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20.109(S19):Evaluate protein purity and concentration (Day4)20.109(S19):Growth of phage-based active (cathode) material (Day1)20.109(S19):Guidelines for working in the tissue culture facility
20.109(S19):Homework20.109(S19):In silico cloning and confirmation digest of protein expression vector(Day1)20.109(S19):Journal club presentations (Day7 and 8)
20.109(S19):Laboratory tour20.109(S19):Module 120.109(S19):Module 2
20.109(S19):Module 320.109(S19):Perform quantitative PCR experiment and explore additional RNA-seq datasets (Day5)20.109(S19):Practice tissue culture techniques and prepare cells for RNA purification (Day1)
20.109(S19):Prep notes for M320.109(S19):Purify RNA and practice RNA-seq data analysis methods (Day3)20.109(S19):Purify phage-based active (cathode) material (Day2)
20.109(S19):Purify protein for secondary assays(Day2)20.109(S19):Research proposal presentation20.109(S19):Test protein activity using peptidyl-prolyl cis-trans isomerase assay (Day5)
20.109(S19):Visualize phage nanowires using TEM (Day4)20.109(S19): Announcements20.109(S19): Assignments
20.109(S19): Data Summary20.109(S19): M1 Mini-presentation20.109(S19): Mini-presentation
20.109(S19): Mini-report20.109(S19): Prep notes, orientation20.109(S19): Prep notes for M1
20.109(S19): Prep notes for M220.109(S19): Research article20.109(S19): Spring 2019 schedule
20.109(S20):Analyze RNA-seq data and select gene targets for quantitative PCR (qPCR) experiment (Day 6)20.109(S20):Analyze SMM data (Day6)20.109(S20):Analyze titration curves (Day5)
20.109(S20):Analyze titration curves (Day6)20.109(S20):Assess purity and concentration of TDP43 protein (Day3)20.109(S20):Characterize clone by titration using flow cytometry (Day4)
20.109(S20):Characterize clone by titration using flow cytometry (Day5)20.109(S20):Class data20.109(S20):Communication
20.109(S20):Complete in silico cloning and induce TDP43 protein expression (Day1)20.109(S20):Enrich candidate clones using fluorescence-activated cell sorter (FACS) (Day1)20.109(S20):Examine TDP43 binders for chemical features (Day7)
20.109(S20):Examine qPCR results and complete data analysis (Day8)20.109(S20):Guidelines for working in the tissue culture facility20.109(S20):Harvest candidate clones (Day2)
20.109(S20):Homework20.109(S20):Identify clone to characterize (Day4)20.109(S20):Identify clones to characterize (Day3)
20.109(S20):Journal club presentation (Day4 and 6)20.109(S20):Journal club presentations (Day4 and 5)20.109(S20):Laboratory tour
20.109(S20):Module 120.109(S20):Module 220.109(S20):Module 3
20.109(S20):Perform qPCR experiment and continue RNA-seq data analysis (Day7)20.109(S20):Perform small molecule microarray (SMM) with TDP43 protein (Day4)20.109(S20):Prepare cells for RNA purification and practice RNA-seq data analysis methods (Day1)
20.109(S20):Prepare clones for sequencing (Day3)20.109(S20):Purify RNA from etoposide-treated cells and and generate cDNA (Day3)20.109(S20):Purify TDP43 protein (Day2)
20.109(S20):Research proposal presentation20.109(S20):Scan SMM slides to identify binders of TDP43 protein (Day5)20.109(S20):Treat cells with etoposide and analyze RNA-seq data (Day2)
20.109(S20): Announcements20.109(S20): Assignments20.109(S20): Data Summary
20.109(S20): Mini-presentation20.109(S20): Mini-report20.109(S20): Prep notes, orientation
20.109(S20): Prep notes for M120.109(S20): Research article20.109(S20): Spring 2020 schedule
20.109(S21):Announcements20.109(S21):Assignments20.109(S21):Communication
20.109(S21):Data Summary20.109(S21):Guidelines for working in the tissue culture facility20.109(S21):Homework
20.109(S21):Journal club presentation20.109(S21):Laboratory tour20.109(S21):M1D1
20.109(S21):M1D220.109(S21):M1D320.109(S21):M1D4
20.109(S21):M1D520.109(S21):M1D620.109(S21):M1D7
20.109(S21):M2D120.109(S21):M2D220.109(S21):M2D3
20.109(S21):M2D420.109(S21):M2D520.109(S21):M2D6
20.109(S21):M2D720.109(S21):M3D120.109(S21):M3D2
20.109(S21):M3D320.109(S21):M3D420.109(S21):M3D5
20.109(S21):Mini-presentation20.109(S21):Mini-report20.109(S21):Module 1
20.109(S21):Module 220.109(S21):Module 320.109(S21):Research article
20.109(S21):Research proposal presentation20.109(S21):Spring 2021 schedule20.109(S22):Assignments
20.109(S22):Class data20.109(S22):Communication20.109(S22):Data Summary
20.109(S22):FYI20.109(S22):Homework20.109(S22):Journal club presentation
20.109(S22):Laboratory tour20.109(S22):M1D120.109(S22):M1D2
20.109(S22):M1D320.109(S22):M1D420.109(S22):M1D5
20.109(S22):M1D620.109(S22):M1D720.109(S22):M1D8
20.109(S22):M2D120.109(S22):M2D220.109(S22):M2D3
20.109(S22):M2D420.109(S22):M2D520.109(S22):M2D6
20.109(S22):M2D720.109(S22):M2D820.109(S22):M3D1
20.109(S22):M3D220.109(S22):M3D320.109(S22):M3D4
20.109(S22):Module 120.109(S22):Module 220.109(S22):Module 3
20.109(S22):Research article20.109(S22):Research proposal presentation20.109(S22):Research talk
20.109(S22):Spring 2022 schedule20.109(S23):Assignments20.109(S23):Class data
20.109(S23):Communication20.109(S23):Data Summary20.109(S23):FYI
20.109(S23):Homework20.109(S23):Journal article presentation20.109(S23):Laboratory tour
20.109(S23):M1D120.109(S23):M1D220.109(S23):M1D3
20.109(S23):M1D420.109(S23):M1D520.109(S23):M1D6
20.109(S23):M1D720.109(S23):M1D820.109(S23):M2D1
20.109(S23):M2D220.109(S23):M2D320.109(S23):M2D4
20.109(S23):M2D520.109(S23):M2D620.109(S23):M2D7
20.109(S23):M2D820.109(S23):M3D120.109(S23):M3D2
20.109(S23):M3D320.109(S23):M3D420.109(S23):Module 1
20.109(S23):Module 220.109(S23):Module 320.109(S23):Research article
20.109(S23):Research proposal presentation20.109(S23):Research talk20.109(S23):Spring 2023 schedule
20.109(S24):Assignments20.109(S24):Class data20.109(S24):Communication
20.109(S24):Data Summary20.109(S24):FYI20.109(S24):Guidelines for working in the tissue culture facility
20.109(S24):Homework20.109(S24):Journal article presentation20.109(S24):Laboratory tour
20.109(S24):M1D120.109(S24):M1D220.109(S24):M1D3
20.109(S24):M1D420.109(S24):M1D520.109(S24):M1D6
20.109(S24):M1D720.109(S24):M1D820.109(S24):M2D1
20.109(S24):M2D220.109(S24):M2D320.109(S24):M2D4
20.109(S24):M2D520.109(S24):M2D620.109(S24):M2D7
20.109(S24):M2D820.109(S24):M3D120.109(S24):M3D2
20.109(S24):M3D320.109(S24):M3D420.109(S24):Module 1
20.109(S24):Module 220.109(S24):Module 320.109(S24):Research article
20.109(S24):Research proposal presentation20.109(S24):Research talk20.109(S24):Spring 2024 schedule
20.109:Lab basics20.109:Module 120.109:Module 2
20.109:Module 320.109:Module 420.109:OWW basics
20.109:People20.109: Spring 2007 schedule20.109 (F07): Phage by design
20.109 (S07): Atomic force microscopy20.109 (S07): Transmission electron microscopy20.109 Main Page
20.309:Course Information20.309:DAQ System20.309:Lab Report Guidelines
20.309:Learning outcomes20.309:Safety20.309: Exam 1 Topics
20.309 Assignment 1: Optics bootcamp20.309 Main Page20.309 development to-do list
20.345:Course Information20.345:Final project proposal20.345:Key Factors Table
20.345:Literature search20.345:Main page20.345: Wiki guidelines
A.Williams: Objectives and Literature Review
AFM
ANOID Project
Additional ResourcesAligning the optical trapAlumni Page
Aperture and field stopsAssignment 1, Part 1: Pre-lab questionsAssignment 1, Part 2: Optics bootcamp
Assignment 1, Part 3: Building your transillumination microscope
Assignment 1, Part 3: Microscope design
Assignment 1, Part 4: Building your transilluminated microscope
Assignment 1, Part 4: Measuring magnification and bead sizeAssignment 10, Part 1: Measuring the osmotic shock response of yeastAssignment 10 Overview
Assignment 11: Tell us about your lab visit
Assignment 1: Microscope design
Assignment 1: Optics bootcamp
Assignment 1: Pre-lab questions
Assignment 1: Transilluminated microscope
Assignment 1: Transillumination microscopy
Assignment 1 Overview: Transillumination microscopyAssignment 2: epi illuminator for fluorescence microscopyAssignment 2: fluorescence microscopy
Assignment 2 Part 1: Noise in imagesAssignment 2 Part 2: Fluorescence microscopyAssignment 2 Part 3: Build an epi-illuminator for your microscope
Assignment 2 Part 4: Fluorescent imaging of actinAssignment 3, Part 1: visualizing actin with fluorescence contrastAssignment 3, Part 2: experimental design with fluorescence
Assignment 3: visualizing actin using fluorescence contrast
Assignment 3: visualizing actin with fluorescence contrast
Assignment 3 Overview
Assignment 4: finding and measuring thingsAssignment 4 part 1: Make a fake imageAssignment 4 part 2: Measure resolution
Assignment 4 part 3: Track microspheres over timeAssignment 5, Part 1: MSD difference tracking and microscope stabilityAssignment 5, Part 1: viscosity and diffusivity in glycerol-water mixtures
Assignment 5, Part 2: live cell particle tracking of endocytosed beadsAssignment 5: Spring 2020
Assignment 5: cellular microrheology
Assignment 5 Overview
Assignment 5 navigation
Assignment 6, Part 1: Pre-lab questions
Assignment 6, Part 1: build a two-color microscopeAssignment 6, Part 2: Electronics bootcampAssignment 6, Part 2: electronics written problems
Assignment 6, Part 3: Identifying unknown filter circuitsAssignment 6 OverviewAssignment 6 Overview: two color microscope
Assignment 7, Part 1: op amp golden rules questionsAssignment 7, Part 2: measure temperature and fluorescenceAssignment 7, Part 3: testing your instrument and measuring a DNA melting curve
Assignment 7: Amplifiers and feedbackAssignment 7 OverviewAssignment 8, Part 0: convolution practice
Assignment 8, Part 1: convolution
Assignment 8, Part 1: fabricate a microfluidic device
Assignment 8, Part 2: build a two-color microscope
Assignment 8, Part 2: fabricate a microfluidic deviceAssignment 8, Part 2: lock-in amplifier and temperature controlAssignment 8, Part 3: add flow control and test your device
Assignment 8 OverviewAssignment 8 Overview: flow channel & two-color microscopeAssignment 9, Part 1: Analyze two-color yeast images
Assignment 9, Part 1: model functionAssignment 9, Part 2: Simulating DNA melting data and testing the model functionAssignment 9, Part 3: Fitting your data
Assignment 9 OverviewAssignment 9 Overview: Analyzing yeast imagesBEECH(F23)
BEECH(F23):Build Communication ToolkitBEECH(F23):Build CommunityBEECH(F23):Build Knowledge
BEECH(F23):Build Your ProjectBEECH(F23):PeopleBEECH(F23): 2023-2024 schedule
BEECH Main PageBE Classroom Computer DocumentationBE TA Training(Su16):Homepage
BE TA Training (Su17)BE TA Training (Su18)BE TA Training (Su19)
Beam Expander ExampleBeechBode plots
Bode plots and frequency responseBryan Hernandez/20.109/Lab notebook/Module 1/Day 2Bryan Hernandez/20.109/Lab notebook/Module 1/Day 3
Bryan Hernandez/20.109/Lab notebook/Module 1/Day 4Bryan Hernandez/20.109/Lab notebook/Module 1/Day 5Bryan Hernandez/20.109/Lab notebook/Module 1/Day 6
Bryan Hernandez/20.109/Lab notebook/Module 2/Day 2CM March14CM March28
CRISPRi module, Part II: Increasing ethanol yield in E. coli MG1655Calculating MSD and Diffusion CoefficientsCapacitors and inductors
Cartridge ManipulationCell PrintingCell Printing Experimentation
Cell ReservationsCellular microrheologyComplex Number Review
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