Jakob Zimmermann

9 Questions 22 Answers 0 Followers

Questions related from Jakob Zimmermann

How can I normalise the network size for export in cytoscape?

I have encoded log2FC by size in STRING networks built with cytoscape (3.7.2). When exporting them, the log2FC key is not comparable across different networks as cytoscape exports either the...

10 April 2020 5,162 0 View

Does anyone have a working protocol for the genotyping PCR of Ahr-deficient mice?

We're looking for a working PCR protocol to genotype Ahr-deficient mice (Schmidt et al., PNAS, 1996). We're facing a few issues with our current protocol and would be grateful for a protocol that...

23 July 2019 6,059 0 View

Does anyone have a working protocol for the genotyping PCR of Il17a-Cre mice?

We're looking for a working PCR protocol to genotype Il17a-Cre mice (Hirota, Nat Immunol, 2011). We're facing a few issues with the protocol recommended on the Jackson website and would be...

14 July 2019 8,387 1 View

DSS concentration in colonic lumen?

Does anyone know a reference for the concentration of dextran sulfate sodium that is reached in the colonic lumen when given to mice in the drinking water as a 1/2/3 % solution?

09 April 2019 2,567 0 View

Is there any analysis of genetic risk for IBD stratified according to microbiota composition?

Is there any study out there where the genetic risk for IBD has been addressed in the context of a certain microbiota composition, say enterotype, or according to presence/absence of indicator...

10 November 2017 1,243 3 View

Can I selectively remove host cells from mouse blood while retaining intact bacteria?

To enumerate the total amount of bacteria per blood volume, I would like to selectively remove host cells from mouse blood while retaining bacteria. Size filtration is unlikely to work as filters...

23 October 2017 6,553 3 View

Preservation of bacterial transcriptome upon cooling?

Is there any study around on how well bacterial transcriptomes are preserved when they are taken out of the "in vivo" situation and kept on ice for varying amounts of time? In other words, how...

13 September 2017 2,678 2 View

RNA integrity of formaldehyde-fixed bacteria?

Has anybody tried isolating RNA from formaldehyde-fixed bacteria, ideally not paraffin-embedded but just in solution? Is the integrity preserved, i.e. clear peaks for the ribosomal RNAs,...

06 September 2016 1,996 2 View

Can anybody recommend an antibody and protocol to stain murine TLR2 in immunofluorescence histology?

We are struggling with the staining of murine TLR2 in PFA-fixed mouse cryosections. There are antibodies that work well for flow but up to now they didn't stain anything at all in PFA-fixed...

27 May 2014 6,588 1 View