Anita Scoones (@anitascoones)

January 2026, The Plant Cell cover

We made the front cover of @theplantcell.bsky.social!

Huge congratulations to co-first authors @katielong.bsky.social and Ashleigh Lister, corresponding author @cristobaluauy.bsky.social and everyone at JIC, @earlhaminst.bsky.social and @vizgen.bsky.social who collaborated on this exciting work 👏

04.02.2026 13:31 👍 24 🔁 13 💬 3 📌 0

In my recent blog @earlhaminst.bsky.social I reflected on delivering the first hands-on single-cell training courses in #LATAM 🧬🌎🇧🇷 Highlighting insights from our recent review in @cellpress.bsky.social on the #singlecell research landscape across #LatinAmerica ! 🔗 ➡️ www.cell.com/cell/abstrac...

05.02.2026 16:01 👍 1 🔁 1 💬 0 📌 0

Latin America is a richly diverse region of the world that holds extraordinary potential for #singlecell and #spatialgenomics research. Yet LatAm countries remain significantly underrepresented in single-cell publications, with limited access to training and development.

29.01.2026 11:01 👍 0 🔁 3 💬 1 📌 0

Anita delivers training during the wet-lab Single-Cell course in Brazil. ©Wellcome Connecting Science

Anita introduces the single-cell team at Earlham Institute.

The programme brought together international scientists to deliver the training. Group photo of the course trainers. ©Wellcome Connecting Science

In 2023, then-PhD student at Earlham Institute - Anita Scoones - was invited to help shape and deliver the first hands-on single-cell #genomics course in Latin America, organised by @connectingscience.bsky.social in collaboration with Brazil's National Cancer Institute.

@anitascoones.bsky.social

29.01.2026 11:01 👍 1 🔁 2 💬 1 📌 0

📣 Abstract submissions are open 📣 for the Norwich Single-Cell & Spatial #Symposium 2026, hosted at @earlhaminst.bsky.social 🧬! We’re bringing together researchers across #singlecell and #spatial #biology for two days of science, discussion, and networking. 🔗Link: www.earlham.ac.uk/events/norwi...

05.02.2026 15:44 👍 1 🔁 1 💬 0 📌 0

Postdoctoral Scientist Anita Scoones with her opening presentation slide which reads "A longer look: benchmarking long-read sequencing for single-cell transcriptomics."

Group Leader Dr Iain Macaulay with Postdoctoral Research Anita Scoones answering questions after her talk.

This morning's single-cell genomics session at #GenomeScience25 chaired by @whatchamacaulay.bsky.social, with @anitascoones.bsky.social presenting her recent study on benchmarking #longread methods for #singlecell transcriptomics. 🧬🖥️

📃 Check out the preprint here: www.biorxiv.org/content/10.1...

10.07.2025 12:55 👍 5 🔁 2 💬 0 📌 0

Arrived at #GenomeScience! Looking forward to catching up with colleagues, meeting new faces, and discussing all things genomics 🙌. Day 2 (12.05pm, G26) presenting our work using #longreads for #scRNAseq - on biorxiv this week📑- otherwise find me @ poster 3/ @earlhaminst.bsky.social stand 🧬 #gsuk25

09.07.2025 11:56 👍 0 🔁 1 💬 0 📌 0

A comparison of long-read single-cell transcriptomic approaches https://www.biorxiv.org/content/10.1101/2025.07.03.662955v1

06.07.2025 07:30 👍 3 🔁 2 💬 0 📌 0

Looking forward to presenting at #GenomeScience this week! ✨- I'll be discussing our work benchmarking #singlecell #longread approaches, freshly on biorxiv as of this morning! 🧬📄

06.07.2025 20:23 👍 0 🔁 2 💬 0 📌 0

A comparison of long-read single-cell transcriptomic approaches. #LongRead #Sequencing #SingleCell #Transcriptomics #ToolsBenchmarking #Genomics #Bioinformatics @anitascoones.bsky.social @biorxiv-bioinfo.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...

06.07.2025 19:05 👍 8 🔁 4 💬 0 📌 0

🧬 We demonstrate that long-read single-cell RNA-seq can enable direct immunoglobulin chain reconstruction and resolve isoform usage in immune cells, while also highlighting that limitations common across all platforms still constrain the complexity we can recover

06.07.2025 20:11 👍 2 🔁 0 💬 0 📌 0

A comparison of long-read single-cell transcriptomic approaches Long-read sequencing enables the incorporation of isoform-level expression into single-cell transcriptomic studies, offering detail beyond those accessible with short-read methods. Although insightful, these approaches have typically been costly and yielded limited data for each individual cell. Recent advances in library preparation approaches and sequencing throughput have brought long-read single-cell studies closer to the mainstream. Here, we present a comparative analysis of commercial approaches for single-cell long-read sequencing. We have performed parallel analyses of the same cDNA material, generated using the 10X genomics platform, on Illumina short-read, and PacBio and Oxford Nanopore long-read platforms. We also demonstrate the impact of CRISPR-based depletion of libraries, to remove highly expressed transcripts, prior to long-read sequencing in these experiments. By analysing single-source cDNA libraries in parallel, we enable a direct comparison of each platform, evaluating standard metrics alongside concordance in clustering and cell type identification. While each approach generates usable gene and isoform expression data, we identify limitations common across platforms, primarily linked to cDNA synthesis inefficiencies and read filtering strategies. Our work demonstrates the increasing utility of single-cell long-read sequencing for isoform-resolved analyses, such as direct immunoglobulin chain reconstruction without additional amplification, and the detection of alternative splicing patterns across immune cell subtypes in CD45, a key gene for immune cell activation and differentiation. Our benchmarking of current platform options provides a foundation for researchers looking to adopt single-cell long-read sequencing into their transcriptomic studies, providing a framework for its integration into diverse biological questions. ### Competing Interest Statement A.P.C. is an inventor on patents filed by Oxford University Innovations for single-cell technologies and is a co-founders of Entelo Bio. All other authors declare no conflict of interest. Cancer Research UK, https://ror.org/054225q67, A26815 Biotechnology and Biological Sciences Research Council, https://ror.org/00cwqg982, BB/CCG1720/1, BB/CCG2220/1, BBS/E/T/000PR9816, BBX011070/1, BB/V016156/1, BB/T008717/1 UK Research and Innovation, EP/X035913/1, 10098097 Biotechnology and Biological Sciences Research Council, BB/M011216/1, BBS/E/ER/23NB0006 Medical Research Council, MR/V010182/1

📝 New preprint on bioRxiv! We compared #longread #singlecell #RNAseq methods (ONT & PacBio) using same-source cDNA to see how they perform in practice. Might be useful for others exploring these approaches 👀 www.biorxiv.org/cgi/content/...

06.07.2025 20:11 👍 3 🔁 1 💬 1 📌 0

A comparison of long-read single-cell transcriptomic approaches Long-read sequencing enables the incorporation of isoform-level expression into single-cell transcriptomic studies, offering detail beyond those accessible with short-read methods. Although insightful, these approaches have typically been costly and yielded limited data for each individual cell. Recent advances in library preparation approaches and sequencing throughput have brought long-read single-cell studies closer to the mainstream. Here, we present a comparative analysis of commercial approaches for single-cell long-read sequencing. We have performed parallel analyses of the same cDNA material, generated using the 10X genomics platform, on Illumina short-read, and PacBio and Oxford Nanopore long-read platforms. We also demonstrate the impact of CRISPR-based depletion of libraries, to remove highly expressed transcripts, prior to long-read sequencing in these experiments. By analysing single-source cDNA libraries in parallel, we enable a direct comparison of each platform, evaluating standard metrics alongside concordance in clustering and cell type identification. While each approach generates usable gene and isoform expression data, we identify limitations common across platforms, primarily linked to cDNA synthesis inefficiencies and read filtering strategies. Our work demonstrates the increasing utility of single-cell long-read sequencing for isoform-resolved analyses, such as direct immunoglobulin chain reconstruction without additional amplification, and the detection of alternative splicing patterns across immune cell subtypes in CD45, a key gene for immune cell activation and differentiation. Our benchmarking of current platform options provides a foundation for researchers looking to adopt single-cell long-read sequencing into their transcriptomic studies, providing a framework for its integration into diverse biological questions. ### Competing Interest Statement A.P.C. is an inventor on patents filed by Oxford University Innovations for single-cell technologies and is a co-founders of Entelo Bio. All other authors declare no conflict of interest. Cancer Research UK, https://ror.org/054225q67, A26815 Biotechnology and Biological Sciences Research Council, https://ror.org/00cwqg982, BB/CCG1720/1, BB/CCG2220/1, BBS/E/T/000PR9816, BBX011070/1, BB/V016156/1, BB/T008717/1 UK Research and Innovation, EP/X035913/1, 10098097 Biotechnology and Biological Sciences Research Council, BB/M011216/1, BBS/E/ER/23NB0006 Medical Research Council, MR/V010182/1

nice to see this one up on bioRxiv - we took at look at various approaches for #longread #singlecell #RNAseq, very much from the perspective of the prospective user - firstly to see for ourselves how they behaved!

www.biorxiv.org/content/10.1...

06.07.2025 16:29 👍 9 🔁 7 💬 1 📌 0

To move forward, we need better benchmarking and pipelines that are optimised for the realities of single-cell data — sparse, noisy, and complex.

Otherwise, we risk missing the very biology we’re trying to uncover 🧬

#SingleCell #LongReads #IsoformResolution #Genomics #Bioinformatics

24.06.2025 21:25 👍 2 🔁 0 💬 0 📌 0

There’s a strong push in the field to maximise cell throughput — but meaningful isoform analysis RELIES on having enough resolution per cell 🔬

It’s a trade-off, and the risk is that depth gets overlooked - even though it’s exactly what’s needed to study splicing and capture transcript diversity.

24.06.2025 21:25 👍 0 🔁 1 💬 1 📌 0

Report: Single Cell & Spatial Buyer's Guide 2025 This report is a free-to-download resource to help keep track of the advances in the single cell and spatial field.

✨🧬 Featured in the Single Cell & Spatial Buyer’s Guide 2025 by Front Line Genomics @flgenomics.bsky.social!

I shared thoughts on applying long-read sequencing to single-cell — isoform diversity, benchmarking challenges, and where we still need to do better.

Read (pp. 36–40): hubs.la/Q03qCBTm0

🧵👇

24.06.2025 21:25 👍 2 🔁 3 💬 1 📌 0

Great to see this new guide out from @flgenomics.bsky.social which includes an interview with Anita Scoones, Postdoctoral Researcher at EI, on the challenges of #longread #singlecell sequencing.

@anitascoones.bsky.social @whatchamacaulay.bsky.social

18.06.2025 15:00 👍 3 🔁 2 💬 0 📌 0

Norwich Single-Cell and Spatial Symposium Now in its eighth year, and extended to a two-day event, the Norwich Single-Cell and Spatial Symposium at Earlham Institute covers single-cell and spatial genomics technologies and their application i...

The Norwich Single-Cell & Spatial Symposium is nearly here! 👏🏻Two packed days of talks across plant, microbial & human systems—covering #singlecell, #spatial & real-world case studies 🧬🦠! In person at the Earlham Institute. Registration closes soon- don’t miss it!🔗
www.earlham.ac.uk/events/norwi...

06.05.2025 11:32 👍 2 🔁 4 💬 0 📌 0

Hi BlueSky 👋🦋 Following suit with a professional migration! Bit about me: I’m a postdoc working on isoform-resolved #singlecell transcriptomics using long-read sequencing. Currently somewhere between protocol optimisation and data chaos😅. Expect science, training bits & memes - of course ☺️

06.05.2025 11:27 👍 9 🔁 1 💬 0 📌 0

Anita Scoones

Latest posts by Anita Scoones @anitascoones