Shreffler:Resources

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Revision as of 14:26, 21 March 2012

Protocols

• Arah2 Tetramer Preparation
• Aseptic Technique
• Bacterial Cell Culture
• Basophil Activation by Flow
  • BioCSI
  • Buhlmann Assay Kit
  • Buhlmann protocol for PNOIT
  • Cisplatin
  • JAX
  • JHU PMCx
  • JHU Mouse SCIT
• Basophil Endocytosis Pilot
• Basophil Sensitization
• CFSE Labeling
• Cell Counting
• Confocal Protocols
• Cryopreserving PBMCs
• Dermal DC isolation
• DNA Isolation for JAX
• Eosinophil Isolation from Buffy Coat
• Culture of Het-1A cells (Human Esophageal Epithelium)
• EthidiumMonoazideBromide
• Fluorochrome-Coated Beads, Preparation
• Hoescht Counterstaining
• FoxP3Intracellular
• Intra-Cellular Staining
• Isolation of PBMCs
• Jurkat Transfection for RA signaling project
• Milk Program Project
• MonocyteDerivedDendriticCells
• Monocyte Phagocytosis
• MurineBmdcAssay
• Oxidative Burst
• Periodate Treatment of PN extract
• Pervanadate preparation
• ProteinLabeling
• RBC Lysis Buffer for Eos
• RT-PCR for JAX Project
• Standard_Buffers_Solutions_Media
• Surfacemarker staining for Flow Cytometry
• TcellSkewing_mDC
• TailVeinInjection
• tSyk measurement in basophils
• T cell allergen stimulation
  • JAX
• attachment:DIG-OVA.doc

Reading List

1. Steinfelder S, Andersen JF, Cannons JL, Feng CG, Joshi M, Dwyer D, Caspar P, Schwartzberg PL, Sher A, and Jankovic D. . pmid:19635859. PubMed HubMed [Steinfelder]
2. Everts B, Perona-Wright G, Smits HH, Hokke CH, van der Ham AJ, Fitzsimmons CM, Doenhoff MJ, van der Bosch J, Mohrs K, Haas H, Mohrs M, Yazdanbakhsh M, and Schramm G. . pmid:19635864. PubMed HubMed [Everts]

   two significant papers on SEA as Th2 adjuvants

3. Suzuki K, Grigorova I, Phan TG, Kelly LM, and Cyster JG. . pmid:19506051. PubMed HubMed [Susuki]

   interesting for methods related to baso confocal project

4. Geiger R, Duhen T, Lanzavecchia A, and Sallusto F. . pmid:19564353. PubMed HubMed [Geiger]

   another methodology paper perhaps for frequency of allergen-specific T cells

5. Campbell JD, Buckland KF, McMillan SJ, Kearley J, Oldfield WL, Stern LJ, Grönlund H, van Hage M, Reynolds CJ, Boyton RJ, Cobbold SP, Kay AB, Altmann DM, Lloyd CM, and Larché M. . pmid:19528258. PubMed HubMed [Campbell]

   madhan's project

6. la Sala A, He J, Laricchia-Robbio L, Gorini S, Iwasaki A, Braun M, Yap GS, Sher A, Ozato K, and Kelsall B. . pmid:19487420. PubMed HubMed [la_Sala]

   mechanisms of CT

7. Duhen T, Geiger R, Jarrossay D, Lanzavecchia A, and Sallusto F. . pmid:19578369. PubMed HubMed [Duhen]

   characterization of a distinct Th subset producing IL-22; relevance to PN adjuvant?, second independent paper also published back-to-back

8. Okamoto M, Van Stry M, Chung L, Koyanagi M, Sun X, Suzuki Y, Ohara O, Kitamura H, Hijikata A, Kubo M, and Bix M. . pmid:19561615. PubMed HubMed [Okamoto]

   new transcriptional regulator for Th2 described, could be useful for Th2 phenotyping

Scripts

R analysis

• Image:Array flinterman.R
  • script used for Flinterman paper -- one of the first 'BATCH' functions for analysis of multiple data files
• Image:Jax pcr.R
  • for analysis of pbmc pcr data in the JAX project -- good use of %in% and grep as well as loops to mash data together from two sources
• Image:Milk mash script.R
  • script used by Wayne and Lara to do interim analysis of milk basophil data
• Image:AAAAI rCode.R
  • Lara's analysis script for her abstract using data file, 20080818_BaselineBasoDataWithClinicalGroups.csv. Example of 2-way ANOVA.
• Image:Duke extract script.R
  • Wayne's analysis of duke peanut mucosal IT data that extracts text files from FlowJo analysis data directory tree and also mashes up baso data with clinical data file and produces time series data with multiple plots using layout for peanut, controls, egg by treatment or placebo

Shell

• Shell script for reformatting data files from Array scanner to be more easily analyzed in R; removes empty spaces, quotation markes, etc. Also eliminates white space from file names. Requires directory containing data files as input.

Media:rmquote.txt

Perl

• Perl script for reformating BiBTeX files exported from Papers so that they have double braces around the Title field in order to preserve capitalization.

  Usage Syntax: format_bib_file.pl file_in.bib file_out.bib

  Saved with '.txt' instead of '.pl' extension so that it could be uploaded here. May want to add that back and make sure the file is executable on your system using 'chmod u+x', or simply copy text and save into file name of your choosing, but will have to make executable

Media:format-bib.txt

Courses

• R analysis 2009

9. Antonicelli L, Micucci C, Mistrello G, Roncarolo D, Zanotta S, Cinti B, Garritani MS, and Bonifazi F. . pmid:18394137. PubMed HubMed [Antonicelli]
10. Hamilton RG, MacGlashan DW Jr, and Saini SS. . pmid:20066506. PubMed HubMed [Bauermeister]
11. Giavina-Bianchi P, Oliveira E, and Kalil J. . pmid:17446345. PubMed HubMed [Flinterman]
12. Quercia O, Stefanini GF, Scardovi A, and Asero R. . pmid:19877563. PubMed HubMed [Giavina-Bianchi]
13. Bauermeister K, Ballmer-Weber BK, Bublin M, Fritsche P, Hanschmann KM, Hoffmann-Sommergruber K, Lidholm J, Oberhuber C, Randow S, Holzhauser T, and Vieths S. . pmid:19800675. PubMed HubMed [Hamilton]
14. Nicolaou N, Poorafshar M, Murray C, Simpson A, Winell H, Kerry G, Härlin A, Woodcock A, Ahlstedt S, and Custovic A. . pmid:20109746. PubMed HubMed [Mittermann]
15. Mittermann I, Zidarn M, Silar M, Markovic-Housley Z, Aberer W, Korosec P, Kosnik M, and Valenta R. . pmid:20466415. PubMed HubMed [Nicolaou]
16. Pittner G, Vrtala S, Thomas WR, Weghofer M, Kundi M, Horak F, Kraft D, and Valenta R. . pmid:15080813. PubMed HubMed [Pittner]
17. Shreffler WG, Beyer K, Chu TH, Burks AW, and Sampson HA. . pmid:15100687. PubMed HubMed [Quercia]
18. Flinterman AE, Knol EF, Lencer DA, Bardina L, den Hartog Jager CF, Lin J, Pasmans SG, Bruijnzeel-Koomen CA, Sampson HA, van Hoffen E, and Shreffler WG. . pmid:18234310. PubMed HubMed [Shreffler]