This was the very first talk I gave in front of a classroom based heavily on my research own personal research. It was 2013, and my audience was a group of students at the Marine Biological Lab in Woods Hole, MA and a group of students who Skyped in from Uruguay. The goal of this talk is to help students better understand when candidate gene approaches are preferred of whole genome approaches and vice versa. You can watch this talk here: http://videocenter.mbl.edu/videos/video/630/in/channel/21/

1. TIME AND MONEY: TECHNIQUES FOR
NEURAL GENE EXPRESSION PROFILING
RAYNA M. HARRIS
HOFMANN LAB, THE UNIVERSITY OF TEXAS AT AUSTIN
HTTP://VIDEOCENTER.MBL.EDU/VIDEOS/CHANNEL/21/
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2. RNAlater
qRT-PCRRNA-seq
O.C.T PFA
immunohistochemistryin situ
hybridization
Common molecular approaches for
neural gene expression profiling
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3. Global gene expression profiling with RNA-seq
• RNA extraction (1-4 hrs)
• Library prep (2 days)
• Sequencing (3 days)
• Bioinformatics (a few days)
• Filter low quality reads
• Map to transcriptome
• Identify differentially expressed genes
• Interpret data (months to years)
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4. Quantitative Real Time PCR
• Primer validation (weeks)
• Store brains in RNALater or
homogenized in buffer
• RNA Extraction (1-4 hrs)
• cDNA synthesis (2 hrs)
– Oligo(dT) for mRNA only
– Random hexamers for all RNA
• qPCR (3 hours)
• Data analysis (~4 hours)
RNAlater
RNA isolation
cDNA synthesis
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qPCR
Data Analysis

5. LMDTissue punches
Increasing spatial resolution of
RNA-seq and qRT-PCR
RNAlater
qRT-PCRRNA-seq
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6. Tissue punches
• A. Freeze in O.C.T (5 min) and
section (30 min/brain)
• B. Slice fresh tissue (5 min)
• Punch regions of interest
(5min)
• Homogenize and freeze tissue
(5 min)
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7. Laser Microdissection
• Freeze tissue in O.C.T (5 min)
• Prepare membrane slides (20 min)
• Histology (5 min/brain)
• Laser microdissection
(~30min/brain)
• RNA extraction (1-4 hrs)
• Optional: RNA amplification
(1-2 days)
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8. Detecting RNA expression with
in situ hybridization
• Riboprobe Synthesis (weeks)
• Freeze brain in O.C.T. (5 min)
• Section brains (hr/brain)
• Hybridization & Detection (3 days)
• Alternatives
– Radioactive
– Fluorescent
• Visualize the signal
– Count silver grains
– Map distribution
Target RNA
Probe & RNA
Add HRP
Blue signal! 8

9. Detecting proteins with
Immunohistochemistry
• Fix and cryoprotect tissue (2 days)
• Section brains (~1hr/brain)
• Bind primary and secondary
antibodies (3 days)
• Visualize the signal
• Quantify cell counts
or map distribution
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10. From the bench to publication
qPCR LMD ISH IHC
$ spent $7,620 $4,161 $12,123 $6,695
# papers 2 1 5 5
$ per paper $3,810 $4,161 $2,425 $1,339
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11. A few questions that may help you choose most
appropriate technique
• What are your molecules of interest?
– mRNA or protein?
– How soon after the stimulus will its activity be altered?
• How big is your experiment?
– How many groups, animals, brain regions, genes/proteins?
• What resources do you have at your fingertips?
– Core facilities and equipment
– Validated PCR primers, riboprobes, antibodies?
– A mentor who can help you collect & analyze the data?
– Bioinformatic and statistical consulting?
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12. Candidate genes vs genomic approaches
• Histological approaches allow for co-localization
• Histological approaches are low throughput
• You may choose the wrong genes
• Candidate genes act in networks that are poorly understand
• Genomics allows systems level view of brain and behavior
• Genomic approaches lack of spatial resolution
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13. Recommended Readings
IHC & ISH Mapping: Munchrath &Hofmann (2010)
Distribution of Sex Steroid Hormone Receptors in the Brain of
an African Cichlid Fish, Astatotilapia burtoni
Double IHC: O’Connell LA, Matthews BJ, Hofmann HA (2012)
Isotocin regulates fatherhood in a monogamous cichlid fish.
qRT-PCR: Matz, Wright, Scott (2013) No Control Genes
Required: Bayesian Analysis of qRT-PCR Data
Sequencing: https://wikis.utexas.edu/display/GSAF/Pricing
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14. Acknowledgments
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