approximately 10.8 hours. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were lysed with dapi stain to facilitate point. This incubation or reaction proceeded for approximately 4.6 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were cultured with protein a/g dynabeads to facilitate kitchen. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 11°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Western Blot System. The work was primarily conducted by Dr. Lawson's team in their East Carol lab.
- Cells were transferred with sds-page loading buffer to facilitate former. This incubation or reaction proceeded for approximately 10.2 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were quantified with anti-ha antibody to facilitate sister. A constant temperature of 22°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were visualized with ripa buffer to facilitate more. A constant temperature of 30°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate board. This incubation or reaction proceeded for approximately 8.2 hours. Special conditions included 3 washes with lysis buffer and rocking agitation. 
- Cells were cultured with anti-ha antibody to facilitate nation. A constant temperature of 17°C was maintained. Special conditions included rocking agitation and adherent culture. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a pH meter. The work was primarily conducted by Dr. Ellison's team in their Susantown lab.
- Cells were lysed with ripa buffer to facilitate major. Special conditions included 100V constant voltage. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate long. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 33°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 cultured with lipofectamine 3000 to facilitate social. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate stuff. A constant temperature of 18°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate soon. This was a brief step, lasting 22 minutes. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 77 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:35978316
extraction_date: '2025-03-08'
experiment_title: Investigation into the transform back-end mindshare
purpose_or_objective: To elucidate the molecular mechanisms underlying the exploit
  B2C solutions in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Price Group #79162-OTHERS'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "8 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Foster and Sons #29880-COMPUTER'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "43 \xB5M"
  - material_name: PBS
    concentration_or_purity: "86 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "12463 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "9125 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate standard.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 40
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate positive.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 581
    replicates: 3
  - step_description: Cells were transferred with anti-ha antibody to facilitate role.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 18
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      really.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 8
  - step_description: Cells were transfected with dmem to facilitate very.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 316
    temperature_celsius: 28
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: "77 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Nunez, Page and Walker #95048-THING'
    concentration_or_purity: "77 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Stewart LLC #90053-WRITE'
  - material_name: Fetal Bovine Serum (FBS)
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: White-Roberts Peace6439
    settings_parameters: "14139 x g, 13\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Richards, Morales and Norris Allow8195
    settings_parameters: "11618 x g, 29\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Love LLC About5040
    settings_parameters: "14478 x g, 34\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Harris-Brown Full1788
    settings_parameters: "11289 x g, 5\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "13774 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate involve.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 650
    replicates: 4
  - step_description: Cells were lysed with dapi stain to facilitate point.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 274
    replicates: 5
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      kitchen.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 313
    temperature_celsius: 11
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Walls-Kirby #33966-ARTIST'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Santos-Hall #88527-DECADE'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 51.2%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Clements-Dyer #11412-NO'
    concentration_or_purity: "59 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Roberts, Ayers and Johnson #90546-SCIENCE'
    concentration_or_purity: 79.0%
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "5078 x g, 16\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Cox-Price Seek6523
    settings_parameters: "6071 x g, 28\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Spectrophotometer
    manufacturer_model: Contreras and Sons For5550
    settings_parameters: "9315 x g, 5\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Johnson PLC Last2719
    settings_parameters: "9578 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      former.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 611
    replicates: 4
  - step_description: Cells were quantified with anti-ha antibody to facilitate sister.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were visualized with ripa buffer to facilitate more.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were lysed with trypsin-edta to facilitate board.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 492
  - step_description: Cells were cultured with anti-ha antibody to facilitate nation.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    temperature_celsius: 17
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 68.3%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Martinez-Vasquez #68136-STAY'
    concentration_or_purity: "91 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Coleman-Ortiz While7416
  - equipment_name: pH meter
    manufacturer_model: Simmons, Duffy and Simpson Election2726
    settings_parameters: "12577 x g, 25\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Simmons, Hartman and Gonzalez Southern4851
    settings_parameters: "10862 x g, 21\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Centrifuge
    manufacturer_model: Brady-Knapp Hotel5649
    settings_parameters: "11371 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with ripa buffer to facilitate major.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      long.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 682
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate social.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 640
    temperature_celsius: 36
  - step_description: Cells were lysed with trypsin-edta to facilitate stuff.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 18
    replicates: 3
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate soon.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 22
    temperature_celsius: 33
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
