Discover and read the best of Twitter Threads about #RNAseq

Most recents (4)

There's been talk about ACE2 and its association with age, sex, smoking etc. as a way to explain #covid19 disease severity. Driving this is intuition that since ACE2 is a receptor for SARS-CoV-2, ⬆️ACE2 => worse disease. My take on this w/@sinabooeshaghi biorxiv.org/content/10.110…
First, if you're going to examine previously published expression data you have to be very careful with ACE2. Expression levels are very low in some organs, e.g. in the lung. This means you have to really worry about how data was processed, normalized, scaled etc.
We looked at mouse single-cell RNA-seq data published by @IliasAngelidis, @lkmklsmn et al. (@fabian_theis and @SchillerLab). Using #scRNAseq from eight 3-month old and seven 24-month old mice we found significantly *less* expression in aged mice.
Read 12 tweets
I read the @biorxivpreprint every day. I've recently been asked by various people what/why/how I read so here is a short thread that may be helpful to others: 1/
@biorxivpreprint I read abstracts of articles on the @biorxivpreprint every morning and every evening, and typically a few times during the day as well. I am sometimes delving into the main paper, usually starting with the supplement. 2/
@biorxivpreprint I search for articles on @Google using keywords (and filtering for "past 24 hours"), my lab has @SlackHQ channels where people post articles, I check @rxivist, and I read and search twitter by keywords for topics I'm interested in every day. I follow @biorxivpreprint. 3/
Read 25 tweets
If you are interested in analyzing #SingleCell #RNAseq data in #Bioconductor using #rstats, please check out our paper Orchestrating single-cell analysis (OSCA) with @Bioconductor that was published in @naturemethods this week! #genomics #scRNAseq #dataviz #methodsmatter
@Bioconductor @naturemethods OSCA is a rich, reproducible, accessible (from beginners to experts!) resource with many #scRNAseq workflows & datasets. The resource is an online #bookdown book that compiles every night to track development by the open-source and open-development @Bioconductor #rstats community
@Bioconductor @naturemethods Now, OSCA is not the only set of packages / workflows for the analysis of #scRNAseq data. #Scanpy (scanpy.readthedocs.io/en/stable/) and #Seurat (satijalab.org/seurat/) and are two incredibly popular packages in #python and #rstats, respectively.
Read 9 tweets
🚨Tweetorial: NTRK 101 🚨Given the data discussed at @asco #ASCO2019 & @sno #SNO2019 on #NTRK fusions in primary brain tumors & brain mets, I thought we could review the background of these fusions, how to find them, and then look at potential options for tx. #btsm
<Disclaimer: I’m a speaker for Bayer (larotrectinib) and a subI for the STARTRK trial using entrectinib. I also have ongoing research work w @carisls > I’m keeping this as bias-free as possible though. Ok, next...
With the increase in tumor profiling & expanded options using #RNAseq, it seems like it is getting easier to find an #NTRK fusion. It can easily feel like Christmas when you do! 🎄 Just remember that an #NTRK MUTATION is not 🚫 fusion. They aren’t = & treatments aren’t the same.
Read 26 tweets

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