How do I visualize the K562 genome in IGV next to hg38?
November 15, 2024 at 7:42 PM
How do I visualize the K562 genome in IGV next to hg38?
Russian Navy Project 0885M Yasen-M/Severodvinsk II-Class nuclear-powered guided missile submarine Arkhangelsk (K-562) leaving Severodvinsk - posted January 26, 2025 #arkhangelsk #k562 SRC: TW-@Saturnax1 / @fotaflota
January 26, 2025 at 2:42 PM
Russian Navy Project 0885M Yasen-M/Severodvinsk II-Class nuclear-powered guided missile submarine Arkhangelsk (K-562) leaving Severodvinsk - posted January 26, 2025 #arkhangelsk #k562 SRC: TW-@Saturnax1 / @fotaflota
@brielin.bsky.social's fantastic work on causal gene network inference from Perturb-seq is published! We estimate total causal effects using guides as instruments, then deconvolve into direct & mediated effects with a directed analog of graphical lasso. Deets: nature.com/articles/s41467-025-64353-7
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells - Nature Communications
The authors give a method for learning causal gene networks using Perturb-seq data. In K562 cells, they find a network with small-world and scale-free properties. Analysis shows a relationship between...
nature.com
November 3, 2025 at 7:09 PM
@brielin.bsky.social's fantastic work on causal gene network inference from Perturb-seq is published! We estimate total causal effects using guides as instruments, then deconvolve into direct & mediated effects with a directed analog of graphical lasso. Deets: nature.com/articles/s41467-025-64353-7
Cell lines frequently develop subclones — the original single cell ATAC paper showed both epigenomic and genetic subclonality in K562
And K562 is relatively stable😬
And K562 is relatively stable😬
January 29, 2025 at 2:43 PM
Cell lines frequently develop subclones — the original single cell ATAC paper showed both epigenomic and genetic subclonality in K562
And K562 is relatively stable😬
And K562 is relatively stable😬
So…my old HPLC is having a minor issue or 2 but parts and are on the way. I’m still getting 60k peptides in 36 min (run to run) from 10ng K562?!? Moving to Whisper zoom gets me to almost 7k protein groups! BPS and DIA-NN are largely in agreement. First real single cells are up next!
March 18, 2025 at 4:55 PM
So…my old HPLC is having a minor issue or 2 but parts and are on the way. I’m still getting 60k peptides in 36 min (run to run) from 10ng K562?!? Moving to Whisper zoom gets me to almost 7k protein groups! BPS and DIA-NN are largely in agreement. First real single cells are up next!
This is something that Alex Marson and I have been working toward for ~8 years. A brilliant postdoc with us, @minetoota.bsky.social, decided to build a proof of principle by using the only current genome-scale Perturb-seq, in K562 cells, to model red blood cell phenotypes such as hemoglobin (MCH)
January 26, 2025 at 12:13 AM
This is something that Alex Marson and I have been working toward for ~8 years. A brilliant postdoc with us, @minetoota.bsky.social, decided to build a proof of principle by using the only current genome-scale Perturb-seq, in K562 cells, to model red blood cell phenotypes such as hemoglobin (MCH)
Sorry for missing some details in the methods section. For A02:01, the antigen presenting cells were mostly T2 cells. For some data they might have been through HEK293T and for some K562-A02:01. For MAGE-A3, we used HEK293T-A01:01 cells because K562 is MAGE-A3+. For all others, they were K562 + MHC
November 24, 2025 at 10:02 PM
Sorry for missing some details in the methods section. For A02:01, the antigen presenting cells were mostly T2 cells. For some data they might have been through HEK293T and for some K562-A02:01. For MAGE-A3, we used HEK293T-A01:01 cells because K562 is MAGE-A3+. For all others, they were K562 + MHC
Mineto proposed that we could use Perturb-seq from K562 cells to interpret -- and even predict! -- gene effects on traits.
To convince us that regulatory effects from experiments are relevant he considered a simple case: regulators of HBA1, which is part of the hemoglobin protein.
To convince us that regulatory effects from experiments are relevant he considered a simple case: regulators of HBA1, which is part of the hemoglobin protein.
January 26, 2025 at 12:13 AM
Mineto proposed that we could use Perturb-seq from K562 cells to interpret -- and even predict! -- gene effects on traits.
To convince us that regulatory effects from experiments are relevant he considered a simple case: regulators of HBA1, which is part of the hemoglobin protein.
To convince us that regulatory effects from experiments are relevant he considered a simple case: regulators of HBA1, which is part of the hemoglobin protein.
Wer hätte das auf der COVID Bingo-Karte?
antibody-dependent enhancement (ADE)
Anti-SARS-CoV-2-Antikörper waren mit DENV-2 kreuzreaktiv, zeigten das Potenzial die DENV-2-Infektion in K562- und U937-Zellen zu verstärken.
antibody-dependent enhancement (ADE)
Anti-SARS-CoV-2-Antikörper waren mit DENV-2 kreuzreaktiv, zeigten das Potenzial die DENV-2-Infektion in K562- und U937-Zellen zu verstärken.
October 11, 2023 at 3:54 PM
Wer hätte das auf der COVID Bingo-Karte?
antibody-dependent enhancement (ADE)
Anti-SARS-CoV-2-Antikörper waren mit DENV-2 kreuzreaktiv, zeigten das Potenzial die DENV-2-Infektion in K562- und U937-Zellen zu verstärken.
antibody-dependent enhancement (ADE)
Anti-SARS-CoV-2-Antikörper waren mit DENV-2 kreuzreaktiv, zeigten das Potenzial die DENV-2-Infektion in K562- und U937-Zellen zu verstärken.
Engineered LSD1 mutant Y391K bypasses H3K14 acetylation inhibition on K4 demethylation. Study in K562 cells deciphers epigenetic crosstalk. #EpigeneticsInsights PMID:38965385, Nat Chem Biol 2025, @nchembio @Harvard https://doi.org/10.1038/s41589-024-01671-9 #Medsky 🧪
Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1 | Nature Chemical Biology
Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation, but its functional significance in cells has been difficult to discern. Previous enzymatic studies revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine-specific demethylase 1 (LSD1). In the present study, we engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. K562 cells with the Y391K LSD1 CRISPR knockin show decreased expression of a set of genes associated with cellular adhesion and myeloid leukocyte activation. Chromatin profiling revealed that the cis-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation, and edited K562 cells show diminished H3 mono-methyl Lys4 near these silenced genes, consistent with a role for enhanced LSD1 demethylase activity. These findings illuminate the functional consequences of disconnecting
doi.org
March 6, 2025 at 10:10 AM
Engineered LSD1 mutant Y391K bypasses H3K14 acetylation inhibition on K4 demethylation. Study in K562 cells deciphers epigenetic crosstalk. #EpigeneticsInsights PMID:38965385, Nat Chem Biol 2025, @nchembio @Harvard https://doi.org/10.1038/s41589-024-01671-9 #Medsky 🧪
Here is slide demonstrating how it works w.r.t. to the highly aneuploid, yet very commonly used cell-line K562.
July 8, 2025 at 6:06 PM
Here is slide demonstrating how it works w.r.t. to the highly aneuploid, yet very commonly used cell-line K562.
The ZenoTOF 8600 paired with Aurora Series columns: a powerful combination showcased by @sciex.bsky.social’s Jean-Baptiste Vincendet at PSI-2025. >10,000 protein group IDs from 250 ng K562 cell line. Eager to see what else researchers achieve as adoption of the ZenoTOF 8600 system continues to grow.
December 22, 2025 at 12:31 AM
The ZenoTOF 8600 paired with Aurora Series columns: a powerful combination showcased by @sciex.bsky.social’s Jean-Baptiste Vincendet at PSI-2025. >10,000 protein group IDs from 250 ng K562 cell line. Eager to see what else researchers achieve as adoption of the ZenoTOF 8600 system continues to grow.
#OTD 1946 the Bell 47 became the first helicopter ever to be civil certified. This quaint 1977 film shows how Bell got there. www.youtube.com/watch?v=k562...
Birth of the Bell Helicopter.mpg
YouTube video by Paul Faltyn
www.youtube.com
March 8, 2025 at 4:48 AM
#OTD 1946 the Bell 47 became the first helicopter ever to be civil certified. This quaint 1977 film shows how Bell got there. www.youtube.com/watch?v=k562...
#FebMusicChallenge25
Your task made me think of the island John Lennon bought off the west coast of Ireland - Dorinish - but I can’t find any songs he wrote there. So I’ll turn to his songwriter partner & offer Mull of Kintyre instead. I was aged 11 when this was no 1: m.youtube.com/watch?v=K562...
Your task made me think of the island John Lennon bought off the west coast of Ireland - Dorinish - but I can’t find any songs he wrote there. So I’ll turn to his songwriter partner & offer Mull of Kintyre instead. I was aged 11 when this was no 1: m.youtube.com/watch?v=K562...
Paul McCartney & WINGS - Mull Of Kintyre (1977)
YouTube video by murphicus
m.youtube.com
February 12, 2025 at 10:30 AM
#FebMusicChallenge25
Your task made me think of the island John Lennon bought off the west coast of Ireland - Dorinish - but I can’t find any songs he wrote there. So I’ll turn to his songwriter partner & offer Mull of Kintyre instead. I was aged 11 when this was no 1: m.youtube.com/watch?v=K562...
Your task made me think of the island John Lennon bought off the west coast of Ireland - Dorinish - but I can’t find any songs he wrote there. So I’ll turn to his songwriter partner & offer Mull of Kintyre instead. I was aged 11 when this was no 1: m.youtube.com/watch?v=K562...
Limitations of existing datasets:
1. They often selected ‘interesting’ elements (e.g., high H3K27ac) or genes (e.g., transcription factors)
2. They have largely focused on 1 cell type (K562 cells)
3. Statistical power was limited due to cost constraints
4/
1. They often selected ‘interesting’ elements (e.g., high H3K27ac) or genes (e.g., transcription factors)
2. They have largely focused on 1 cell type (K562 cells)
3. Statistical power was limited due to cost constraints
4/
September 19, 2025 at 3:03 AM
Limitations of existing datasets:
1. They often selected ‘interesting’ elements (e.g., high H3K27ac) or genes (e.g., transcription factors)
2. They have largely focused on 1 cell type (K562 cells)
3. Statistical power was limited due to cost constraints
4/
1. They often selected ‘interesting’ elements (e.g., high H3K27ac) or genes (e.g., transcription factors)
2. They have largely focused on 1 cell type (K562 cells)
3. Statistical power was limited due to cost constraints
4/
Super nice to see that kind of amazing performance from 8600 with ZT Scan! Close to 6k proteins @ 200 SPD with CV < 20% at 50ng of K562 (not HeLa!) - just wow. And this seems to be Evosep One, not Eno. Btw, even lib-free (!) with 5ng@500 SPD works pretty well with DIA-NN 2.2.
June 2, 2025 at 1:49 PM
Super nice to see that kind of amazing performance from 8600 with ZT Scan! Close to 6k proteins @ 200 SPD with CV < 20% at 50ng of K562 (not HeLa!) - just wow. And this seems to be Evosep One, not Eno. Btw, even lib-free (!) with 5ng@500 SPD works pretty well with DIA-NN 2.2.
This is an interesting paper. The connection between splicing and R-loop formation (or lack of formation) is really fascinating.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
SF3B1-targeted Splicing Inhibition Triggers Transcriptional Stress Response and Global Alterations in R-Loop Landscape
Efficient co-transcriptional splicing is thought to suppress genome-destabilizing R-loops. Inhibition of SF3B1, a core U2 spliceosome component, by Pladienolide B (PladB) in human K562 cells caused wi...
www.biorxiv.org
May 13, 2025 at 2:57 PM
This is an interesting paper. The connection between splicing and R-loop formation (or lack of formation) is really fascinating.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
K562 digest curve on the Astral with @ionopticks.bsky.social column, no trap. 25pg to 5000pg on column. DIA RAW files are on Dropbox here: www.dropbox.com/scl/fo/9kont...
If you download and process please share results on this thread. I'll dig ours out and post those also.
#Proteomics
If you download and process please share results on this thread. I'll dig ours out and post those also.
#Proteomics
Dropbox
www.dropbox.com
December 14, 2024 at 7:43 PM
K562 digest curve on the Astral with @ionopticks.bsky.social column, no trap. 25pg to 5000pg on column. DIA RAW files are on Dropbox here: www.dropbox.com/scl/fo/9kont...
If you download and process please share results on this thread. I'll dig ours out and post those also.
#Proteomics
If you download and process please share results on this thread. I'll dig ours out and post those also.
#Proteomics
In a wonderful collaboration with @marsonlab.bsky.social our postdoc @minetoota.bsky.social realized that he could use the K562 data to model red blood cell traits measured by UK Biobank, including hemoglobin.
Could we use this as a proof-of-principle to measure gene effects flowing through GRNs?
Could we use this as a proof-of-principle to measure gene effects flowing through GRNs?
December 11, 2025 at 5:54 PM
In a wonderful collaboration with @marsonlab.bsky.social our postdoc @minetoota.bsky.social realized that he could use the K562 data to model red blood cell traits measured by UK Biobank, including hemoglobin.
Could we use this as a proof-of-principle to measure gene effects flowing through GRNs?
Could we use this as a proof-of-principle to measure gene effects flowing through GRNs?
#OTD 1946 the Bell 47 became the first helicopter ever to be civil certified. This quaint 1977 film shows how Bell got there. www.youtube.com/watch?v=k562...
Birth of the Bell Helicopter.mpg
YouTube video by Paul Faltyn
www.youtube.com
March 8, 2026 at 9:08 PM
#OTD 1946 the Bell 47 became the first helicopter ever to be civil certified. This quaint 1977 film shows how Bell got there. www.youtube.com/watch?v=k562...
Shin et al 2026. CTCF demarcates H3K9me2 or H3K9me3 chromatin domains and restricts the spreading of these modifications faseb.onlinelibrary.wiley.com/doi/abs/10.1...
▶️Related to our previous paper which showed that CTCF forms boundaries of H3K9me2/H3K9me3 nanodomains www.nature.com/articles/s41...
▶️Related to our previous paper which showed that CTCF forms boundaries of H3K9me2/H3K9me3 nanodomains www.nature.com/articles/s41...
CTCF‐Binding Sites Demarcate Chromatin Domains Enriched With Histone H3K9me2 or H3K9me3 and Restrict the Spreading of These Modifications in Human Cells
To investigate the role of CTCF in chromatin domains enriched with histone H3K9me2 or H3K9me3, we analyzed the distribution of these modifications around CTCF-binding sites in human K562 cells. Genom...
faseb.onlinelibrary.wiley.com
January 7, 2026 at 11:31 PM
Shin et al 2026. CTCF demarcates H3K9me2 or H3K9me3 chromatin domains and restricts the spreading of these modifications faseb.onlinelibrary.wiley.com/doi/abs/10.1...
▶️Related to our previous paper which showed that CTCF forms boundaries of H3K9me2/H3K9me3 nanodomains www.nature.com/articles/s41...
▶️Related to our previous paper which showed that CTCF forms boundaries of H3K9me2/H3K9me3 nanodomains www.nature.com/articles/s41...
In this case it's simple: it's predicting the creation of a weak GATA1::TAL1 motif. If the model came from K562 it's not surprising given the prevalence of this motif in that cell type.
February 13, 2025 at 3:20 AM
In this case it's simple: it's predicting the creation of a weak GATA1::TAL1 motif. If the model came from K562 it's not surprising given the prevalence of this motif in that cell type.
ENCODE GRAMMAR is now on the UCSC Genome Browser! 🧬 Base-resolution deep learning predictions, sequence contribution scores & motif instances (BPNet, ChromBPNet, ProCapNet, ReporterNet) across thousands of ENCODE experiments. Explore on hg38: genome.ucsc.edu/s/Lo...
August 17, 2026 at 9:31 PM
ENCODE GRAMMAR is now on the UCSC Genome Browser! 🧬 Base-resolution deep learning predictions, sequence contribution scores & motif instances (BPNet, ChromBPNet, ProCapNet, ReporterNet) across thousands of ENCODE experiments. Explore on hg38: genome.ucsc.edu/s/Lo...
…and we don’t have this matrix at good completeness & precision, despite many efforts (including our own 👇). Hopefully we will in not too distant future, but given the difficulty of this task, I’m not holding my breath regarding virtual cells. pubmed.ncbi.nlm.nih.gov/41173850/
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells - PubMed
Inference of directed biological networks is an important but notoriously challenging problem. The recent proliferation of large-scale CRISPR perturbation data provides a new opportunity to tackle this problem by leveraging the transcriptional response to the presence of a gene-targeting guide. Here …
pubmed.ncbi.nlm.nih.gov
December 27, 2025 at 4:58 PM
…and we don’t have this matrix at good completeness & precision, despite many efforts (including our own 👇). Hopefully we will in not too distant future, but given the difficulty of this task, I’m not holding my breath regarding virtual cells. pubmed.ncbi.nlm.nih.gov/41173850/
Curious about artificial deamidation? Check out our updated preprint! tinyurl.com/ms6fz3sn
Now with PBS as a 6th buffer + new K562 data + N-terminal Q -> pyro-Glu investigations.
Take home message: Zwitterionic buffers like HEPES minimize unwanted artifacts!
@riley-research.bsky.social
Now with PBS as a 6th buffer + new K562 data + N-terminal Q -> pyro-Glu investigations.
Take home message: Zwitterionic buffers like HEPES minimize unwanted artifacts!
@riley-research.bsky.social
December 20, 2024 at 2:59 PM
Curious about artificial deamidation? Check out our updated preprint! tinyurl.com/ms6fz3sn
Now with PBS as a 6th buffer + new K562 data + N-terminal Q -> pyro-Glu investigations.
Take home message: Zwitterionic buffers like HEPES minimize unwanted artifacts!
@riley-research.bsky.social
Now with PBS as a 6th buffer + new K562 data + N-terminal Q -> pyro-Glu investigations.
Take home message: Zwitterionic buffers like HEPES minimize unwanted artifacts!
@riley-research.bsky.social