Phenol saturation (Instructions for preparing saturated phenol from solid phenol)

Respirometer Protocol (Instructions for set-up, operation, and data analysis)

Maui hybridization and wash system (Instructions for GeoChip hybridization using the Maui system)

Community DNA Preparation through hydridization

aRNA Amplification

3. RNA Direct Labeling Protocol using Alexa Dye 每 protocol includes clean up procedures and Microarray processing

4. dsDNA quantification with PicoGreen

5. Environmental sample cloning 每 Protocols for molecular analysis of bacterial functional gene, including PCR, Ligation, Transformation, and screening

6. Manual hybridization protocol

7. PourMatic plate pouring directions 每 Instructions for how to use the New Brunswick Plate pourer

8. DMSO Printing 每 This protocol describes the method for making microarray printing plates in a 96-well format in DMSO

9. FACE Sampling Protocol 每 Sampling design that allows for the collection of enough samples both for gene surveys and later use in microarray studies

10. FBR Sampling Protocol 每 Protocol describes procedures for collecting samples and snap freezing them in the field

11. FGA 每 DNA labeling and Hybridization 每 Protocol created June 2003 (removed)

12. ArrayStat 1.0 每 Direction on how to use the software ArrayStat 1.0 to analyze microarray data

13. Groundwater sampling protocol 1 每 Basic groundwater microbial sampling protocol

14. Groundwater sampling protocol 2 每 Slightly modified groundwater microbial sampling protocol

15. Hybridization 每 This protocol describes the hybridization of a Cy labeled cDNA probe onto coated slide spotted with PCR amplified cDNA 每 Created 2001 (removed)

16. Labeling 每 This protocol describes the labeling of eukaryotic RNA with aminoallyl labeled nucleotides via first strand cDNA synthesis followed by a coupling of the aminoallyl groups to either Cy3 or Cy5 fluorescent molecules 每 Created 2001

17.  Media 每 The chart contains recipes for media used in the lab, including DSMZ Medium 463, Denitrifying media, Nitrolotriacetic Acid Media with glucose, Ethylenedinitrilotetracetic acid, and TAE

18. Media Recipes 每 Includes recipes for LB, SOB, SOC, and LM media

19. Microarray Fabrication Protocol 每 This protocol describes the making of Shewenella oneidensis microarrays, including Primer Pair plate creation, PCR amplification of gDNA, dilution of PCR Amplicons, Re-Amplification, and Purification

20. Microarrayprotocl_cDNA (Telechemslides) 每 This protocol describes the microarray processing steps including post-processing slides, TRIzol RNA extraction, RNeasy, probe labeling, hybridization, washes, and scanning

21. MoBio Soil Extraction 每 MoBio＊s Soil extraction protocol modified by Jost Liebich (removed)

22. MoBio_HMW_112904 每 MoBio＊s Soil Extraction protocol modified for HMW DNA on 11/28/04 (removed)

23. MR-1 Minimal Medium 每 Recipe for Modified M1 Medium

24. MR-1 HBa Media 每 Recipe for MR-1 HBa Minimal Media

25. MSU PRL Protocols 每 All protocols used for DNA Microarray by Arabidopsis Functional Genomics Consortium and prepared by the AFGC Microarray Laboratory

26. NEW Clone Library Sequencing Protocol 每 Included TA Cloning and transformation, PCR template stocks and glycerol preservation, M13 PCR amplification, Cycle sequencing, purification, setting up the 3700 sequencer

27. PCR Protocol for pmoA 每 Recipe for PCR reaction and PCR Program

28. PCR_Purification 每 This protocol describes PR amplification of eukaryotic cDNA plasmid inserts, gel electrophoresis, purification, and storage of PCR products

29. pDS Mutagenesis method 每 Protocol for in-frame deletion mutagenesis

30. POPO Stain 每 protocol for staining with POPO

31. Preparation of Electro-competent cells 每 Protocol for making electrocompetent cells

32. Preparing a run for the sequencer 每 protocol for sequencing

33. Primer Dilutions for MSU ordered primers 每 Description of how to dilute primers from MSU

34. Protocol for cell harvesting on batch culture 每 Describes how to harvest cells on batch-grown cells from different TEA＊s

35. Protocol for cleaning hydra syringes 每 Describes how to clean and maintain syringes on Hydra Machine

36. Protocol for isolation of DNA from Soil and Gram-negative Bacteria 每 Dr. Zhou＊s published protocol for DNA extraction from soil and marine sediment (removed)

37. Protocol for Large Scale bacterial Genomic DNA Extraction 每 Dr. Zhou＊s protocol for DNA  isolation (removed)

38. Protocol for PET slides 05-17-04 每 Describes slide preparation, printing, immobilization, washing, pre-treatment, hybridization and post washing on PET slides (removed)

39. R. palustris Protocol 每 Includes formation of primer pair plates, 8x PCR amplification of all ORFs, visual inspection of amplicons, product QC and sizing, purification, quantification, transfer to 384 well plates, and deposition onto coated slides

40. Real time quantitative PCR 每 includes preparation of gene-specific primer sets, calibrating iCycler, preparation of samples for standard curves, total cellular RNA extraction and cDNA preparation, and Real Time PCR

41. Rhodopseudomonas Recipes 每 Includes PCR reaction buffer, Taq Polymerase buffer, DNA Ladder, Gel Loading buffer, nucleotide working stock, Magnesium Chloride for PCR, TAE Buffer, and 1.25% agarose gel

42. Taq Polymerase Protocol 每 This protocol describes how to purify Taq polymerase

43. Template Prep 每 Microarray cDNA clone growth and template miniprepping 每 Describes clone handling, plate replication, and DNA template preparation in 96-well format

44. Zhou Lab Protocol for Microarraying (Genomic DNA) 每 Protocols include Rehydration and Snap Drying, Crosslinking, blocking, denaturation, SYBR Green DNA staining, Genomic DNA labeling, Hybridization, and Washing

45. Zhou Lab Rarifaction Analysis 每 Zhou Lab accepted protocols for PCR Amplification of genes, gene cloning, and determining clone patterns

46. Array Hybridization 每 Describes the manual method for microarray hybridization (removed)

47. Array Hybridization TECAN 每 Describes how to hybridize microarrays using the TECAN station (removed)

48. Chromosome DNA isolation from bacteria 每 describes how to isolate genomic DNA from bacterial cells as done by Aifen Zhou

49. PCR Protocol FGA II 每 Describes how to set up PCR reactions and purify the products

50. Universal Hybridization System 每 TECAN 每 Corning GAPS document describing how to use TECAN with their slides

51. gDNA Labeling 每 Labeling genomic DNA for Microarrays by Zhili He