Julien Jarroux (@jjarroux) header
Julien Jarroux (@jjarroux) profile picture

Julien Jarroux

@jjarroux

RNA enthusiast. PhD. Before : Institut Curie. Current : Tilgner lab at Weill Cornell Medicine

 New York, NY
Joined November 2013
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Photo by Julien Jarroux (@jjarroux)Photo by Julien Jarroux (@jjarroux)Photo by Julien Jarroux (@jjarroux)Photo by Julien Jarroux (@jjarroux)Photo by Julien Jarroux (@jjarroux)Photo by Julien Jarroux (@jjarroux)Photo by Julien Jarroux (@jjarroux)Photo by Julien Jarroux (@jjarroux)
Our review of single-cell isoform work is out: tandfonline.com/doi/full/10.… By @noush_joglekar @CareenFoord @jjarroux and Shaun Pollard (not on twitter) #LongRead #RNA @iRnaCosi #nanopore #pacbio #genomics #Transcripomics #RNAseq #Splicing
From words to complete phrases: insight into single-cell isoforms using short and long reads

From words to complete phrases: insight into single-cell isoforms using short and long reads

The profiling of gene expression patterns to glean biological insights from single cells has become commonplace over the last few years. However, this approach overlooks the transcript contents tha...

tandfonline.com
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- finally cell-type specific exon inclusion in mouse hippocampus is largely conserved in human hippocampus, but human brain has turned extra exons that are constitutive in mouse into cell-type specific alternative exons in human.
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- developmental changes (of matched cell types) stronger than brain-region differences (of matched cell types), and especially the P21-to-P28 transition stands out.
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- for brain-region variability: some gene classes stand out, including neurotransmitter release and reuptake as well as synapse turnover - for glia strong poly(A)-site regulation between brain regions, - for neurons, also strong regulation at TSS
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main results: - for 3/4 of genes full-length isoform expression varies between brain regions (matched cell types), development (matched cell types) or between subtypes of a high-level cell type. - on top: strong splicing variation between high-level cell types
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Our preprint on single-cell long-read isoforms across mouse brain regions, developmental time points as well as human hippocampi is here: biorxiv.org/content/10.1101/… Great team work with contributions by many but led by @noush_joglekar, who invested almost 3 years into this.
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Check out the exciting new paper from the Tilgner Lab, looking at alternative splicing in the brain!
Anoushka (@noush_joglekar) profile pictureAnoushka@noush_joglekar5 Apr 2023
I'm so excited to FINALLY present the latest preprint from the @hagentilgner lab where we look at alternative splicing in the brain across "space and time" biorxiv.org/content/10.1101/…
Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell...

Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell...

RNA isoforms influence cell identity and function. Until recently, technological limitations prevented a genome-wide appraisal of isoform influence on cell identity in various parts of the brain....

biorxiv.org
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Julien Jarroux retweeted
Anoushka (@noush_joglekar) profile picture
Anoushka@noush_joglekar5 Apr 2023
This was of course a culmination of many years of effort - many many thanks to all the brilliant friends, collaborators, and colleagues (on and off this platform) who made this happen: @rainryuhei_wen @MarkDiekhans @GSheynkman @ofedrigo @erichjarvis
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Anoushka (@noush_joglekar) profile picture
Anoushka@noush_joglekar5 Apr 2023
I'll stop before I belabor this analogy, but go check out our preprint if you want to be blown away at the sheer amount of stuff that happens in the brain. I had a blast scrutinizing this amazing data from every angle 😍
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Anoushka (@noush_joglekar) profile picture
Anoushka@noush_joglekar5 Apr 2023
And it seems that no matter where you are, teenagers (cell types in adolescent mice in this case) are wacky and rebellious, but they're ultimately just trying to find their identity
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Anoushka (@noush_joglekar) profile picture
Anoushka@noush_joglekar5 Apr 2023
Splicing happens everything everywhere all at once. It's almost dizzying, the number of ways a gene can change its form depending on what environment it's being expressed in
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Anoushka (@noush_joglekar) profile picture
Anoushka@noush_joglekar5 Apr 2023
We collected some very cool data to study isoforms across multiple scales in the brain: cell (sub)types, spatially distinct regions, and developmental timepoints. Very succinctly, what we found is that
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Julien Jarroux retweeted
Anoushka (@noush_joglekar) profile picture
Anoushka@noush_joglekar5 Apr 2023
I'm so excited to FINALLY present the latest preprint from the @hagentilgner lab where we look at alternative splicing in the brain across "space and time" biorxiv.org/content/10.1101/…
Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell...

Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell...

RNA isoforms influence cell identity and function. Until recently, technological limitations prevented a genome-wide appraisal of isoform influence on cell identity in various parts of the brain....

biorxiv.org
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After 12yrs in #longreads, the method of 2022 tinyurl.com/mwt52tsd is a treat! Thanks @naturemethods for letting us write about it (link to follow). Led by @CareenFoord+@JustineKCH+@jjarroux. See also Andrey+Alla’s long-read software tinyurl.com/yyupucph
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WCM Neurogenetics (@WCM_CNG) profile picture
WCM Neurogenetics@WCM_CNG3 Jan 2023
Congratulations to Dr. Hagen Tilgner, Dr. Anoushka Joglekar, and Dr. Julien Jarroux, for their newly published paper, out today in Nature Biotechnology! nature.com/articles/s41587-0…
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Ever wandered how to get the best out of your long read RNA-seq? Whether you use @nanopore or @PacBio, give IsoQuant a go for accurate isoform prediction! More in our newest paper from the @hagentilgner lab. nature.com/articles/s41587-0…
Accurate isoform discovery with IsoQuant using long reads

Accurate isoform discovery with IsoQuant using long reads

Nature Biotechnology - IsoQuant predicts novel isoforms from long-read RNA sequencing.

nature.com
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Out in @NatureBiotech: What isoforms are really in your @PacBio or @nanopore run? Andrey&Alla (with help by @noush_joglekar, AS, @jjarroux &AL) have precise answers: nature.com/articles/s41587-0… #LongRead #RNA @iRnaCosi #nanopore #pacbio #genomics #Transcripomics #RNAseq #Splicing
Accurate isoform discovery with IsoQuant using long reads

Accurate isoform discovery with IsoQuant using long reads

Nature Biotechnology - IsoQuant predicts novel isoforms from long-read RNA sequencing.

nature.com
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On Saturday, we welcomed girl scouts troop 2848 at @WCM_CNG and @WCM_BMRI for a session of Saturday Science. From strawberry DNA extraction to single-cell brain biology. So great to see these girls' enthusiasm and great work by @noush_joglekar @jjarroux and @rainryuhei_wen
Image from Hagen Tilgner / @hagentilgner@genomic.social (@hagentilgner)
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ScisorWiz is out! New paper from the @hagentilgner lab with a tool to visualize single-cell isoform expression, by @astein7 with @noush_joglekar and @cheesepuuff academic.oup.com/bioinformat…
ScisorWiz: visualizing differential isoform expression in single-cell long-read data

ScisorWiz: visualizing differential isoform expression in single-cell long-read data

AbstractSummary. RNA isoforms contribute to the diverse functionality of the proteins they encode within the cell. Visualizing how isoform expression diffe

academic.oup.com
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New paper from our lab in @NatureBiotech! If you're interested in RNA sequencing, isoforms, single-cell and single-nuclei transcriptomics, and gene expression in the brain, this is the one for you! nature.com/articles/s41587-0…
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

Nature Biotechnology - Complete RNA isoforms are captured by a new single-nuclei sequencing method.

nature.com
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At @WCM @WCM_BMRI, in @hagentilgner's lab with superstars @si_hardwick, @rainryuhei_wen and @noush_joglekar!
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