Table of contents
No headersThe following resource lists includes Powerpoint slides, PDF files of important papers, lab manuals, Web links, and other resources.
Powerpoints:
Transposon Mutagenesis in Thiomicrospira (Forward Genetics_Random Mutagenesis Of Thiomicrospira Crunogena.pptx)
Reverse Genetics in Thiomicrospira (Reverse genetics.pptx)
Functional Complementation of Biochemical Pathways (Agro FC project.ppt)
Gene Ontology & CACAO Program (ASM-JGI-CACAO_2011.ppt)
Overview of Functional Genomics Using Agrobacterium (Agro Functional Genomics Overview Slides.ppt)
Overview of Transposon Mutagenesis in Agrobacterium (TransposonMutagenesis2010.ppt)
Protein Expression & Purification (HiramProteinExpressionTalk.ppt)
Transcriptional Analysis in Thiomicrospira (Transcription of csome genes by Tcru.pptx)
IMG-ACT Genome Annotation (What_is_Annotation_slides MGAN v3.ppt)
Example of Functional Genomics in a New Model Organism - Meiothermus ruber (Lori Scott Example of Functional Genomics Augustana College.ppt)
Organism Resources:
Thiomicrospira crunogena XCL-2 genome paper (Tcru genome.pdf)
Thiomicrospira crunogena carbonic anhydrases (Tcru carbonic anhydrases.pdf)
Agrobacterium tumefaciens C58 genome mapping paper (Goodneretal99.pdf)
Agrobacterium tumefaciens C58 genome papers (Goodner et al[1].pdf, woodetal.pdf)
Agrobacterium genomic diversity paper (J. Bact. Agro genomes.pdf)
Functional Genomics Protocols & Lab Manuals:
Construction of Tn5RL27 (Metcalf_plasposon.pdf)
Forward Genetics in Thiomicrospira (Random mutagenesis mutagenesis method.docx)
USF course notes on random mutagenesis (01.1_Random mutagenesis by mating.docx)
USF course notes on picking transconjugants from matings (01.2_Picking transconjugants from mating plates.docx)
USF course notes on screening transconjugants from matings (01.3_Screening transconjugant T. crunogena for carbon dioxide sensitivity.docx)
Forward Genetics in Agrobacterium (ForwardGeneticsAgro 2010 - Institute.doc)
Reverse Genetics in Thiomicrospira (Site-directed mutagenesis method.docx)
Overview of approach (Site directed mutagenesis overview.docx)
Paper on mating plasmid used in reverse genetics (mating plasmid for sdm.pdf)
USF course notes on chemotaxis (04_chemotaxis.docx)
USF course notes on PCR primer design (05_primer design.docx)
USF course notes on isolating genomic DNA (06_genomic DNA purification.docx)
USF course notes on PCR (07_PCR.docx)
USF course notes on making mutation in cloned gene (08_interrupting a gene with a transposon.docx)
USF course notes on transformation (09_transforming E coli.docx)
USF course notes on putting a mutated gene back into the host organism (10_mating a mutated gene into a target organism.docx)
USF course notes on verification of double crossovers (11_verifying a mutated genes presence.docx)
USF course notes on screening knockout mutants for phenotypes (12_screening phenotype.docx)
Reverse Genetics in Agrobacterium (AgroReverseGenetics2010 - Institute.doc)
Functional Complementation in Thiomicrospira (Chemotaxis assay method.docx)
Paper on E. coli MCP mutant strains (Parkinson mcp constructs.pdf)
Paper on expression plasmids (pNP1 & pRR48.pdf)
Paper on minimal swim plates (minimal swim plates.pdf)
Paper on H1 medium (H1 medium.pdf)
Functional Complementation in Agrobacterium (ArginineFunctionalComplementationProject - Institute.doc)
Transcriptional Analysis in Thiomicrospira (02.1_Transcription of citric acid cycle genes RNA prep and verification.docx)
AMBION Ribopure RNA kit (RiboPure Bacterial RNA Prep Manual.pdf)
Semiquantitative RT-PCR (02.2_Semiquantitative RT-PCR.docx)
QIAGEN RT-PCR kit (QIAGEN _OneStep_RT-PCR_Kit_Handbook-1.pdf)
Web Resources & Tools:
CACAO: http://gowiki.tamu.edu/wiki/index.php/Main_Page
CACAO manual (File_ASM-JGI_manual.pdf)
IMG-ACT: http://img-act.jgi-psf.org/user/login
IMG-ACT student genome annotation program description paper (IMG-ACT PLoS Biology Article 2010.pdf)
GENI: http://geni-science.org/
Phenotypic Landscape of E. coli: http://ecoliwiki.net/colipedia/index...henotype_Tools
GALAXY high-throughput genome analysis: http://main.g2.bx.psu.edu/
Other Resources:
Easier way to get ready for making double crossover gene knockouts (Easier Way for Double Recombination.ppt)
Large-scale mutant characterization in E. coli paper (PhenotypicLandscapeOfABacterium.pdf)
Impact of testing conditions on finding auxotrophs paper (AreEssentialGenesReallyEssential.pdf)
A sampling of Brad's favorite recipes
CherryPecanGoatCheeseSpread.doc
ChickenEnchiladas.doc
SausageBalls.doc
Potato Gnocchi & Brad's Mushroom Sauce.doc
- Tag page
- What links here
Files 55
| File | Size | Date | Attached by | |||
|---|---|---|---|---|---|---|
 | AgroReverseGenetics2010 - Institute.doc lab manual from Hiram College | 671 kB | 11:26, 20 Jul 2011 | goodnerbw | Actions | |
| ArginineFunctionalComplementationProject - Institute.doc lab manual from Hiram College | 758 kB | 11:26, 20 Jul 2011 | goodnerbw | Actions | |
| ForwardGeneticsAgro2010 - Institute.doc lab manual from Hiram College | 1133.5 kB | 11:26, 20 Jul 2011 | goodnerbw | Actions | |
| Goodner et al[1]..pdf C58 genome - Cereon/Hiram College/Univ. Richmond effort | 394.7 kB | 11:28, 20 Jul 2011 | goodnerbw | Actions | |
| woodetal.pdf C58 genome - Dupont/Univ. of Washington/TIGR effort | 461.27 kB | 11:28, 20 Jul 2011 | goodnerbw | Actions | |
| Goodneretal99.pdf C58 genome mapping by undergrads | 176.06 kB | 11:31, 20 Jul 2011 | goodnerbw | Actions | |
| IMG-ACT PLoS Biology Article 2010.pdf description of IMG-ACT student genome annotation program | 556.39 kB | 11:31, 20 Jul 2011 | goodnerbw | Actions | |
| Easier Way for Double Recombination.ppt method developed in Australia for gene knockouts | 166 kB | 11:59, 20 Jul 2011 | goodnerbw | Actions | |
| Tcru genome.pdf T cru genome paper | 1006.61 kB | 11:59, 20 Jul 2011 | goodnerbw | Actions | |
| Tcru Carbonic Anhydrases.pdf T cru carbonic anhydrase characterization | 468.82 kB | 11:59, 20 Jul 2011 | goodnerbw | Actions | |
| Agro FC Project.ppt functional complementation of biochemical pathways | 2.43 MB | 12:02, 20 Jul 2011 | goodnerbw | Actions | |
| File_ASM-JGI_manual.pdf CACAO User Manual | 161.45 kB | 14:55, 20 Jul 2011 | goodnerbw | Actions | |
| ASM-JGI-CACAO_2011.ppt CACAO slides | 4.6 MB | 14:55, 20 Jul 2011 | goodnerbw | Actions | |
| AreEssentialGenesReallyEssential.pdf Paper on how best to look for auxotrophs | 351.17 kB | 21:01, 20 Jul 2011 | goodnerbw | Actions | |
| PhenotypicLandscapeOfABacterium.pdf Paper on large-scale mutant characterization in E. coli | 2.87 MB | 21:27, 20 Jul 2011 | goodnerbw | Actions | |
| Agro Functional Genomics Overview Slides.ppt Overview of functional genomics efforts in Agrobacterium | 375.5 kB | 22:00, 20 Jul 2011 | goodnerbw | Actions | |
| TransposonMutagenesis2010.ppt Use of transposon mutagenesis in Agrobacterium | 935.5 kB | 22:00, 20 Jul 2011 | goodnerbw | Actions | |
| Forward genetics_Random mutagenesis of Thiomicrospira crunogena.pptx Slides on transposon mutagenesis in Tcru | 872.34 kB | 07:33, 21 Jul 2011 | goodnerbw | Actions | |
| metcalf_plasposon.pdf Paper describing Tn5RL27 | 169.95 kB | 07:33, 21 Jul 2011 | goodnerbw | Actions | |
| Random mutagenesis mutagenesis method.docx Methods for transposon mutagenesis in Tcru | 15.16 kB | 07:33, 21 Jul 2011 | goodnerbw | Actions | |
| 01.1_Random mutagenesis by mating.docx USF course notes on random mutagenesis | 187.49 kB | 07:40, 21 Jul 2011 | goodnerbw | Actions | |
| 01.2_Picking transconjugants from mating plates.docx USF course notes on picking transconjugants | 171.63 kB | 07:40, 21 Jul 2011 | goodnerbw | Actions | |
| 01.3_Screening transconjugant T. crunogena for carbon dioxide sensitivity.docx USF course notes on screening transconjugants | 146.76 kB | 07:40, 21 Jul 2011 | goodnerbw | Actions | |
| Reverse genetics.pptx Slides on reverse genetics in Tcru | 2.61 MB | 07:45, 21 Jul 2011 | goodnerbw | Actions | |
| Site directed mutagenesis overview.docx Overview of reverse genetics in Tcru | 141.7 kB | 07:45, 21 Jul 2011 | goodnerbw | Actions | |
| 04_Chemotaxis.docx USF course notes on chemotaxis | 194.09 kB | 07:46, 21 Jul 2011 | goodnerbw | Actions | |
| 05_PCR primer design.docx USF course notes on primer design | 292.51 kB | 07:50, 21 Jul 2011 | goodnerbw | Actions | |
| 06_Genomic DNA purification.docx USF course notes on genomic DNA isolation | 16.06 kB | 07:50, 21 Jul 2011 | goodnerbw | Actions | |
| 07_PCR.docx USF course note on PCR | 15.21 kB | 07:50, 21 Jul 2011 | goodnerbw | Actions | |
| 08_Interrupting a gene with a transposon.docx USF course notes on "site directed" transposon mutagenesis | 157.06 kB | 07:57, 21 Jul 2011 | goodnerbw | Actions | |
| 09_Transforming E coli.docx USF course notes on transformation | 18.48 kB | 07:57, 21 Jul 2011 | goodnerbw | Actions | |
| 10_Mating a mutated gene into a target organism.docx USF course notes on mating in mutated gene | 148.1 kB | 07:57, 21 Jul 2011 | goodnerbw | Actions | |
| 11_Verifying a mutated gene’s presence.docx USF course notes on verifying construction of mutant | 200.15 kB | 07:59, 21 Jul 2011 | goodnerbw | Actions | |
| 12_Screening phenotype.docx USF course notes on screening for mutant phenotype | 18.91 kB | 08:00, 21 Jul 2011 | goodnerbw | Actions | |
| Site-directed mutagenesis method.docx Overall methods for reverse genetics in Tcru | 17.03 kB | 08:00, 21 Jul 2011 | goodnerbw | Actions | |
| mating plasmid for sdm.pdf Paper on mating plasmid used in reverse genetics | 147.35 kB | 08:07, 21 Jul 2011 | goodnerbw | Actions | |
| Tcru chemotaxis genes into E coli.pptx Slides on functional complementation of chemotaxis | 3.09 MB | 08:07, 21 Jul 2011 | goodnerbw | Actions | |
| Chemotaxis assay method.docx Method for chemotaxis assay | 16 kB | 08:07, 21 Jul 2011 | goodnerbw | Actions | |
| Parkinson mcp constructs.pdf Paper on E. coli MCP mutant strains | 255.38 kB | 08:09, 21 Jul 2011 | goodnerbw | Actions | |
| pNP1 & pRR48.pdf Paper on expression plasmids | 16.91 kB | 08:09, 21 Jul 2011 | goodnerbw | Actions | |
| minimal swim plates.pdf Paper on swim plates | 53.32 kB | 08:09, 21 Jul 2011 | goodnerbw | Actions | |
| H1 medium.pdf Paper on H1 media | 6.82 kB | 08:11, 21 Jul 2011 | goodnerbw | Actions | |
| Transcription of csome genes by Tcru.pptx Slides on transcriptional analysis of Tcru genes | 1118.91 kB | 08:11, 21 Jul 2011 | goodnerbw | Actions | |
| 02.1_Transcription of citric acid cycle genes RNA prep and verification.docx Methods for transcriptional analysis of Tcru genes | 910.79 kB | 08:11, 21 Jul 2011 | goodnerbw | Actions | |
| 02.2_Semiquantitative RT-PCR.docx Method for semiquantitative RT-PCR | 236.57 kB | 08:13, 21 Jul 2011 | goodnerbw | Actions | |
| RiboPure Bacteria RNA prep manual.pdf Instruction manual for RNA isolation kit from Ambion | 498.61 kB | 08:13, 21 Jul 2011 | goodnerbw | Actions | |
| QIAGEN_OneStep_RT-PCR_Kit_Handbook-1.pdf Instruction manual for RT-PCR kit from QIAGEN | 142.49 kB | 08:13, 21 Jul 2011 | goodnerbw | Actions | |
| HiramProteinExpressionTalk.pptx Slides on protein expression & purification | 3.55 MB | 09:35, 21 Jul 2011 | goodnerbw | Actions | |
| What_is_Annotation_slides MGAN v3 with written script.ppt Overview of IMG-ACT and genome annotation | 2.23 MB | 16:12, 21 Jul 2011 | goodnerbw | Actions | |
| CherryPecanGoatCheeseSpread.doc Great party spread for crackers | 25 kB | 16:24, 21 Jul 2011 | goodnerbw | Actions | |
| ChickenEnchiladas.doc My take on chicken enchiladas | 28.5 kB | 16:24, 21 Jul 2011 | goodnerbw | Actions | |
| Potato Gnocchi & Brad's Mushroom Sauce.doc Homemade pasta easy to make | 31.5 kB | 16:24, 21 Jul 2011 | goodnerbw | Actions | |
| Sausage Balls.doc New Year's Day finger food or for any party | 28 kB | 16:24, 21 Jul 2011 | goodnerbw | Actions | |
| Pistachio Shortbread Trees (Wayne Reeve).doc Wayne munchy little party number | 31.5 kB | 20:07, 23 Jul 2011 | waynereeve | Actions | |
| Lori Scott Example of Functional Genomics Augustana College.pptx Work done by 2010 FG Institute participant Lori Scott & her students | 1316.27 kB | 19:33, 24 Jul 2011 | goodnerbw | Actions | |