Yo #bioinformatics peeps, besides the #cmap dataset, are there are any other good examples of Sample metadata organization?

I'm thinking specifically of ways to capture different experimental variables which can then be used for differential gene expression, but not only, in #Transcriptomics. E.g. fields such as multiple treatments and concentrations, genotypes, siRNA Target, time point, etc.

I have a pretty good idea but I fear that I might be reinventing the wheel.

#datamanagement

Now Siddharth Dey, UCSB
https://deylab.com/

Photo-sensitive barcodes combined with topologically imposed light gradients enable spatially-resolved #SingleCell #transcriptomics and #epigenomics

a new technology: scSTAMP-seq which enables use of light patterning to achieve dynamic spatial resolution

adaptation of STAMP-seq

also applying to DNA methylation
https://www.biorxiv.org/content/10.1101/2023.05.06.539708v1

#CSSingleCells23

Rong Fan at Yale
https://www.fan-lab.org/

Spatial Multi-Omics Sequencing at Cellular Level via Deterministic Barcoding in Tissue

first slide called "2006--the ice age of single-cell biology," referring to review article by Johanna Joyce

Recent great technical advance: spatial CITE-seq
https://www.nature.com/articles/s41587-023-01676-0

and spatial ATAC-seq

#Transcriptomics
#Epigenetics
#CSSingleCells23

"predicts new biology missed by today's genomics"
#spatial #transcriptomics #genomics
#scrnaseq
#CSSingleCells23

works by unified detection of sample-specific sequence variation... sample can be different cells, sequence is raw reads

method chooses an "anchor" sequence then looks for neighboring sequence that varies. thus is independent of any reference genome

https://www.biorxiv.org/content/10.1101/2022.06.24.497555v4
https://www.biorxiv.org/content/10.1101/2023.03.17.533189v2

New insights into universally expressed human genes
https://www.biorxiv.org/content/10.1101/2022.12.06.519414v1

2/3

Rosalind Xu is up!
From Moffitt lab at Harvard Med and Children's Hospital
https://moffittlab.github.io/people.html

"A single-cell spatial atlas of the mouse gut reveals spatial- and microbiota-dependent sensation"

Using MERFISH which was developed for brain, so she had to develop protocol that works in gut

#SingleCell
#CSSingleCells23
#microbiota
#intestinal
#Transcriptomics

I'm excited to be at my first conference since I joined @PLOS last year:

The Conceptual Power of Single-Cell Biology

Fun fact: my friend and colleague Quincey Justman and I conceived of this conference when we were both at Cell Press, sometime in 2018.

I'll be tooting as often as I can, at #CSSingleCells23. Hope to attract some others to toot instead of using the MAGA plutocrat's toy.

#SingleCell
#genomics
#Transcriptomics
#CellAtlas
#CSSingleCells23

https://www.cell-symposia.com/conceptual-single-cells-2023/

The ABACBS national seminar series is returning Aug 31st. Featuring Clara Jiang using RNASeq to study potential anti-depressive mechanisms of statins & @Psy_Fer_ on nanopore analysis with SLOW5

Register -> https://sahmri.zoom.us/meeting/register/tZ0vd--uqT8vE933U3H9fXcr2Uw8LI5jqJwr#/registration

More info -> https://mailchi.mp/a59746e8a1fc/abacbs-newsletter-august-2023?e=865ac655bf

#bioinformatics #genomics #transcriptomics #RNA

Image-seq - cool tech for #spatial #transcriptomics though looks like it needs a fancy laser micro-dissection microscope. Need to read more about it...#Science #immunology
https://www.nature.com/articles/s41577-023-00912-7?utm_source=nri_etoc&utm_medium=email&utm_campaign=toc_41577_23_8&utm_content=20230727

Monday, July 24, between 18:00 CEST and 19:00 CEST

#TransMed Track #ibd #transcriptomics
@SusanneIbing
A-190: Intestinal Tissue Transcriptomics Over Time in Inflammatory Bowel Disease

Single-cell #transcriptomics of dynamic cell behaviour in rodent airways. https://elifesciences.org/articles/76645?utm_source=mastodon&utm_medium=social&utm_campaign=organic

We welcome attendees, particularly with a view to developing collaborations relating to #sequencing, #genomics, #transcriptomics, #spatial omics and #scRNAseq. At the Pirbright Institute, we generate a lot of #biological and omic data and wish to work more effectively to deliver data-driven insights into tackling livestock #disease.

Improving anxiety research in rodents for a better understanding of human chronic ('trait') #anxiety.

Nándor Lipták covers a #preprint from the #MikicsLab combining behavioural tests with corticosterone measurements, #transcriptomics & #bioinformatics.

#preLight 👉 https://prelights.biologists.com/highlights/improving-anxiety-research-novel-approach-to-reveal-trait-anxiety-through-summary-measures-of-multiple-states/

SAVE THE DATE: We are happy to announce that the Workshop on Genomics 2024 will take place on the 7-20th of January.

Save it in your calendars, and share it with those interested! More info to come soon!

https://evomics.org/2024-workshop-on-genomics/

#genomics #workshop #bioinformatics #transcriptomics #phylogenomics #popgen #savethedate #unix #r

Today is the LAST DAY to apply for our joint CBW-IMPACTT Microbiome Analysis Workshop at the early-bird rate! July 5-7, 2023 at the University of Calgary. Apply here: https://bioinformatics.ca/workshops-all/2023-cbw-impactt-microbiome-analysis/

#bioinformatics #workshop #16S #18S #sequencing #shotgunsequencing #metagenomics #genomics #transcriptomics #metatranscriptomics #longread #markergene #functionalannotation #tutorial #statistics #biostatistics #microbiome #microbiota #microbialecology #diversity #betadiversity #differentialabundance

RT @AhmedMoustafa
NCBI just released the count matrices for thousands of RNA-Seq 🧬 experiments on GEO 🎉 an amazing resource 🤩 #RNASeq #Transcriptomics #Bioinformatics #OpenScience #OpenData https://ncbiinsights.ncbi.nlm.nih.gov/2023/04/19/human-rna-seq-geo/

New method tracks #gene #expression in single #cells over space and time.

#mRNA #TEMPOmap #transcriptomics

https://phys.org/news/2023-04-method-tracks-gene-cells-space.html

RT @juanmobovi@twitter.com

Very excited that our paper is now published in Microbial Biotechnology (@MicrobialBiote1
)! Finding the time point of BGC transcription and #NaturalProduct production in a #myxobacteria by linking #genomics, #transcriptomics, and #metabolomics

🐦 🔗 https://twitter.com/juanmobovi/status/1641776788312293376

#ExperimentalEvolution of the halophilic #alga #Dunaliella reveals evolution of reduced #plasticity in less predictable environments across 3 biological levels – #epigenomics, #transcriptomics & cell morphology. Christelle Leung, @Lmchev &co #PLOSBiology https://plos.io/3FTyejq

#ExperimentalEvolution of the halophilic #alga #Dunaliella reveals evolution of reduced #plasticity in less predictable environments across 3 biological levels – #epigenomics, #transcriptomics & cell morphology. Christelle Leung, @Lmchev &co #PLOSBiology https://plos.io/3FTyejq

#ExperimentalEvolution of the halophilic #alga #Dunaliella reveals evolution of reduced #plasticity in less predictable environments across 3 biological levels – #epigenomics, #transcriptomics & cell morphology. Christelle Leung, @Lmchev &co #PLOSBiology https://plos.io/3FTyejq