We have recently expanded our single-cell epigenetics assays!
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQa
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQa
November 5, 2026 at 8:26 PM
We have recently expanded our single-cell epigenetics assays!
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQa
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQa
Hans took it a step further and did a coinfection, we can see each phage but the rate of coinfection was higher than standard Poisson would predict. Suggestive of some factor that means if 1 phage can get in so can another. We’re moving from petriseq to PIPSEQ method thanks to recent MIRA 3/3
October 2, 2026 at 12:51 PM
Hans took it a step further and did a coinfection, we can see each phage but the rate of coinfection was higher than standard Poisson would predict. Suggestive of some factor that means if 1 phage can get in so can another. We’re moving from petriseq to PIPSEQ method thanks to recent MIRA 3/3
We have recently expanded our single-cell epigenetics assays!
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQao
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQao
September 30, 2026 at 7:20 PM
We have recently expanded our single-cell epigenetics assays!
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQao
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQao
We have recently expanded our single-cell epigenetics assays!
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQao
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQao
September 10, 2026 at 3:45 PM
We have recently expanded our single-cell epigenetics assays!
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQao
Our Emulsion scCUT&Tag assay is now compatible with the Illumina PIP-seq platform
#SingleCell #EpigenomeTech #PairedTag #Multiomics #Epigenetics #scCUTandTag #PIPseq
Learn more here: u.epigenome.us/NYjSGQao
Full post here : www.linkedin.com/posts/cathar...
A Promising Single Cell Alternative | Catharine Aquino
A Promising Single Cell Alternative
Before we roll out any new service, internal benchmarking is a must. This time we tested Illumina’s Single Cell 3' RNA prep kit (which I will call PIPseq) against t...
www.linkedin.com
July 27, 2025 at 7:07 PM
Full post here : www.linkedin.com/posts/cathar...
Verdict:
If your study hinges on squeezing out every cell, go with GEMX. But if you are balancing budget and performance, PIPseq might be something to consider. We now added PIPseq to our services.
If your study hinges on squeezing out every cell, go with GEMX. But if you are balancing budget and performance, PIPseq might be something to consider. We now added PIPseq to our services.
July 27, 2025 at 7:07 PM
Verdict:
If your study hinges on squeezing out every cell, go with GEMX. But if you are balancing budget and performance, PIPseq might be something to consider. We now added PIPseq to our services.
If your study hinges on squeezing out every cell, go with GEMX. But if you are balancing budget and performance, PIPseq might be something to consider. We now added PIPseq to our services.
Bottom line
GEMX has the edge in cell detection, but PIPseq performs respectably at roughly half the price. For many experiments, that trade off could be worth it.
GEMX has the edge in cell detection, but PIPseq performs respectably at roughly half the price. For many experiments, that trade off could be worth it.
July 27, 2025 at 7:07 PM
Bottom line
GEMX has the edge in cell detection, but PIPseq performs respectably at roughly half the price. For many experiments, that trade off could be worth it.
GEMX has the edge in cell detection, but PIPseq performs respectably at roughly half the price. For many experiments, that trade off could be worth it.
A Promising Single Cell Alternative
Before we roll out any new service, internal benchmarking is a must. This time we tested Illumina’s Single Cell 3' RNA prep kit (which I will call PIPseq) against the reigning champ, 10x Genomics GEMX 3' Gene Expression kit (GEMX for short).
What we found:
Before we roll out any new service, internal benchmarking is a must. This time we tested Illumina’s Single Cell 3' RNA prep kit (which I will call PIPseq) against the reigning champ, 10x Genomics GEMX 3' Gene Expression kit (GEMX for short).
What we found:
July 27, 2025 at 7:07 PM
A Promising Single Cell Alternative
Before we roll out any new service, internal benchmarking is a must. This time we tested Illumina’s Single Cell 3' RNA prep kit (which I will call PIPseq) against the reigning champ, 10x Genomics GEMX 3' Gene Expression kit (GEMX for short).
What we found:
Before we roll out any new service, internal benchmarking is a must. This time we tested Illumina’s Single Cell 3' RNA prep kit (which I will call PIPseq) against the reigning champ, 10x Genomics GEMX 3' Gene Expression kit (GEMX for short).
What we found:
Intrinsic molecular identifiers enable robust molecular counting in single-cell sequencing https://www.biorxiv.org/content/10.1101/2024.10.04.616561v1
Intrinsic molecular identifiers enable robust molecular counting in single-cell sequencing https://www.biorxiv.org/content/10.1101/2024.10.04.616561v1
Particle-templated instant partition sequencing (PIPseq), is an emerging approach for massively scal
www.biorxiv.org
October 6, 2024 at 2:33 AM
Intrinsic molecular identifiers enable robust molecular counting in single-cell sequencing https://www.biorxiv.org/content/10.1101/2024.10.04.616561v1
Join us TODAY for the latest Ramaciotti Centre for Genomics Monthly Seminar, where cutting-edge science meets cost-effective innovation. Featuring Ivonne Petermann showcasing Illumina's PIPseq and Tsz (Andrew) Ho Li from UNSW Biotechnology & Biomolecular Sciences. See you soon! #SingleCell #Illumina
June 25, 2025 at 1:37 AM
Join us TODAY for the latest Ramaciotti Centre for Genomics Monthly Seminar, where cutting-edge science meets cost-effective innovation. Featuring Ivonne Petermann showcasing Illumina's PIPseq and Tsz (Andrew) Ho Li from UNSW Biotechnology & Biomolecular Sciences. See you soon! #SingleCell #Illumina
#Singlecellsequencing at the Ramaciotti Centre! 🚀Announcing our pioneering Fluent PIP-seq V single-cell project, for @katequinlan.bsky.social of @unswbabs.bsky.social The #pipseq technology is simple, scalable, cost-effective NGS workflow recently acquired by #Illumina - check our LinkedIn for info🧬
April 16, 2025 at 5:56 AM
#Singlecellsequencing at the Ramaciotti Centre! 🚀Announcing our pioneering Fluent PIP-seq V single-cell project, for @katequinlan.bsky.social of @unswbabs.bsky.social The #pipseq technology is simple, scalable, cost-effective NGS workflow recently acquired by #Illumina - check our LinkedIn for info🧬
2/2
10x Genomics v3.1
10x Genomics Flex.
Evercode v2 Parse Bio.
PIPseq v5.0 Fluent Bio.
Smart-Seq3xpress
10x Genomics v3.1
10x Genomics Flex.
Evercode v2 Parse Bio.
PIPseq v5.0 Fluent Bio.
Smart-Seq3xpress
May 22, 2025 at 1:31 PM
2/2
10x Genomics v3.1
10x Genomics Flex.
Evercode v2 Parse Bio.
PIPseq v5.0 Fluent Bio.
Smart-Seq3xpress
10x Genomics v3.1
10x Genomics Flex.
Evercode v2 Parse Bio.
PIPseq v5.0 Fluent Bio.
Smart-Seq3xpress
#Illumina #Single-Cell 3’ RNAPrep, formerly #Fluent PipSeq V is now official 🎉. A highly efficient, affordable, accurate workflow with #DRAGEN and #Partek Flow to scale experiments from hundreds to millions of cells on #NoveSeqX #NovsSeq6000 #NextSeq platforms
RM: www.illumina.com/products/by-...
RM: www.illumina.com/products/by-...
Illumina Single Cell 3' RNA Prep
Accessible and highly scalable single-cell RNA-Seq solution for mRNA capture, barcoding, and library prep without complex workflows or microfluidics
www.illumina.com
January 7, 2025 at 8:25 PM
#Illumina #Single-Cell 3’ RNAPrep, formerly #Fluent PipSeq V is now official 🎉. A highly efficient, affordable, accurate workflow with #DRAGEN and #Partek Flow to scale experiments from hundreds to millions of cells on #NoveSeqX #NovsSeq6000 #NextSeq platforms
RM: www.illumina.com/products/by-...
RM: www.illumina.com/products/by-...
My frustration again is that the PIPseq V data has never been released afaik; hence we wanted to get this out there to see if anyone could crack it
March 14, 2025 at 5:53 PM
My frustration again is that the PIPseq V data has never been released afaik; hence we wanted to get this out there to see if anyone could crack it
Possibilities that I'm thinking thru:
- PCR bottlenecks / multiple IMIs per original transcript gives false count density in PIPseq (would reflect poorly on this product)
- More diversity of the transcript being covered so can resolve ambiguous mappings hidden in 10x data (would be good for PIPseq)
- PCR bottlenecks / multiple IMIs per original transcript gives false count density in PIPseq (would reflect poorly on this product)
- More diversity of the transcript being covered so can resolve ambiguous mappings hidden in 10x data (would be good for PIPseq)
March 14, 2025 at 5:53 PM
Possibilities that I'm thinking thru:
- PCR bottlenecks / multiple IMIs per original transcript gives false count density in PIPseq (would reflect poorly on this product)
- More diversity of the transcript being covered so can resolve ambiguous mappings hidden in 10x data (would be good for PIPseq)
- PCR bottlenecks / multiple IMIs per original transcript gives false count density in PIPseq (would reflect poorly on this product)
- More diversity of the transcript being covered so can resolve ambiguous mappings hidden in 10x data (would be good for PIPseq)
I'd be particularly excited if folks could take this and figure out anything re: gene detection / quantification differences. It's not obvious to me yet if expression in PIPseq or GEM-X but not the other is due to wet- or dry- lab differences in the protocols/recommended processing /14
March 14, 2025 at 1:29 PM
I'd be particularly excited if folks could take this and figure out anything re: gene detection / quantification differences. It's not obvious to me yet if expression in PIPseq or GEM-X but not the other is due to wet- or dry- lab differences in the protocols/recommended processing /14
I found it frustrating that the PIPseq V paper (www.biorxiv.org/content/10.1...) did not provide data for V technology publicly (www.fluentbio.com/datasets/ stops at v4; 'available upon request' is not acceptable in 2025). It's hard to use new tech where data isn't easily accessible! /11
March 14, 2025 at 1:29 PM
I found it frustrating that the PIPseq V paper (www.biorxiv.org/content/10.1...) did not provide data for V technology publicly (www.fluentbio.com/datasets/ stops at v4; 'available upon request' is not acceptable in 2025). It's hard to use new tech where data isn't easily accessible! /11
As I've been doing single-cell for ~10 years now, I can confidently say that GEM-X is just a really, really good product and the platform where you'll see the next few developments from us. That said, the fact that PIPseq looks promising on our first try is encouraging for future products. /10
March 14, 2025 at 1:29 PM
As I've been doing single-cell for ~10 years now, I can confidently say that GEM-X is just a really, really good product and the platform where you'll see the next few developments from us. That said, the fact that PIPseq looks promising on our first try is encouraging for future products. /10
The differences start to emerge when you look a bit more closely. In terms of molecular complexity, PIPseq performed pretty well, but there's a pretty massive difference compared to GEM-X. At similar cell numbers and sequencing depth, we get about 63% more UMIs / cell with GEM-X over PIPseq V /7
March 14, 2025 at 1:29 PM
The differences start to emerge when you look a bit more closely. In terms of molecular complexity, PIPseq performed pretty well, but there's a pretty massive difference compared to GEM-X. At similar cell numbers and sequencing depth, we get about 63% more UMIs / cell with GEM-X over PIPseq V /7
We designed a basic head-to-head experiment using a cryovial of PBMCs from a healthy donor, split and profiled via 10x GEM-X 3' and PIPseq V (T20). @karolisk.bsky.social masterfully generated data on his first try with the Single-cell Analytics Innovation Lab (SAIL) here at MSKCC. /3
March 14, 2025 at 1:29 PM
We designed a basic head-to-head experiment using a cryovial of PBMCs from a healthy donor, split and profiled via 10x GEM-X 3' and PIPseq V (T20). @karolisk.bsky.social masterfully generated data on his first try with the Single-cell Analytics Innovation Lab (SAIL) here at MSKCC. /3
We've been using 10x products for profiling and technology development for several years now. With new products coming online for single-cell profiling, we wanted to get first-hand experience with PIPseq as it's (imo) the tech that could most easily be integrated into our existing workflows. /2
March 14, 2025 at 1:29 PM
We've been using 10x products for profiling and technology development for several years now. With new products coming online for single-cell profiling, we wanted to get first-hand experience with PIPseq as it's (imo) the tech that could most easily be integrated into our existing workflows. /2
Trying a slightly new model (for us at least) of #openscience. With @ronanchaligne.bsky.social and @karolisk.bsky.social, we pitted 10x Genomics Chromium GEM-X against Illumina PIPseq V head-to-head to understand these two platforms for single-cell genomics. Some thoughts off the bleeding edge: /1
a baby is eating a piece of food while sitting on the ground .
ALT: a baby is eating a piece of food while sitting on the ground .
media.tenor.com
March 14, 2025 at 1:29 PM
Trying a slightly new model (for us at least) of #openscience. With @ronanchaligne.bsky.social and @karolisk.bsky.social, we pitted 10x Genomics Chromium GEM-X against Illumina PIPseq V head-to-head to understand these two platforms for single-cell genomics. Some thoughts off the bleeding edge: /1
One billion cell atlas project from #Illumina and collaborators AstraZeneca, Eli Lily and Merck
#singlecell #perturbseq #PIPseq
www.illumina.com/company/news...
#singlecell #perturbseq #PIPseq
www.illumina.com/company/news...
Illumina introduces Billion Cell Atlas to accelerate AI and drug discovery
www.illumina.com
January 17, 2026 at 7:16 AM
One billion cell atlas project from #Illumina and collaborators AstraZeneca, Eli Lily and Merck
#singlecell #perturbseq #PIPseq
www.illumina.com/company/news...
#singlecell #perturbseq #PIPseq
www.illumina.com/company/news...
A little video intro into Illumina Single Cell 3' RNA Prep protocols. It has begun!!
#singlecell
#transcriptomics
#PIPSeq
#illumina
#singlecell
#transcriptomics
#PIPSeq
#illumina
🧬Two updated technical videos demonstrating T2 and T20 workflows on newly released #Illumina Single-Cell 3' RNA Prep
T2: www.youtube.com/watch?v=4i5k...
T20: www.youtube.com/watch?featur...
📰 www.prnewswire.com/news-release...
T2: www.youtube.com/watch?v=4i5k...
T20: www.youtube.com/watch?featur...
📰 www.prnewswire.com/news-release...
January 13, 2025 at 7:54 AM
A little video intro into Illumina Single Cell 3' RNA Prep protocols. It has begun!!
#singlecell
#transcriptomics
#PIPSeq
#illumina
#singlecell
#transcriptomics
#PIPSeq
#illumina
Didn’t think I’d be interested in droplets/partitions/emulsions again after leaving Bio Rad. But, I’m back on the droplet wagon at #illumina with #PIPSeq V #singlecell
November 29, 2024 at 8:37 PM
Didn’t think I’d be interested in droplets/partitions/emulsions again after leaving Bio Rad. But, I’m back on the droplet wagon at #illumina with #PIPSeq V #singlecell