Shreffler:Resources

Protocols

 * Aseptic Technique
 * Bacterial Cell Culture
 * Basophil Activation by Flow
 * BioCSI
 * Buhlmann/ALPCO
 * Cisplatin
 * JAX
 * JHU PMCx
 * Basophil Sensitization
 * CFSE Labeling
 * Cell Counting
 * Confocal Protocols
 * Cryopreserving PBMCs
 * Dermal DC isolation
 * Eosinophil Isolation from Buffy Coat
 * 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
 * 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
// two significant papers on SEA as Th2 adjuvants // interesting for methods related to baso confocal project // another methodology paper perhaps for frequency of allergen-specific T cells // madhan's project // mechanisms of CT // characterization of a distinct Th subset producing IL-22; relevance to PN adjuvant?, second independent paper also published back-to-back // new transcriptional regulator for Th2 described, could be useful for Th2 phenotyping
 * 1) Steinfelder pmid=19635859
 * 2) Everts pmid=19635864
 * 1) Susuki pmid=19506051
 * 1) Geiger pmid=19564353
 * 1) Campbell pmid=19528258
 * 1) la_Sala pmid=19487420
 * 1) Duhen pmid=19578369
 * 1) Okamoto pmid=19561615

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
[[Media:rmquote.txt]]
 * 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.

Perl
[[Media:format-bib.txt]]
 * 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

Courses

 * R analysis 2009


 * 1) Antonicelli pmid=18394137
 * 2) Bauermeister pmid=20066506
 * 3) Flinterman pmid=17446345
 * 4) Giavina-Bianchi pmid=19877563
 * 5) Hamilton pmid=19800675
 * 6) Mittermann pmid=20109746
 * 7) Nicolaou pmid=20466415
 * 8) Pittner pmid=15080813
 * 9) Quercia pmid=15100687
 * 10) Shreffler pmid=18234310