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Single Cell Media retweeted
I very much regret that "Requiem for A Spike" was deleted from the title of this paper when it was published.
(I just googled "requiem for a spike" - no dice to this!)
nature.com/articles/nature09…
Single Cell Media retweeted
Mitochondrial respiration atlas reveals differential changes in mitochondrial function across sex and age
biorxiv.org/content/10.1101/…
Single Cell Media retweeted

iMeta@iMetaScience2 Apr 2024
🇯🇵!
JapanConnected via China App StoreLocation may be affected by a proxy or VPN.Account-level information, not a live location or per-post device.
Updated #fastp: an ultrafast one‐pass #FASTQ data #preprocessing, quality control, and deduplication tool
onlinelibrary.wiley.com/doi/…
#Bioinformatics #datamining #sequencing #NGS #QC
@wileymicrobio @wileyinresearch
Single Cell Media retweeted
We just published a short paper on @iMetaScience to introduce SeqKit's new functionality, performance optimizations, and improved user-friendliness, since the initial publication 7 years ago. onlinelibrary.wiley.com/doi/…
Single Cell Media retweeted
1/ We are extremely excited to share our new manuscript published @Cancer_Cell! Kudos to co-first authors @AvishaySpitzer, @GritschSimon and @M_Nomura for seminal work, to co-PIs @MarioSuva, Dan P. Cahill and @KeithLigon5 and to all contributors.
Online Now: Mutant IDH inhibitors induce lineage differentiation in IDH-mutant oligodendroglioma dlvr.it/T57X2F
Single Cell Media retweeted
Are you looking for #EEG datasets focused on linguistic processing, especially with raw EEG data and #eye-tracking? Excited to share our recent preprint: A Chinese Linguistic Corpora EEG Dataset for Semantic Alignment and Neural Decoding. biorxiv.org/content/10.1101/…
Single Cell Media retweeted
Large-scale whole-exome sequencing of neuropsychiatric diseases and traits in 350,770 adults
nature.com/articles/s41562-0…
Single Cell Media retweeted
Let’s discuss the Informational Theory of Aging proposed by @davidasinclair and colleagues?
doi.org/10.1038/s43587-023-0…
On a phenotype level it looks very believable. Indeed progressive erosion of epigenetic landscape seems to play a central role in aging.
However, my issue is with mechanistical explanation authors propose. They believe that maintaining the right epigenetic pattern depends on ability of chromatin modifying proteins (CMPs) to return every time to a right “default” or “home” genome loci after their work is done. If this “home” return mechanism is disrupted CMPs start putting epigenetic marks into wrong places.
Authors suggest that double strand DNA breaks (DSBs) and subsequent reparation compromise CMPs ability to recognize their “home” loci. Hence, DSBs are actually the primary cause of aging.
DNA damage is not my expertise, but as far as I know, DSBs are rare events and what is more important are know to be caused only by ionizing radiation, oxidative damage and specific modifications of DNA, caused by ROS. If it’s true and there is no other robust sources of DSBs, then mechanistical explanation proposed by authors looks insufficient. We know that different classes of antioxidants were tested and gave no conclusive evidence that reduction of ROS production could prolong lifespan.
There could be several explanations for this discrepancy.
1. There are other robust sources of DSBs besides oxidative stress and IR. I would highly appreciate comments on this from people with deep knowledge in this field.
2. Antioxidants that were tested are not efficient in precluding nuclear DNA damage. DNA damage is not my expertise, so again will highly appreciate if you know studies proving or disproving this. However, theoretically it could be the case because majority of ROS are extremely short lived (with H2O2 being one of rare exceptions). Thus ROS production could elicit microdomain activity and without antioxidants targeted to these microdomains we fail to interfere with it. I’m not sure if there are ROS generating enzymes in nucleus, but maybe we need antioxidants targeted specifically to the nucleus?
3. Other mechanisms besides DSBs mediate erosion of epigenetic landscape. This explanation seems most feasible for me. Here could several possibilities:
i) could it be that CMPs are not very accurate? If yes then erosion of epigenetic landscape with age would be just the consequence of chronological age.
ii) Non-enzymatic acetylation and methylation.
iii) could single nucleotide mutations disrupt ability of CMPs to recognize their DNA binding sites?
iv) CMPs activity as well as affinity with their DNA and protein consequences are regulated by posttranslational modifications. Hence one can suggest that that misslocalization of CMPs could be result of “inappropriate” signaling cascade. Once wrongly located epigenetic marks further misbalance intracellular signaling networks affecting CMPs even more. Hence a positive feedback loop created.
4. Antioxidants effectively prevent DSBs formation, but erosion of epigenetic landscape is just one of the hallmarks of aging.
What’re your thoughts?
Single Cell Media retweeted
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments | Nature Methods
nature.com/articles/s41592-0…
Single Cell Media retweeted
Check out our lab’s recent work on visual learning and representations at the #cosyne24 #cosyne2024 workshops:
Add these workshop sessions to your agenda to see recent work from the Pachitariu-Stringer lab at #cosyne24:
whova.com/portal/webapp/cosy…
whova.com/portal/webapp/cosy…
whova.com/portal/webapp/cosy…
Work by @NunezKant , @Lin_Zhong_ion , @FarahDu6 and @computingnature.
Single Cell Media retweeted
LAST CALL: Closing date: 1st March 2024. Would your Research Team like to win a #singlecell #Multiomics Project worth up to £10,000? #clinicalresearch #NGS #personalisedmedicine #precisionmedicine #genomics #sequencing @WesternHSCTrust @hiranihealth
Single Cell Media retweeted
That's a wrap for #singlecellgenomicsday 2023! Thanks to our amazing speakers, and to all of you for tuning in!
Its a privilege to celebrate the state of the field for the 7th year in a row, and we look forward to seeing you next year!
(And thanks @ATJCagan for illustrating!)
Single Cell Media retweeted
Interested in single cell genomics but need help getting started? Check out the full agenda for our Single Cell Genomics Day next Friday (4/7). All talks will be live-streamed (no registration required) at satijalab.org/scgd23
Single Cell Media retweeted
This week in @Nature we present our #SingleCell dissection of #ApoE4, the strongest genetic variant for #Alzheimers.
ApoE4 impairs #cholesterol #transport, leading to #oligodendrocyte ER accumulation, decreased #myelination.
Restoring transport restores mouse cognition.
#Hope #AD
Single Cell Media retweeted
#scRNAseq of diseased #heart muscle cells is helping us understand the genetic causes of hypertrophic cardiomyopathy. Read here: hubs.ly/Q01t0nnF0
Single Cell Media retweeted
Learn about the innovative DRAGEN pipelines for scRNA-Seq and scATAC-Seq for discovery research studies. Download our poster from Single Cell Genomics 2022 Conference (#SCG2022).
#singlecell #ATACseq #DRAGEN bit.ly/3EdHPRD
Single Cell Media retweeted
This Knowledge Exchange guided users through the process of demultiplexing & conducting preliminary analyses of Oxford Nanopore single-cell transcriptomics data, using the wf-single-cell open-source bioinformatic pipeline. Watch now: bit.ly/3S1OGl1
Single Cell Media retweeted
Single-Cell RNA sequencing explores petite cell fate in rat during organ transplantation
Single Cell Media retweeted
LR TEQ Super Saiyan Goku ft. Bird is worse than me, they can't even regenerate from a single cell.
Single Cell Media retweeted
If you missed the amazing talk by @SadeWill93 on the single cell resolution IVD immune responses following degeneration in the rat, fear not! She has a great poster (#38) on the single-cell resolution acute inflammatory and regenerative responses in a mouse model! #ORSPSRS2022


































