tvalerius + biology   121

Cell Size and Scale - Biology
Zoomable graphic to show the size relationships between visible items and cells, molecules, down to atoms.
biology  science  education 
april 2015 by tvalerius
CDC - Biosafety in Microbiological and Biomedical Laboratories (BMBL) 5th Edition
THE manual for biosafety in the lab in the US. NIH training will require referencing this manual.
bwh  biology  biosafety 
september 2013 by tvalerius
Protocols Used in the EUCOMM and KOMP-CSD ES Cell Production Pipelines
As the title says, all the protocols used to expand KOMP/EUCOMM ES cells for microinjection as well as protocols/recommendations for injecting them into blastocysts.
es-cells  komp  protocol  microinjection  biology 
september 2013 by tvalerius
Nature ENCODE : Nature Publishing Group : A landmark in the understanding of the human genome
This is the gateway site created for the ENCODE project. Many ways in to the data generated and the place to get started.
biology  bioinformatics  research  ENCODE 
august 2013 by tvalerius
MGI-Genealogy Chart of Inbred Strains
Published in 2000 showing the lineage relationships of laboratory mouse strains.
mouse  reference  lineage  biology  mouse-workshop 
august 2013 by tvalerius
Frozen section technique III
Many tips on thickness, curling etc. Start here for common problems and use the surrounding pages form this site.

Many good pictures illustrating problem sections.
histology  biology  protocol 
august 2013 by tvalerius
The Art of Embedding Tissue for Frozen Section: Pathology Leaders
Describes technique for small thin stripes of tissue. (Called "super flat" in some articles.)
histology  biology  protocol 
august 2013 by tvalerius
JCB -- Instructions for Authors
Within these instructions are very useful guidelines regarding image preparation (see Data Presentation).
biology  imaging  figure 
april 2013 by tvalerius
What's in a picture? The temptation of image manipulation
Clear and useful editorial about image manipulation in figures. Though this dates to 2004, everything discussed perfectly relevant in 2013.
biology  imaging  imageJ  confocal 
april 2013 by tvalerius
OBA - NIH Guidelines - rDNA policies
NIH Guidelines for recombinant DNA (rDNA) research. In these are how biosafety levels are determined for different kinds of research in humans and animals.
biology  nih  lab  reference 
december 2010 by tvalerius
NCI BAC recombineering Protocols
Protocols from NCI for the SW series of BAC recombineering reagents.
science  protocol  resources  biology  recombineering  bac 
september 2010 by tvalerius
Valerius Lab - Home
Webpage for my work- Kidney and liver development.
biology  kidney  devbio  science 
march 2010 by tvalerius
Mouse Development Staging Definitions
Theiler stages, embryonic day, and somite number. Links to schematics as well. Use this all the time.
biology  devbio  mouse  reference 
february 2010 by tvalerius
NCBI Taxonomy Homepage
Links to all Taxonomy IDs used in Genbank/NCBI.
biology  science  reference  database  ncbi  taxonomy 
december 2009 by tvalerius
Addgene - A Better Way To Share Plasmids
Plasmid repository and distribution company. The idea is to add published reagents to this repository to remove the burden of filling requests yourself. I have ordered a few plasmids from them and the system works well. They streamline the ever more burdensome MTA process and things go quickly.
plasmid  research  dna  biology  vector  database 
december 2009 by tvalerius
DBTSS HOME
Transcriptional Start Site database. Tools look interesting but need to test a few examples. Data based on work in NIH3T3 cells. A place to check when designing constructs.
biology  transgenics  transgenic  database  molecular  molecularbiology 
november 2009 by tvalerius
Protocols (Valerius - Lab Protocols)
BAC recombination and wholemount in situ protocols. (so far)
recombineering  protocol  biology 
august 2009 by tvalerius
Recombineering Website
Maps and sequence files for the recombineering plasmids. The annotated text files are laid out as proper Genbank files, but the idiotic VectorNTI app I use cannot see them correctly.
science  plasmid  resources  biology  recombineering 
may 2009 by tvalerius
Sanger Institute Gene Trap Resource
Vectors used in SIGTR gene traps. These vectors include splice-acceptor-LacZ (Bgeo) cassettes that express LacZ in the endogenous domain of the trapped gene. Vectors - pGT0lxf and pGT0lxr.
science  vector  biology  genetics  transgenic 
february 2009 by tvalerius
Gudmap Gene Expression Database
This database includes microarrays and in situ hybridizations of the urogenital system. Focused on the developing kidney. This is all mouse data.
science  biology  database  datamining  kidney 
january 2009 by tvalerius
Contents ‎(Resources‎)
Plasmid maps and protocols from Akio.
biology  protocol  plasmid 
january 2009 by tvalerius
Mouse BLAT Search
BLAT for comparing a DNA sequence to the mouse genome.
biology  genomics  science  resource 
april 2008 by tvalerius
KOMP DCC
The gene lists for targeting in mice.
genetics  knockout  mouse  nih  biology  science 
february 2008 by tvalerius
NIH Knock Out Mouse Project (KOMP)
Taking orders (suggestions) for what genes to target.
biology  genetics  mouse  nih 
february 2008 by tvalerius
Human Protein Atlas
Few thousand antibodies used for IHC in a screen of human tissue biopsies. Images of the results shown with high resolution viewers, expression scored and searchable.
biology  database  histology  protein  science  antibodies  resource 
november 2007 by tvalerius
Theiler Stages
List of the Theiler stage and the corresponding d.p.c. age. Links to images also.
science  biology  anatomy  devbio  reference 
november 2007 by tvalerius
S. Steven Potter, PhD, Cincinnati Children's Hospital Medical Center
S. Steven Potter, Ph.D. is a member of the faculty and staff of Childrens Hospital Medical Center, Cincinnati involved in Developmental Biology.
kidney  research  biology  science 
october 2007 by tvalerius
BACPAC Resources Center Home Page
Place to get BAC clones. These are sequence mapped onto Ensembl.
libraries  research  biology  clones  genomics 
october 2007 by tvalerius
PerlPrimer
Great program for designing real time pcr primer sets that span intron/exon boundries. This prevents amplifying contaminating DNA vs transcript in RTPCR reactions.
biology  science  pcr  tools  primerdesign 
september 2007 by tvalerius
Allen Brain Atlas
Gene expression atlas of the mouse brain.
science  biology  insitu  devbio 
august 2007 by tvalerius
THE KIDNEY DEVELOPMENT DATABASE
Jamie's site of know gene expression patterns.
science  biology  kidney  database 
august 2007 by tvalerius
WebCite
A solution to the dead link problem related to science. Good idea for publishing some gene lists that the journal may not host, or you want to share outside of a published paper.
academic  bibliography  blog  education  reference  citations  metadata  biology 
july 2007 by tvalerius
OME - Open Microscopy Environment
Attempt at a comprehensive image management solution for microscopy. I installed this on a OSX system as a local server and it functions just fine. Limitation is in direct imports from our confocal - no plugin yet so too much retyping. Needs to mature.
imaging  metadata  microscopy  database  biology 
july 2007 by tvalerius
CellProfiler cell image analysis software
Software to categorize cell phenotype resulting from high throughput (HT) chemical screens.
biology  cellculture  phenotype 
july 2007 by tvalerius
3D Slicer
Software that builds 3d models from section data.
3d  freeware  graphics  imaging  modeling  rendering  visualization  software  biology 
may 2007 by tvalerius
Slicer:Feedback - NAMIC
Wiki for Slicer software that builds 3d models from section data.
imaging  3d  modeling  rendering  visualization  software  biology 
may 2007 by tvalerius
Index of /ofc/Archive
FANTOM2 information for the DNAbook. Metadata for all the clones in the collection.
biology  clones  bioinformatics  database  genes  cdna 
may 2007 by tvalerius
Index of ftp://ftp.informatics.jax.org/pub/reports/
FTP site for flat files of MGI. See the index link for more description.
bioinformatics  database  biology 
may 2007 by tvalerius
Pharyngula: Patterning the nervous system with Bmp
Meyer's take on the media's interest on BMPs and neural patterning - why the fuss?
devbio  biology  bmp 
may 2007 by tvalerius
Mechanism to Organize Nervous System Conserved in Evolution
BMPs and dorso-ventral patterning of the CNS. News article referencig a PLOS-Biology paper.
biology  devbio  bmp  signaling 
may 2007 by tvalerius
Papars
Write up of the Delta-Notch signaling pathway.
biology  signaling  notchpathway 
may 2007 by tvalerius
MGI_3.53 - References Query Results (Details)
Another Notch signaling pathway member. Include with others for in situ studies.
checkgene  biology 
may 2007 by tvalerius
UCSC Genome Browser Home
Excellent online sequence info with ability to add custom tracks and export high quality results for presentations.
genomics  database  mouse  biology  sequence 
may 2007 by tvalerius
Soriano Lab - ROSA 26
All you need to know about the ROSA26 locus. Ideal for targeting etc.
mouse  genetics  strain  biology 
may 2007 by tvalerius
NIH Guide: MURINE ATLAS OF GENITOURINARY DEVELOPMENT
The original RFA for the GUDMAP consortium poroject.
gudmap  nih  grants  biology 
may 2007 by tvalerius
Procuring Genome-scale Nucleic Acid Collections
Discussion on the "completeness" of the available clone collections.
biology  science  genomics  genes  clones  resources 
may 2007 by tvalerius
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