Shreffler:Resources

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(Protocols)
(Protocols)
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==Protocols==
==Protocols==
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* [[Shreffler:Arah2_tetramers|Arah2 Tetramer Preparation]]
* [[Shreffler:Aseptic_Technique|Aseptic Technique]]
* [[Shreffler:Aseptic_Technique|Aseptic Technique]]
* [[Shreffler:Bacterial_Cell_Culture|Bacterial Cell Culture]]
* [[Shreffler:Bacterial_Cell_Culture|Bacterial Cell Culture]]
* [[Shreffler:Basophil_Activation|Basophil Activation by Flow]]
* [[Shreffler:Basophil_Activation|Basophil Activation by Flow]]
** [[Shreffler:BioCSI_Basophil_Activation|BioCSI]]
** [[Shreffler:BioCSI_Basophil_Activation|BioCSI]]
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** [[Shreffler:Buhlmann_BAT_assay_kit|Buhlmann/ALPCO]]
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** [[Shreffler:Buhlmann_BAT_assay_kit|Buhlmann Assay Kit]]
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** [[Shreffler: Buhlmann_PNOIT|Buhlmann protocol for PNOIT]]
** [[Shreffler:Cisplatin_Allergen|Cisplatin]]
** [[Shreffler:Cisplatin_Allergen|Cisplatin]]
** [[Shreffler:JAX_Basophil_Activation|JAX]]
** [[Shreffler:JAX_Basophil_Activation|JAX]]
** [[Shreffler:PM_Basophil_Activation|JHU PMCx]]
** [[Shreffler:PM_Basophil_Activation|JHU PMCx]]
 +
** [[Shreffler:SCIT_Basophil_Activation|JHU Mouse SCIT]]
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* [[Shreffler: Basophil_Endocytosis|Basophil Endocytosis Pilot]]
* [[Shreffler:Basophil_Sensitization| Basophil Sensitization]]
* [[Shreffler:Basophil_Sensitization| Basophil Sensitization]]
 +
* [[Shreffler:BCell_Staining | B Cell Staining]]
* [[Shreffler:CFSE Labeling | CFSE Labeling]]
* [[Shreffler:CFSE Labeling | CFSE Labeling]]
* [[Cell Counting]]
* [[Cell Counting]]
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* [[Shreffler:Cryopreservation | Cryopreserving PBMCs]]
* [[Shreffler:Cryopreservation | Cryopreserving PBMCs]]
* [[Shreffler:DC Isolation from skin | Dermal DC isolation]]
* [[Shreffler:DC Isolation from skin | Dermal DC isolation]]
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* [[Shreffler:DNA_Cleanup | DNA Cleanup]]
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* [[Shreffler:DNA Isolation for JAX | DNA Isolation for JAX]]
* [[Shreffler:Eosinophil Isolation | Eosinophil Isolation from Buffy Coat]]
* [[Shreffler:Eosinophil Isolation | Eosinophil Isolation from Buffy Coat]]
 +
* [[Shreffler:Culturing_Het1A | Culture of Het-1A cells (Human Esophageal Epithelium)]]
* EthidiumMonoazideBromide
* EthidiumMonoazideBromide
* [[Shreffler: Fluorochrome_Beads | Fluorochrome-Coated Beads, Preparation]]
* [[Shreffler: Fluorochrome_Beads | Fluorochrome-Coated Beads, Preparation]]
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* [[Shreffler: Hoescht_Counterstaining | Hoerscht Counterstaining]]
+
* [[Shreffler: Hoerscht_Counterstaining | Hoescht Counterstaining]]
* FoxP3Intracellular
* FoxP3Intracellular
* [[Shreffler:Intra_Cellular_Staining|Intra-Cellular Staining]]
* [[Shreffler:Intra_Cellular_Staining|Intra-Cellular Staining]]
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* [[Shreffler:Milk_Program|Milk Program Project]]
* [[Shreffler:Milk_Program|Milk Program Project]]
* MonocyteDerivedDendriticCells
* MonocyteDerivedDendriticCells
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* [[Shreffler:Monocyte_Phagoflow | Monocyte Phagocytosis]]
* MurineBmdcAssay
* MurineBmdcAssay
* [[Shreffler:Oxidative_Burst | Oxidative Burst]]
* [[Shreffler:Oxidative_Burst | Oxidative Burst]]
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* [[Shreffler:Pervanadate | Pervanadate preparation]]
* [[Shreffler:Pervanadate | Pervanadate preparation]]
* ProteinLabeling
* ProteinLabeling
 +
* [[Shreffler:RBC Lysis Buffer for Eos | RBC Lysis Buffer for Eos]]
* [[Shreffler:RTPCR | RT-PCR for JAX Project]]
* [[Shreffler:RTPCR | RT-PCR for JAX Project]]
 +
* [[Shreffler: SDS-PAGE | SDS-PAGE]]
* [[Shreffler:Standard_Buffers_Solutions_Media|Standard_Buffers_Solutions_Media]]
* [[Shreffler:Standard_Buffers_Solutions_Media|Standard_Buffers_Solutions_Media]]
* [[Shreffler:SurfaceStaining | Surfacemarker staining for Flow Cytometry]]
* [[Shreffler:SurfaceStaining | Surfacemarker staining for Flow Cytometry]]

Revision as of 12:38, 2 April 2012

Image:Shrefflab.png

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Contents

Protocols

Reading List

Error fetching PMID 19635859:
Error fetching PMID 19635864:
Error fetching PMID 19506051:
Error fetching PMID 19564353:
Error fetching PMID 19528258:
Error fetching PMID 19487420:
Error fetching PMID 19578369:
Error fetching PMID 19561615:
  1. Error fetching PMID 19635859: [Steinfelder]
  2. Error fetching PMID 19635864: [Everts]
    two significant papers on SEA as Th2 adjuvants

  3. Error fetching PMID 19506051: [Susuki]
    interesting for methods related to baso confocal project

  4. Error fetching PMID 19564353: [Geiger]
    another methodology paper perhaps for frequency of allergen-specific T cells

  5. Error fetching PMID 19528258: [Campbell]
    madhan's project

  6. Error fetching PMID 19487420: [la_Sala]
    mechanisms of CT

  7. Error fetching PMID 19578369: [Duhen]
    characterization of a distinct Th subset producing IL-22; relevance to PN adjuvant?, second independent paper also published back-to-back

  8. Error fetching PMID 19561615: [Okamoto]
    new transcriptional regulator for Th2 described, could be useful for Th2 phenotyping

All Medline abstracts: PubMed HubMed

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

Error fetching PMID 18394137:
Error fetching PMID 20066506:
Error fetching PMID 17446345:
Error fetching PMID 19877563:
Error fetching PMID 19800675:
Error fetching PMID 20109746:
Error fetching PMID 20466415:
Error fetching PMID 15080813:
Error fetching PMID 15100687:
Error fetching PMID 18234310:
  1. Error fetching PMID 18394137: [Antonicelli]
  2. Error fetching PMID 20066506: [Bauermeister]
  3. Error fetching PMID 17446345: [Flinterman]
  4. Error fetching PMID 19877563: [Giavina-Bianchi]
  5. Error fetching PMID 19800675: [Hamilton]
  6. Error fetching PMID 20109746: [Mittermann]
  7. Error fetching PMID 20466415: [Nicolaou]
  8. Error fetching PMID 15080813: [Pittner]
  9. Error fetching PMID 15100687: [Quercia]
  10. Error fetching PMID 18234310: [Shreffler]
All Medline abstracts: PubMed HubMed
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