#scATACseq
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alejofraticelli.bsky.social
4-year expired scATACseq kit…. Worked like a charm.
May 21, 2026 at 8:17 AM
lcolladotor.bsky.social
I'd like to thank 🙏🏽 @cynthiasc.bsky.social for her 3 years at @lieberinstitute.bsky.social working in my team analyzing data generated by @kr-maynard.bsky.social et al.

Cynthia led our first foray into the world of multi-omics data (snRNA-seq + snATAC-seq)

#multiome #snRNAseq #scATACseq
December 17, 2025 at 11:24 PM
bartdeplancke.bsky.social
Superb work by Wouter @Zouters & @OlgaPushkarev developing ChromatinHD, two scale-adaptive #machinelearning models & interpretation tools that use #scRNAseq + #scATACseq data to better understand how chromatin accessibility relates to gene expression doi.org/10.1038/s414...

Happy 2025 everyone 🎆 !
ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning - Nature Communications
Functional chromatin changes occur at different scales. Here, the authors introduce ChromatinHD, a method that characterises differential and predictive chromatin accessibility changes in a scale-adap...
doi.org
January 6, 2025 at 2:05 PM
haoyin.bsky.social
Single-cell omics🐭#OvarianAging
scRNAseq scATACseq
12- vs 3-mo

#Aging
1⃣Mesenchymal Phox2B/ESRRγ/HoxB7-TGFβ2➡️ #Fibrosis (steroidogenic stroma, fibroblast, theca, but NOT pericyte)
2⃣Granulosa cell HSPA5 #ATF3 ATF4➡️#ERStress

Any #VascularAging?

#GeroScience 2025
link.springer.com/article/10.1...
March 11, 2025 at 1:09 AM
haoyin.bsky.social
Want to visualize & create a website for your omics data (incld CITEseq, scATACseq, #SpatialTranscriptomics)?

Try ShinyCell2!😆

Compatible with data formats Seurat Signac ArchR Scanpy

vs cellxgene WebAtlas Vitessce

github.com/the-ouyang-l...

bioRxiv 2024
www.biorxiv.org/content/10.1...
May 5, 2025 at 6:50 PM
haoyin.bsky.social
#SpatialOmics #MultiOMics

MaxFuse

Integration of spatial & single-cell data across modalities with weakly linked features

Fuzzy Smoothing
Iterative cycles of coembedding, graph-smoothing & matching

tri-omic scRNAseq scATACseq CODEX integration

#NatBiotech 2023
www.nature.com/articles/s41...
April 27, 2025 at 12:08 AM
haoyin.bsky.social
Human brain #Organoid
scRNAseq + scATACseq + single-cell transcription factor perturbation (CROP-seq, lentiviral gRNA library for 20 TFs, 3 gRNAs/TF, 1 gRNA/cell in >22k cells) in

GLI3-HES1 antagonism for dorsoventral patterning in human telencephalon

#Nature 2023
www.nature.com/articles/s41...
September 6, 2025 at 7:28 PM
minashaigan.bsky.social
Great conversations and inspiring vibes at @events.embl.org — felt amazing to share my work and hear from incredible speakers!
#EESAgeing #SingleCell #Aging #ATACseq #RNAseq #Immunology #Multiomics #scRNAseq #scATACseq
June 11, 2025 at 3:45 PM
chadweldy.bsky.social
But how does this relate to human disease?? Through an awesome collaboration with the @anshulkundaje.bsky.social lab, we trained ChromBPNet models with scATACseq datasets for each cell type and vascular site, and predict human variant effect on a cell type/site basis @soumyakundu.bsky.social
September 10, 2025 at 3:54 PM
robp.bsky.social
Alevin-fry 0.11.0 was just released (last night). This speed up permit-list generation by making it multithreaded, but much more importantly, adds the `atac` command allowing barcode correction and counting & BED generation directly in the main branch of alevin-fry. 1/3 #scRNAseq #scATACseq
December 7, 2024 at 2:46 PM
elena-dvoretskova.bsky.social
How is the progression of maturation regulated in forebrain inhibitory neurons? Excited to share our new study from the Mayer lab — stable differentiation, dynamic maturation, and stage-specific chromatin changes in GABAergic neurons.

#GABA #Neuroscience #scATACseq #scRNAseq
July 9, 2025 at 6:20 AM
cynthiasc.bsky.social
🚀 Sharing insights on ArchR, a powerful tool for single-cell chromatin accessibility analysis! 🎯 ArchR excels in large datasets and integrates scATACseq with scRNAseq for cutting-edge multi-modal studies.
🎥 Dive deeper with the video: youtu.be/XNZx5Dlp6jY?...

#Bioinformatics #10xGenomics #LIBD
[2024-12-11] ArchR journal club
YouTube video by Leonardo Collado Torres
youtu.be
December 12, 2024 at 3:01 PM
jsantoyo.bsky.social
MuMu: a sample multiplexing protocol for droplet-based simultaneous single nuclei RNA- and ATAC-seq systems. #SingleNuclei #MultiplexingProtocol #10X #scRNAseq #scATACseq @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
source: https://www.biorxiv.org/content/10.1101/2024.11.27.625728v1
December 1, 2024 at 7:41 PM
tommytang.bsky.social
I used that to plot single-cell ATACseq tracks github.com/crazyhottom..., more examples rpubs.com/crazyhottom...
GitHub - crazyhottommy/scATACutils: R/Bioconductor package for working with 10x scATACseq data
R/Bioconductor package for working with 10x scATACseq data - crazyhottommy/scATACutils
github.com
March 2, 2026 at 2:45 PM
tommytang.bsky.social
chatomics! PCA analysis on scATACseq data. In this blog post, I will show you how the first PC is correlated with sequencing depth divingintogeneticsandgenomics.com/post/pca-sc...
February 9, 2025 at 3:15 PM
haoyin.bsky.social
De novo detection of Somatic Mutations in scRNAseq & scATACseq data

SComatic

github.com/cortes-ciria...

Tracing human Clonal Heterogeneity (& even Lineage!?🤓)

#NatureBiotech 2024
www.nature.com/articles/s41...
August 3, 2026 at 1:06 PM
svanuytven.eurosky.social
If this piques your interest, the (unedited, early-access) manuscript is up now:
www.nature.com/articles/s41...
#EMT #CancerResearch #SingleCell #scRNAseq #scATACseq #Metastasis (20/20)
Single cell multiomics unravel the transcription networks controlling the different EMT tumor states - Nature Communications
Epithelial-to-mesenchymal transition (EMT) involves cancer cells shifting between different states linked to tumor progression. Here, the authors use single-cell multiomics and CRISPR/Cas9-mediated lo...
www.nature.com
July 13, 2026 at 9:01 AM
cynthiasc.bsky.social
Hi ! I am new here and I like to present my interests with this video from our Journal Club! This is an overview of the multiome analysis for scATACseq and scRNAseq using several
#CellRanger pipelines. This is inspired by our work at #LIBD and resources from 10x Genomics. youtu.be/fHVLi9-sftM?...
[2024-10-11] An overview of the CellRanger-ARC Pipeline Analysis
YouTube video by Leonardo Collado Torres
youtu.be
November 8, 2024 at 8:29 PM
haoyin.bsky.social
#Atherosclerosis #FoamCell heterogeneity 2/2

Meta-analysis 37 scRNAseq libraries + 44 scATACseq datasets->
5 Foam cell states

ICAM1+ inflammatory
FOLR2+ phagocytic
MMP9+ matrix-remodeling
ANGPTL4+ hypoxic
COL1A2+ fibroblastic

#Biomol_MDPI 2024
www.mdpi.com/2218-273X/14...
September 7, 2025 at 12:57 PM
jsantoyo.bsky.social
OmnibusX: A unified platform for accessible multi-omics analysis. #MultiOmics #DataAnalysis #RNAseq #scRNAseq #scATACseq #SpatialTranscriptomics #BMCcomputationalBiology
journals.plos.org/ploscompbiol...
September 11, 2025 at 8:31 AM
minashaigan.bsky.social
🔬 Your immune system doesn’t just weaken with age—it evolves. We mapped how.
📊 We used single-cell multi-omics (RNA + ATAC) + bulk ATAC on PBMCs to build a cell-by-cell map of aging.
👉 Poster 83, EMBO | EMBL Symposium
#SingleCell #Aging #EMBL #Multiomics #scRNAseq #scATACseq
June 10, 2025 at 10:39 AM
haoyin.bsky.social
Spatially-resolved MultiOmics of🐭fetal #Cardiomyocyte
snRNAseq scATACseq 10X Visium
13 CM subsets
NFYa marks CM4-like subsets

CM NFYa KO🐭->
Embryonic death
#CardiacNoncompaction/Hypertrabeculation
⏬Proliferation
⏬Mitochondrial respiration

#DevCell 2023
www.sciencedirect.com/science/arti...
December 2, 2023 at 8:08 PM
chr-mayer.bsky.social
This shift was mirrored in chromatin accessibility.

scATAC-seq revealed stage-specific enhancer activation, with late-born cells opening distinct regulatory elements — especially in distal regions. A dynamic change in the regulatory landscape.
#Chromatin #Epigenetics #scATACseq
(4/n)
July 8, 2025 at 12:04 PM
haoyin.bsky.social
Multiomic Atlas of Human Tonsil
scRNAseq
scATACseq
CITEseq

#SpatialTranscriptomics #Visium

Marginal Reticular Cells, not fibroblastic reticular cells, are high in PDGFRβ, #FibrillarCollagen, Proteoglycan core proteins & DIO2

#Immunity 2024
www.cell.com/immunity/ful...
February 1, 2024 at 12:53 PM
tommytang.bsky.social
This normalizes the data and extracts regulatory variation for downstream clustering and visualization.

Read my blog post on how to implement LSI from scratch within R. divingintogeneticsandgenomics.com/post/pca-sc...
PCA analysis on scATACseq data | Chatomics
To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. In my last post, I showed you how to use PCA for bulk RNAseq data. Today, let’s see how we can use it for scATACseq data. Download the example dataset from 10x genomics https://support.10xgenomics.com/single-cell-atac/datasets/1.1.0/atac_pbmc_5k_v1 The dataset is 5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v1.0). Download the atac_pbmc_5k_v1_filtered_peak_bc_matrix.tar.gz file and unzip it.
divingintogeneticsandgenomics.com
February 5, 2025 at 2:15 PM