Difference between revisions of "20.109(S13):Preparing cells for analysis (Day4)"
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+ | <font color=red>Done. Light edits completed Monday morning.</font color> | ||
==Introduction== | ==Introduction== | ||
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Folks trying to engineer cartilage tissue have been in interested in this and similar questions for some time. After all, the more closely an ''in vitro'' or ''in vivo'' model construct can mimic natural tissue and promote its development, the more successful it may be for wound and disease repair. Engineering tissue thus requires an expert understanding of what the native tissue is like. Articular cartilage is a water-swollen protein network consisting of >50% collagen Type II, along with small amounts of collagen Types IX and XI. The collagen fibrils vary in diameter, cross-linking density, and orientation (random or aligned) depending on the depth of the tissue cross-section that is examined (see figure). Unlike cartilage, many other connective tissues are composed primarily of collagen Type I. | Folks trying to engineer cartilage tissue have been in interested in this and similar questions for some time. After all, the more closely an ''in vitro'' or ''in vivo'' model construct can mimic natural tissue and promote its development, the more successful it may be for wound and disease repair. Engineering tissue thus requires an expert understanding of what the native tissue is like. Articular cartilage is a water-swollen protein network consisting of >50% collagen Type II, along with small amounts of collagen Types IX and XI. The collagen fibrils vary in diameter, cross-linking density, and orientation (random or aligned) depending on the depth of the tissue cross-section that is examined (see figure). Unlike cartilage, many other connective tissues are composed primarily of collagen Type I. | ||
− | Extracellular matrix (ECM) proteins such as the collagens must be synthesized by cells. Chondrocytes readily synthesize collagen II, while fibroblasts and mesenchymal stem cells primarily synthesize collagen I. Thus, the expression and production of different collagens is one way to distinguish these cells types. To study collagen at the gene transcript level, you will break open and homogenize your cells using a lysis reagent and column (QIAshredder) and then isolate RNA using an RNeasy kit from Qiagen. The RNeasy kit includes silica gel columns, similar to the ones you used to purify DNA in Module 1, that selectively bind RNA (but not DNA) that is >200 bp long under appropriate buffer conditions. Due to size exclusion, the resultant RNA is somewhat enriched in mRNAs relative to rRNA and tRNA. To further purify for mRNA, one could use a polyT affinity column to capture the polyA tail of this RNA type, but we will not do this today. | + | Extracellular matrix (ECM) proteins such as the collagens must be synthesized by cells. Chondrocytes readily synthesize collagen II, while fibroblasts and mesenchymal stem cells primarily synthesize collagen I. Thus, the expression and production of different collagens is one way to distinguish these cells types. To study collagen at the gene transcript level, you will break open and homogenize your cells using a lysis reagent and column (QIAshredder) and then isolate RNA using an RNeasy kit from Qiagen. The RNeasy kit includes silica gel columns, similar to the ones you used to purify DNA in Module 1, that selectively bind RNA (but not DNA) that is >200 bp long under appropriate buffer conditions. Due to size exclusion, the resultant RNA is somewhat enriched in mRNAs relative to rRNA and tRNA. To further purify for mRNA, one could use a polyT affinity column to capture the polyA tail of this RNA type, but we will not do this step today. |
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− | After eluting and measuring your total RNA, you will perform a reverse transcription (RT) reaction to make cDNA from the mRNA. Next time you will amplify the gene transcripts of interest, namely those for the collagen I and collagen II alpha chains, by PCR. In previous iterations of this module, we used | + | After eluting and measuring your total RNA, you will perform a reverse transcription (RT) reaction to make cDNA from the mRNA. Next time you will amplify the gene transcripts of interest, namely those for the collagen I and collagen II alpha chains, by PCR. In previous iterations of this module, we used a 1-step RT-PCR kit, and then ran the amplified cDNA products out on an agarose gel to compare the changes in collagen II and I expression for the two culture conditions. However, as you may have noticed by now, agarose gels do not have a large dynamic range. Moreover, end-point PCR is prone to error should the conditions (e.g., amount of RNA) deviate from those used to optimize the assay. For these reasons, we now use a more sensitive method for quantifying the transcripts, called real-time-PCR or sometimes RT-PCR, confusingly! The method is also called qPCR, for quantitative PCR. |
In qPCR, the amount of DNA is measured after each cycle of PCR, in contrast to an end-point PCR assay. The DNA is detected by using a dye that fluoresces only when it binds to DNA (similar to ethidium bromide staining), or even a tagged primer that fluoresces only when it binds to the desired product. As the DNA is amplified, fluorescence is repeatedly measured and increases exponentially over time. Finally, cDNA product renaturing competes with primer annealing and the fluorescence intensity plateaus rather than growing. Comparisons between samples are done using data in the exponential regime. | In qPCR, the amount of DNA is measured after each cycle of PCR, in contrast to an end-point PCR assay. The DNA is detected by using a dye that fluoresces only when it binds to DNA (similar to ethidium bromide staining), or even a tagged primer that fluoresces only when it binds to the desired product. As the DNA is amplified, fluorescence is repeatedly measured and increases exponentially over time. Finally, cDNA product renaturing competes with primer annealing and the fluorescence intensity plateaus rather than growing. Comparisons between samples are done using data in the exponential regime. | ||
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When measuring changes in gene expression, primer design must be appropriate for a cDNA rather than genomic DNA. For example, a single primer that includes sequence from two neighbouring exons (along with a second primer that has sequence from just one exon) will amplify mRNA but not genomic DNA, which may be present as a contaminant (see also figure at right). What will happen if each primer contains sequence from only one exon? Primer design and quality control for qPCR also entail further consideration, particularly if tagged primers are used. In our case, the true efficiency of the primers needed to be measured (maximum efficiency is 2, i.e., perfectly exponential growth) to enable later quantification of transcript level changes. You will learn more about qPCR analysis in the coming week. | When measuring changes in gene expression, primer design must be appropriate for a cDNA rather than genomic DNA. For example, a single primer that includes sequence from two neighbouring exons (along with a second primer that has sequence from just one exon) will amplify mRNA but not genomic DNA, which may be present as a contaminant (see also figure at right). What will happen if each primer contains sequence from only one exon? Primer design and quality control for qPCR also entail further consideration, particularly if tagged primers are used. In our case, the true efficiency of the primers needed to be measured (maximum efficiency is 2, i.e., perfectly exponential growth) to enable later quantification of transcript level changes. You will learn more about qPCR analysis in the coming week. | ||
− | Next time (day 5) | + | Next time (day 5) we ll initiate an assay called ELISA to observe collagen at the protein (rather than transcript) level and also begin analysis of the data collected thus far. |
==Protocols== | ==Protocols== | ||
− | <font color=purple>If you got to go to the TC room first on Day 2, you will go in the second cohort today (and vice-versa). If you are in the second group, use the time that you are waiting to prepare your RNase-free area, label tubes that you will need, etc.</font color> | + | <font color=purple>If you got to go to the TC room first on Day 2, you will go in the second cohort today (and vice-versa). If you are in the second group, use the time that you are waiting to complete your research idea discussion, and if you have time to also prepare your RNase-free area, label tubes that you will need, etc.</font color> |
− | ===Part 1: Prepare cell lysates=== | + | ===Part 1: Research idea discussion=== |
+ | |||
+ | Before (second TC cohort) or after (first TC cohort) your wet-lab work today, take some time to discuss the five research results you wrote up for homework with your lab partner, guided by the instructions below. | ||
+ | |||
+ | Writing a research proposal requires that you identify an interesting topic, spend lots of time learning about it, and then design some clever experiments to advance the field. It also requires that you articulate your ideas so any reader is convinced of your expertise, your creativity and the significance of your findings, should you have the opportunity to carry out the experiments you ve proposed. To begin you must identify your research question. This may be the hardest part and the most fun. Fortunately you started by finding a handful of topics to share with your lab partner. Today you should discuss and evaluate the topics you ve gathered. Consider them based on: | ||
+ | * your interest in the topic | ||
+ | * the availability of good background information | ||
+ | * your likelihood of successfully advancing current understanding | ||
+ | * the possibility of advancing foundational technologies or finding practical applications | ||
+ | * if your proposal could be carried out in a reasonable amount of time and with non-infinite resources | ||
+ | |||
+ | It might be that not one of the topics you ve identified is really suitable, in which case you should find some new ideas. It s also possible that through discussion with your lab partner, you ve found something new to consider. Both of these outcomes are fine but by the end of today s lab you should have settled on a general topic or two so you can begin the next step in your proposal writing, namely background reading and critical thinking about the topic. '''Check in with Thomas and get his feedback about your ideas for a few minutes before leaving today.''' | ||
+ | |||
+ | A few ground rules that are 20.109 specific: | ||
+ | *You should not propose any research question that has been the subject of your UROP or research experience outside of 20.109. This proposal must be original. | ||
+ | *You should keep in mind that this proposal will be presented to the class, so try to limit your scope to an idea that can be convincingly presented in a twelve minute oral presentation. | ||
+ | |||
+ | Once you and your partner have decided on a suitable research problem, it s time to become an expert on the topic. This will mean searching the literature, talking with people, generating some ideas and critically evaluating them. To keep track of your efforts, you should start a wiki catalog on your OpenWetWare user page. How you format the page is up to you but check out the [http://openwetware.org/wiki/Yeast_rebuild | yeast rebuild ] or the [http://openwetware.org/wiki/T7.2 | T7.2 ] wiki pages on OpenWetWare for examples of research ideas in process. As part of a later FNT assignment, you will have to print out your wiki page specifying your topic, your research goal and at least two helpful references that you ve read and summarized. | ||
+ | |||
+ | ===Part 2: Prepare cell lysates=== | ||
You will prepare cell-bead samples in three different ways: one will allow you to count your cells, and is suitable for RNA preparation, while the other two will involve more stringent bead/matrix dissolution for better protein or proteoglycan recovery. Split up the work with your partner whatever way is most convenient. '''Remember to label your samples carefully at every step.''' | You will prepare cell-bead samples in three different ways: one will allow you to count your cells, and is suitable for RNA preparation, while the other two will involve more stringent bead/matrix dissolution for better protein or proteoglycan recovery. Split up the work with your partner whatever way is most convenient. '''Remember to label your samples carefully at every step.''' | ||
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#Before proceeding, briefly observe the cell-bead constructs under the microscope and note any changes from Day 3. | #Before proceeding, briefly observe the cell-bead constructs under the microscope and note any changes from Day 3. | ||
#*Let the teaching faculty know if you have difficulty focusing within a bead. | #*Let the teaching faculty know if you have difficulty focusing within a bead. | ||
− | #Remove the culture medium from each of your samples. Be careful not to suck up the beads; it will help to use a serological pipet just as you did when washing your freshly synthesized beads. A | + | #Remove the culture medium from each of your samples. Be careful not to suck up the beads; it will help to use a serological pipet just as you did when washing your freshly synthesized beads. Tipping the plate will help the beads settle in a cluster and allow you to remove medium elsewhere. |
+ | #*A 5 mL pipet size should work well for rigid beads, while for more delicate beads, you should use a 2 mL serological pipet or even a P1000. If your beads are falling apart, you can transfer the beads according to steps 3-5 below without trying to remove medium first. | ||
#*If you are concerned about your bead amount, talk to the teaching faculty. You might skip the proteoglycan assay and focus on the other two instead. | #*If you are concerned about your bead amount, talk to the teaching faculty. You might skip the proteoglycan assay and focus on the other two instead. | ||
#About 1/3 of your beads will be used to measure protein content: move these to an eppendorf tube. The goal is about 10-15 (2-3 mm) beads per tube. | #About 1/3 of your beads will be used to measure protein content: move these to an eppendorf tube. The goal is about 10-15 (2-3 mm) beads per tube. | ||
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#Rinse the transferred bead-cell constructs with 4 mL of warm PBS, then aspirate the buffer. | #Rinse the transferred bead-cell constructs with 4 mL of warm PBS, then aspirate the buffer. | ||
#*If your beads are very fragile, you might want to skip the PBS rinse, and directly proceed to step 2. | #*If your beads are very fragile, you might want to skip the PBS rinse, and directly proceed to step 2. | ||
− | #Add 3 mL of EDTA-citrate buffer, and incubate at 37 °C for 10 min. | + | #Add 3 mL of pre-warmed EDTA-citrate buffer, and incubate at 37 °C for 10 min. |
− | #*Meanwhile, prepare the beads for the protein and proteoglycan assays as described below. | + | #*Meanwhile, prepare the beads for the protein and proteoglycan assays as described below. All the materials that you need are in eppendorf tubes in the fridge. |
#Now recover your cells: | #Now recover your cells: | ||
#*Add 3 mL of warm complete culture medium, pipet up and down to break up the beads (you may find this easier with a 1 mL pipetman rather than a serological pipet), and transfer to a 15 mL conical tube. | #*Add 3 mL of warm complete culture medium, pipet up and down to break up the beads (you may find this easier with a 1 mL pipetman rather than a serological pipet), and transfer to a 15 mL conical tube. | ||
#*Spin the cells down at 1900g for 6 min (using the centrifuge that is in the TC room). | #*Spin the cells down at 1900g for 6 min (using the centrifuge that is in the TC room). | ||
#Resuspend in ~ 1-1.5 mL of culture medium, and ''write down'' what you use. Mix thoroughly by pipetting, then set aside a 90 μL aliquot of your cells for counting, and put the rest of the cells into another eppendorf tube. | #Resuspend in ~ 1-1.5 mL of culture medium, and ''write down'' what you use. Mix thoroughly by pipetting, then set aside a 90 μL aliquot of your cells for counting, and put the rest of the cells into another eppendorf tube. | ||
− | #*If you have very few cells based on your Day 3 observations and/or having very few beads, you might consider skipping the cell count, and instead keeping all of the cells for RNA isolation. If you have too few cells to get a reliable cell count, you are not losing valuable information for your report in any case. And if you have so few cells that taking some of them for a count compromises your other data, that would not be preferable to missing the cell count. | + | #*If you have very few cells based on your Day 3 observations and/or having very few beads, you might consider skipping the cell count, and instead keeping all of the cells for RNA isolation. If you have too few cells to get a reliable cell count, you are not losing valuable information for your report in any case. And if you have so few cells that taking some of them for a count compromises your other data, then that outcome would not be preferable to missing the cell count. |
− | #While one of you begins the spin in the main lab (see Part 2), the other should count your cell aliquot as on Day 2, at a 9:1 ratio with Trypan blue. Separately calculate the approximate numbers of live and of dead cells. | + | #While one of you begins the spin in the main lab (see Part 2), the other should count your cell aliquot as on Day 2, at a 9:1 ratio with Trypan blue. '''Separately''' calculate the approximate numbers of live (yellowish) and of dead (blue) cells. |
− | #*Recall that you must multiply by 10,000 (and your dilution factor) to convert a cell count to a cells/mL concentration. | + | #*Recall that you must multiply by 10,000 (and your dilution factor) to convert a hemacytometer cell count to a cells/mL concentration. |
====Samples for Protein Extraction==== | ====Samples for Protein Extraction==== | ||
− | #Per eppendorf tube (typically 10-15 beads), add 133 μL of EDTA-citrate buffer, and pipet up and down for 20-30 seconds to dissolve the beads. The resulting solution may be viscous. | + | #Per eppendorf tube (typically 10-15 beads), add 133 μL of cold EDTA-citrate buffer, and pipet up and down for 20-30 seconds to dissolve the beads. Be thorough while limiting bubbles as best you can. The resulting solution may be viscous. |
#Pipet 33 μL of 0.25 M acetic acid into each eppendorf tube. | #Pipet 33 μL of 0.25 M acetic acid into each eppendorf tube. | ||
− | #Finally, pipet 33 μL of 1 mg/mL pepsin in 50 mM acetic acid into each tube and mix well. | + | #Finally, pipet 33 μL of 1 mg/mL pepsin (in 50 mM acetic acid) into each tube and mix well. |
− | #Move your eppendorf tubes into the rack in the 4 °C fridge. Tomorrow | + | #Move your eppendorf tubes into the rack in the 4 °C fridge. Tomorrow the teaching faculty will move them to an elastase solution (also at 4 °C) to break down the polymeric collagen to more readily measured monomeric collagen. |
====Samples for Proteoglycan Extraction==== | ====Samples for Proteoglycan Extraction==== | ||
+ | #Soak your beads for a few minutes in pre-warmed PBS, and then remove as much of the PBS as possible. Shoot to have '''no''' pink tint to the beads, as it is known to interfere with the proteoglycan assay. | ||
#Add 250 μL of papain solution to your beads. The papain is in an EDTA-citrate buffer base. | #Add 250 μL of papain solution to your beads. The papain is in an EDTA-citrate buffer base. | ||
#When the first partner goes to the main lab, s/he should take this tube to the 60 °C heat block. After 24 hours, the samples will be moved to the fridge. | #When the first partner goes to the main lab, s/he should take this tube to the 60 °C heat block. After 24 hours, the samples will be moved to the fridge. | ||
− | + | ===Part 3: RNA isolation and measurement=== | |
− | + | Because you are preparing RNA, you will have to take special precautions during this part. RNA is strikingly different from DNA in its stability. Consequently it is more difficult to work with RNA in the lab. It is not the techniques themselves that are difficult; indeed, many of the manipulations are nearly identical to those used for DNA. However, RNA is rapidly and easily degraded by RNases that exist everywhere. There are several rules for working with RNA. They will improve your chances of success. Please follow them all. | |
+ | *Use warm water on a paper towel to wash lab equipment, such as microfuges, before you begin your experiment. Then wipe them down with RNase-away solution. | ||
+ | *Wear gloves when you are touching anything that will touch your RNA. | ||
+ | *Change your gloves often. | ||
+ | *Before you begin your experiment, clean and prepare your work area: (1) remove all clutter, (2) wipe down the benchtop with warm water and RNase-away, and (3) lay down a fresh piece of benchpaper and/or mark off the area with tape. This last step serves as a reminder to always wear your gloves when touching items in that area. | ||
+ | *Use RNA-dedicated solutions and if possible RNA-dedicated pipetmen. | ||
+ | *Get a new box of pipet tips from the RNA materials area and label their lid RNase FREE if the lid is not yet labeled. | ||
#Pellet the cells for RNA isolation back in the main lab (8 min at 500 g). | #Pellet the cells for RNA isolation back in the main lab (8 min at 500 g). | ||
− | + | #Remove the supernatant from your cell pellets using pipet tips from an RNase free tip box. | |
− | #Remove the supernatant from your cell pellets using pipet tips from an RNase free tip box. | + | #*Discard this and other supernatants in a conical waste tube. As you may remember from Module 1, the lysis reagent you will use shortly is not compatible with bleach. |
− | #Now, in the fume hood, add 350 μL RLT with β-mercaptoethanol to each cell sample | + | #Now, in the fume hood, add 350 μL RLT with β-mercaptoethanol to each cell sample |