Microarray introduction
This page has four parts, in the order you use them. Part 1 is what you need to know. Part 2 says what to do, in plain English. Part 3 shows the work done once on a case that is not yours. Part 4 is your own work and where to turn it in.
Open your materials, follow the steps, then turn in your work.
Explain how a microarray uses hybridization to test many genes at once and where it differs from PCR.
Optional: listen or watch a unit review▸
Part 1 of 4 · Background and definitions▸
💡 Big idea: A reads fluorescence where labeled cDNA made from the sample's mRNA hybridizes to matching probes, so one chip can report the expression of thousands of genes at once.
- • : fluorescently labeled cDNA from a sample binds to complementary probe sequences on the chip; fluorescence indicates which genes are expressed.
- • A bright spot means the gene is expressed (mRNA present in sample); a dark spot means little or no expression.
- • Microarrays survey thousands of genes at once but require specialized equipment and bioinformatics; is targeted and gel is the readout, not a scanner.
acts as a sieve and is pulled by charge, so smaller fragments travel farther and band position becomes a readable size map.
A reads fluorescence where labeled cDNA made from the sample's mRNA hybridizes to matching probes, so one chip can report the expression of thousands of genes at once.
Driving question: and a gel handle one target at a time. How does a chip the size of a stamp test thousands of genes in a single run?
What you already know: acts as a sieve and is pulled by charge, so smaller fragments travel farther and band position becomes a readable size map.
New idea: A reads fluorescence where labeled cDNA made from the sample's mRNA hybridizes to matching probes, so one chip can report the expression of thousands of genes at once.
Visual or model: No figure is attached to this lesson. The readings, the worked example and E1 to E3 carry the evidence.
- Observe or measure the relevant feature in introduction.
- Organize the observation with a stable evidence ID.
- Apply this rule: Stored information can be copied, read, and converted into a functional product.
- Choose the option the evidence supports and state the limit of the conclusion.
Real biomedical example: Genetic-testing teams audit whether consent, sample identity, result interpretation, and follow-up evidence are documented before a result informs the . Source: MedlinePlus: What is genetic testing?.
What the evidence supports: E1 to E3 support the daily take-home when the response meets the stated success criteria.
What it cannot prove: The package does not support claims beyond this lesson's or any real patient diagnosis.
- • : A short single strand of that binds to a target sequence and gives DNA polymerase a starting point to build a new strand, as in .
- • : A bacterial that cuts at a specific sequence, leaving clean or sticky ends used to splice genes together.
- • : A lab method that uses an electric field to pull fragments through a gel so they separate by size and show up as bands.
- • : A chip holding thousands of tiny spots that lets scientists measure the activity of many genes at once by detecting which spots light up.
- • : The pairing of two single or RNA strands with matching base sequences into a double strand, used in tests to detect a specific gene.
- • marker: A measurable feature, molecule, or gene used to identify a cell, organism, or condition, like a flag that signals something specific.
Use it now: Choose one decision option. Cite E1 and E3, then explain how the rule connects the evidence to your choice. This is thinking practice for the one turn-in named under Turn in, not a second submission.
Go further, optional: The source links below are optional enrichment. Every fact required for today's local evidence decision appears in this lesson package.
A gene-expression comparison describes relative signal patterns across the supplied conditions, and interpretation depends on normalization, replication, controls, measurement range, and the difference between association and causation.
Limit: A classroom expression table can support a bounded pattern claim but cannot diagnose disease, prove a regulatory mechanism, or establish clinical significance.
Stored information can be copied, read, and converted into a functional product.
Limit: Genes are regulated biological sequences, not conscious instructions, and one gene rarely determines a whole trait alone.
You can explain how a reads many genes by .
Limit: E3 defines the classroom product or success criterion. It is not independent scientific evidence and cannot justify a clinical or causal claim.
Today's decision · Simulated classroom evidence scenario
Your role: medical interventions team member
Decision: Your team must decide what the evidence from introduction supports before submitting the vocabulary application named on today's page.
- • Check the controls and replicates before calling a bright spot a real expression difference between the supplied conditions.
- • Explain each glowing spot as labeled cDNA from the sample's mRNA hybridizing to a matching probe, which reports the genes expressed in that sample.
- • Treat the as a faster gel whose colored spots report the size of each fragment in the sample.
Response: State one choice, cite at least two evidence IDs, explain the rule that connects them, and add one limitation. Use it inside the one turn-in named under Turn in; it is not a separate submission.
Claim ceiling: Today's evidence supports a classroom claim about introduction. It cannot prove causation, diagnose a real patient, or justify action outside this room.
Students often think a is just a faster version of a gel, or that the colored spots show the size of fragments the way gel bands do. The trap: A does not measure size at all. Its spots report which genes are expressed based on where labeled sample binds by complementary . Confusing it with a gel means you miss that a microarray answers what is expressed, not how big the fragment is.
- CER:
- Claim, Evidence, Reasoning: make a claim, back it with evidence, explain your reasoning.
- SOP:
- Standard Operating Procedure, the exact steps to follow (especially in a lab).
- Tracker:
- Your PLTW progress log where you record completed evidence.
- myPLTW:
- The PLTW course site where you do the online activities. Find it in Clever with your Microsoft sign-in, right next to Schoology.
Tap the speaker to hear a term. Add two of these to your notebook glossary with a definition and an example in your own words.
Pick just 2 or 3 words from today and make them yours: write what each one means in your own words, name the context clue or evidence that helped, then give one example from what you actually did in Microarray introduction. Try your own words first; the glossary is there if you get stuck. This is voluntary and counts as extra credit, so keep it short.
Saved on this device. Show Mr. Mendoza or add these to your notebook glossary to claim the extra credit.
Part 2 of 4 · Directions in plain English▸
2.1 Open your materials
Use the materials named in the first step below. Open lesson resources.
2.2 Start the work
Define hybridization and explain how a labeled sample binds to spots on a microarray.
Show all 5 required steps
- Define hybridization and explain how a labeled sample binds to spots on a microarray.
- Describe what a colored spot versus a dark spot tells you about a gene.
- Compare in one row each: PCR, gel, and microarray, listing what each method is best for.
- Write one limit of microarrays that gel or PCR does not share.
- Submit your method comparison as your daily evidence.
Lost your place? Check which steps are done: hybridization defined, bright versus dark spot explained, the PCR-gel-microarray comparison row filled in, and one microarray limitation written. Pick up at the first one missing.
- 0-8Hook: image; introduce concept
- 8-25Define ; explain spot color as expression signal
- 25-50Build comparison table: , gel, (purpose, scale, limit, output)
- 50-65Write one limit of microarrays not shared by or gel
- 65-75Partner quiz: cover one column; name the method from description
- 75-80Submit comparison table in Schoology; keep it as your methods reference
- • Hook: Show a image and ask: how many tests do you think this represents?
- • Why it matters: Microarrays accelerated genomics by shifting from one-gene-at-a-time to genome-wide profiling.
- • Today's work: You build a comparison table that stays your study reference for the methods quiz later in this unit.
- • Exit goal: Method comparison table with one limit submitted before the bell.
PLTW connection and today's work
Open Activity 3.1.4 DNA Microarray in myPLTW and build your PCR-gel-microarray method comparison table.
Today's stopping point: Gel data table should be done; method comparison table due today.
PLTW activity titles identify the course connection. If your account will not open, use the posted materials for today and tell Mr. Mendoza. Do not mark an online activity complete unless you completed it.
Use the turn-in directions in Part 4 of this page. Do not create a second submission unless your teacher asks for one.
Show another explanation or a smaller first step
Need help? Choose a starting point
Part 3 of 4 · Worked example▸
This is a parallel case, not your own. Read it for the order of the work, then do your own in Part 4.
Hybridization in my words: A microarray is covered with single-stranded probe sequences. Labeled cDNA made from the sample's mRNA washes over it, and each piece sticks (hybridizes) only where it finds its complementary probe. A bright, colored spot means that gene was expressed in the sample (its mRNA was present); a dark spot means it was not.
Method comparison: I compared PCR, gel, and microarray by what each is best for.
Microarray limit not shared by the others: A microarray needs specialized scanning equipment and bioinformatics software to read thousands of spots, while a PCR product or a gel can be set up and read with much simpler tools.
| Method | Best for | Output |
|---|---|---|
| PCR | Amplifying one target sequence | Many copies of one region |
| Gel | Separating fragments by size | Bands showing fragment sizes |
| Microarray | Surveying thousands of genes at once | Spot pattern showing expression |
This model shows the level of evidence and organization needed to complete: Completes the methods comparison: a three-row table contrasting PCR, gel, and microarray by purpose plus one sentence on a microarray limit the others do not share.
- Define the term in plain scientific language.
- Connect it to the current investigation.
- Use it accurately in a new example or contrast.
Keep the structure. Replace the question, facts, measurements, and evidence. Then recheck units, vocabulary, and whether the conclusion goes beyond the evidence.
Also due today: Submit your comparison table in Schoology.
A library keeps a master plan protected while working copies guide production at different stations.
- Why protect the master copy?
- What information moves?
- Where can an error change the final product?
Stored information can be copied, read, and converted into a functional product.
Genes are regulated biological sequences, not conscious instructions, and one gene rarely determines a whole trait alone.
- • Master plan maps to .
- • Working copy maps to RNA.
- • Production output maps to or a regulated cell function.
Part 4 of 4 · Your work▸
Check your work before submitting
- You'll be able to explain how a microarray reads many genes by hybridization.
- You'll be able to compare PCR, gel, and microarray by purpose and limit.
4.1 Turn in your work
DueCheck the Schoology assignment for this day- Hand in
- Three-row method comparison table (PCR, gel, microarray) plus one sentence on a microarray limit not shared by the other two methods.
How to submit and name your file
Submit as one PDF in Schoology.
In Schoology, open your course and the assignment for this lesson. Attach your file, select Submit, and check that it appears in the submission.
PDF upload helpYou get two school days for every day you were absent, so this deadline moves with you.
Today's lesson is in Schoology
Each school day has one lesson page in Schoology that holds everything for the day: the goal, the story so far, every table and data value, the numbered steps, and what to turn in. Open it first and work from it. The other rows for this day, if any, are the score line for a paper quiz or test and the John Carroll debate item; they do not add work. Check Schoology for each deadline.
- Today's Lesson · Mon 10/26 · Wk10 · Set up the PCR reaction, then predict how HaeIII cuts taster and nontaster DNA(today's lesson page: the goal, the data, the steps, and what to turn in are all on it)
Link will not open? Open Schoology, choose your course and section, and find the title shown above.
- CompleteEvery required part of the artifact is present, nothing left blank.
- AccurateThe science and the data are correct and match the evidence.
- Scientific reasoningYou explain your claim with evidence and reasoning (CER), not just an answer.
- Professional communicationClear, organized, labeled, and written the way a clinician or scientist would.
- SubmittedGo to Schoology to turn this in. Submit one PDF. Schoology attaches your name to your upload; on the page itself, write your period and code. Name the file: FirstName LastName - Assignment Title - YYYY-MM-DD.pdf. If you cannot get in, see Mr. Mendoza. Do not skip the work.
How this lesson connects
Keep using what you learned last class: Agarose acts as a sieve and DNA is pulled by charge, so smaller fragments travel farther and band position becomes a readable size map. Today: A microarray reads fluorescence where labeled cDNA made from the sample's mRNA hybridizes to matching probes, so one chip can report the expression of thousands of genes at once.
Practice: try a question, then check your answer▸
Claim ceiling for this check: Today's evidence supports a classroom claim about introduction. It cannot prove causation, diagnose a real patient, or justify action outside this room.
On a microarray, a spot for a gene glows bright. What does that tell you about that gene in the sample, and what does the brightness come from?
Write an answer and pick a confidence to unlock the key.
Fast retrieval with instant answers, not the commit-then-reveal check above. Try each from memory first: write what you remember about the earlier units, then check yourself here.
Missed class or ready for more?▸
Optional practice for this unit's lab skills. Nothing in it is due today.
What today's skills lead to. These are real health-science careers this course builds toward. Tap one to see, on the US Department of Labor's O*NET site, what the job actually involves, what it pays, and how fast it is growing.
Use to test how conserved is across humans, mice, and zebrafish.
Goes with: BLAST: is IRF6 conserved across species?
Search ClinVar for which changes are known to cause disease.
Goes with: ClinVar: which IRF6 changes cause disease?
Today is individual work you can do from home: complete the same target above, then submit your Vocabulary task.
Go to Schoology to turn this in. Submit one PDF. Schoology attaches your name to your upload; on the page itself, write your period and code. Name the file: FirstName LastName - Assignment Title - YYYY-MM-DD.pdf. If you cannot get in, see Mr. Mendoza. Do not skip the work.
Class still runs. Complete today's work as this page describes (it is self-guided). Need the concept taught without a teacher? Use this authoritative explainer:
Genetic Science Learning Center: Gel ElectrophoresisThe optional extra-credit track is open. Complete reserved-unit work from home, including virtual labs, for extra credit. Each item shows its correct submission route.
Open the extra-credit trackSources: slides, readings, and resources▸
The deck carries the prior idea forward, lets you inspect an analogy, maps the rule to biology, and ends with the same evidence decision and exit ticket used on this page.
Classroom documents for this lesson are posted in Schoology. Open Clever, then Schoology, and find each one by the name shown on its card.
Open this when the class reaches this activity and use it to complete the required lesson artifact.
Use this if you were absent, got stuck, or need another pass before you submit the lesson artifact.
Use this after the required lesson work when you are ready for a harder application or a deeper connection.
Sign in to Clever with your district Microsoft account to open Schoology or myPLTW. Follow today's posted steps. If myPLTW will not open, use the posted alternative and tell Mr. Mendoza. Turn in your completed work through the Schoology assignment.
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