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Christian MayerWe also saw a shift in TF activity.Footprinting showed increased NFI binding, especially NFIB, in late-born cohorts. These neurons activate maturation modules faster — possibly guided by chromatin remodeling during neurogenesis. <a href="https://fediscience.org/tags/NewsMayerlab" class="mention hashtag" rel="nofollow noopener" target="_blank">#NewsMayerlab</a> <a href="https://fediscience.org/tags/TFfootprints" class="mention hashtag" rel="nofollow noopener" target="_blank">#TFfootprints</a> <a href="https://fediscience.org/tags/TranscriptionFactors" class="mention hashtag" rel="nofollow noopener" target="_blank">#TranscriptionFactors</a> <a href="https://fediscience.org/tags/scATACseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scATACseq</a> (5/7)

Christian MayerThis 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. <a href="https://fediscience.org/tags/NewsMayerlab" class="mention hashtag" rel="nofollow noopener" target="_blank">#NewsMayerlab</a> <a href="https://fediscience.org/tags/Chromatin" class="mention hashtag" rel="nofollow noopener" target="_blank">#Chromatin</a> <a href="https://fediscience.org/tags/Epigenetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Epigenetics</a> <a href="https://fediscience.org/tags/scATACseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scATACseq</a>(4/7)

Gabriele Pollara<a href="https://qoto.org/@cyrilpedia" class="u-url mention">@cyrilpedia</a> sadly this is an absolute classic when new technologies emerge, then it turns out they're not as good as each other, and then someone tries to benchmark & rank them! <a href="https://med-mastodon.com/tags/scatacseq" class="mention hashtag" rel="tag">#scatacseq</a>

Arjan Boltjes"NB cells signal to the BM microenvironment, rewiring via macrophage migration inhibitory factor and <a href="https://mastodon.social/tags/midkine" class="mention hashtag" rel="nofollow noopener" target="_blank">#midkine</a> signaling specifically <a href="https://mastodon.social/tags/monocytes" class="mention hashtag" rel="nofollow noopener" target="_blank">#monocytes</a> ..."<a href="https://mastodon.social/tags/Neuroblastoma" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuroblastoma</a> paper by Fetahu et al., the latest publication from the Taschner-Mandl lab in Vienna.Going through this right now - very alike our own work - and talking to a few team members on Wednesday while they visit our center.<a href="https://mastodon.social/tags/macrophages" class="mention hashtag" rel="nofollow noopener" target="_blank">#macrophages</a> <a href="https://mastodon.social/tags/scATACseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scATACseq</a> <a href="https://mastodon.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://mastodon.social/tags/OpenAccess" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenAccess</a> <a href="https://mastodon.social/tags/cancer" class="mention hashtag" rel="nofollow noopener" target="_blank">#cancer</a> <a href="https://mastodon.social/tags/immunology" class="mention hashtag" rel="nofollow noopener" target="_blank">#immunology</a> Data available on EGA, behind a DAC.

Brendan InnesAnyone know a good review paper / learning resource for building gene regulatory networks <a href="https://genomic.social/tags/GRN" class="mention hashtag" rel="nofollow noopener" target="_blank">#GRN</a> from <a href="https://genomic.social/tags/scATACseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scATACseq</a> <a href="https://genomic.social/tags/ATACseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#ATACseq</a> and/or <a href="https://genomic.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> data? Thanks!

Haojia WuA new multiomics study from Satija Rahul's lab identified a unique population of CD8+ T cells after COVID-19 vaccination. These cells are the SARS-CoV-2 antigen specific and capable of rapid clonal expansion. The relative frequency and differentiation of these cells can predict clinical outcomes for COVID-19 patients. <a href="https://mastodon.haojia-wu.com/tags/covid" class="mention hashtag" rel="nofollow noopener" target="_blank">#covid</a> <a href="https://mastodon.haojia-wu.com/tags/multiomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#multiomics</a> <a href="https://mastodon.haojia-wu.com/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://mastodon.haojia-wu.com/tags/scATACseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scATACseq</a> <a href="https://mastodon.haojia-wu.com/tags/CITEseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#CITEseq</a> <a href="https://mastodon.haojia-wu.com/tags/ASAPseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#ASAPseq</a> <a href="https://mastodon.haojia-wu.com/tags/TCR" class="mention hashtag" rel="nofollow noopener" target="_blank">#TCR</a> <a href="https://www.biorxiv.org/content/10.1101/2023.01.24.525203v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2023.01.24.525203v1</a>

Haojia WuscFates: a python package for pseudotime analysis from single cell data <a href="https://mastodon.haojia-wu.com/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://mastodon.haojia-wu.com/tags/scATACseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scATACseq</a> <a href="https://mastodon.haojia-wu.com/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://mastodon.haojia-wu.com/tags/python" class="mention hashtag" rel="nofollow noopener" target="_blank">#python</a> <a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac746/6832042" rel="nofollow noopener" target="_blank">https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac746/6832042</a>

Haojia WuSComatic: a new <a href="https://mastodon.jiaworkspace.com/tags/singlecell" class="mention hashtag" rel="nofollow noopener" target="_blank">#singlecell</a> tool to detect somatic mutation from <a href="https://mastodon.jiaworkspace.com/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://mastodon.jiaworkspace.com/tags/scATACseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scATACseq</a> data. <a href="https://mastodon.jiaworkspace.com/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://mastodon.jiaworkspace.com/tags/python" class="mention hashtag" rel="nofollow noopener" target="_blank">#python</a> <a href="https://qoto.org/@biorxivpreprint" class="u-url mention" rel="nofollow noopener" target="_blank">@biorxivpreprint</a> <a href="https://www.biorxiv.org/content/10.1101/2022.11.22.517567v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2022.11.22.517567v1</a>

Haojia WuSingle cell best practices from Theis lab, a free online book that guides you through every detail of the single cell analysis. <a href="https://mastodon.jiaworkspace.com/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://mastodon.jiaworkspace.com/tags/scATACseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scATACseq</a> <a href="https://www.sc-best-practices.org/preamble.html" rel="nofollow noopener" target="_blank">https://www.sc-best-practices.org/preamble.html</a>

Haojia WuscFates: a python package for pseudotime analysis from single cell data <a href="https://mastodon.jiaworkspace.com/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scRNAseq</a> <a href="https://mastodon.jiaworkspace.com/tags/scATACseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#scATACseq</a> <a href="https://mastodon.jiaworkspace.com/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://mastodon.jiaworkspace.com/tags/python" class="mention hashtag" rel="nofollow noopener" target="_blank">#python</a> <a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac746/6832042" rel="nofollow noopener" target="_blank">https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac746/6832042</a>

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