๐Ÿ“ฃ๐Ÿ“ฃ๐Ÿ“ฃ Latest news from the NephroLab Cologne โ€“ more specifically, from our ๐Ÿฆ› Hippo- Team:
Our snRNA-Seq study on YAP and TAZ in kidney podocytes is now online open access in JASN! ๐Ÿฅณ ๐ŸŽ‰ ๐Ÿ™
Huge thanks to everyone on the team and the incredibly thorough reviewers at JASN!

Link: https://journals.lww.com/jasn/abstract/9900/transcriptional_regulators_yap_and_taz_have.598.aspx

#HippoSignaling #YAP #TAZ #Kidney #Kidneydisease #Science #snRNASeq #cellsignaling #FSGS #podocyte #Nephrology #Niere #Nephrolab #Nephrologie

@ukkoeln @UniKoeln @CECAD

I don't know if someone is doing #Bioinformatics and #scRNASeq / #snRNASeq stuff here with #R package #Seurat . Seems like with Seurat V5 coming, they are doing something like #Python 2 to 3 transition, where things you used for like a century began to falling apart here and there ๐Ÿคท๐Ÿปโ€โ™‚๏ธ

#Introduction time it is!

Hi everyone, just moved instances following really good advice (thanks @jonny ! ๐Ÿ˜‰).

I'm a postdoc at the Instituto de Neurociencias (Alicante, Spain) working on the neural circuits of itch sensation at the level of the spinal cord dorsal horns and how these circuits are affected during chronic diseases cursing with pruritus (a major unmet medical need, for those of you far from this field). I'm currently analizing a #snRNAseq dataset I generated in a mouse model of chronic itch which we published a couple years ago from my work at the Max Planck Institute for Neurobiology (Munich, Germany) together with my then supervisor Rรผdiger Klein. The aim is to identify the specific subpopulation of neurons responsible for the madly intense scratching phenotype.

Very interested also in behavioral analysis, we are trying to identify specific motor patterns in chronic itch mouse models using #deeplearning #SLEAP pose estimation and behavioral motif classification.

My background in neurodevelopmental biology, specifically axon guidance, also pushes me towards analyzing the developmental origin of spinal neurons populations in order to understand the emergence of these circuits during embryonic stages with the idea that knowing where we come from we might better try to fix broken things!

See you all around!!

@posnienlab
Nice and important work. Batch effects due to processing seems to get mostly ignored until now in #scRNAseq .

Nice to see that #snRNAseq seems to solve part of the problem.

Conclusion: For most applications, isolation of single nuclei followed by #snRNAseq is best choice if material is limited (e.g. early #development, tissue needs to be collected in the wild). Moreover, nuclei isolation protocol is much shorter and thus better reproducible. 7/8
Some cell types (e.g. second mitotic wave) were more efficiently identified in #snRNAseq data and generally, we observed different contributions of both datasets to different cell types when we integrated both datasets. 6/8
Direct comparison of #scRNAseq and #snRNAseq data showed highly reduced heat shock, ribosomal and mitochondrial gene expression in snRNAseq data (compare x- and y-axis in post 3/8). Marker gene expression was very comparable between both datasets. 5/8
A protocol based on the use of multiple RNase inhibitors was most efficient for fresh and snap frozen discs (protocol based on https://dx.doi.org/10.17504/protocols.io.veae3ae) and subsequent #snRNAseq revealed most relevant cell types. 4/8
Single Cell and Single Nuclei Analysis Human Heart Tissue

This protocol provides a walk through for complex processing of fresh human cardiac tissue followed by tissue dissociation for single cell RNA sequencing and nuclei isolation fo...

protocols.io

Hey #snRNAseq experts: We plan to transplant human cells in a mouse brain and sort+sequence the grafted nuclei 1mo after transplantation.

There are many protocols around, Which procedures can you recommend? Is there anything to watch out for? Please retweet โ˜บ๏ธ๐Ÿ™