title: scRNA-seq analysis of mouse utricular sensory epithelium at embryonic day 14 and postnatal day 2

summary: To determine the BMP4 expression levels during inner ear development, we performed a single-cell RNA sequencing (scRNA-seq) analysis of mouse utricular sensory epithelium at embryonic day 14 (E14) and postnatal day 2 (P2).

overall_design: Utricles were harvested from E14 and P2 mice, followed by the careful mechanical removal of the otolithic membranes. Subsequently, the tissues were incubated with thermolysin to facilitate the detachment of the sensory epithelium.


title: RNA-seq Analysis of Wild-Type and Dcaf8 Knockout LT-HSCs in Mice

status: Public on Oct 04 2025

city: Shanghai

first: Pengfei

last: Xu

address: Ruijin Rd. II

country: China

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

type: Expression profiling by high throughput sequencing

summary: Hematopoietic stem cell aging leads to dysfunction of hematopoietic and immune systems, which in return contribute to organismal aging and the development of aging-related diseases. Understanding the molecular mechanisms of HSC aging is critical for developing interventions to treat and prevent aging-related diseases. Here, we show that DCAF8, a substrate receptor of E3 ubiquitin ligases, is highly expressed in HSCs and undergoes a progressive decline with age. Loss of DCAF8 in mice results in aging-like phenotype in HSCs, characterized by increased number of HSCs, decreased self-renewal capacity, cellular senescence and elevated DNA damage. Mechanistically, DCAF8 mediates the degradation of DOCK11, a guanine nucleotide exchange factor for CDC42. In the absence of DCAF8, DOCK11 accumulates, leading to elevated CDC42 activity and consequential loss of polarity of HSCs. Knocking out of Dock11 mitigates the senescence, DNA damage, and self-renewal defects of Dcaf8-/- HSCs. This study highlights a critical role of DCAF8 in regulating HSC aging via the DOCK11-CDC42 axis and suggests potential therapeutic targets for preventing the age-related decline in HSC functions.

overall_design: To explore the mechanisms by which Dcaf8 knockout leads to functional defects in HSCs, we performed RNA-sequencing on LT-HSCs sorted from 3 Dcaf8 knockout mice and 3 WT controls at young ages.

first: Xiuli

last: Zhang

first: Donghe

last: Li

first: Ruibao

last: Ren

first: Ping

last: Liu


title: The chromatin remodeler CHD1L controls human cortical neurogenesis  and contributes to distal 1q21.1 deletion/duplication syndrome [CUT&RUN]

status: Public on Sep 25 2025

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Background/objectives: Deletions and duplications of the distal 1q21.1 region are associated with syndromic forms of autism (MIM612474, 612475). Variable phenotypes have been reported, including congenital heart defects, autism, schizophrenia, head circumference and height defects. Methods: To elucidate which gene(s) are responsible for the 1q21.1 duplication/deletion- associated phenotypes, we performed gene manipulation in zebrafish and mice. We deciphered the function of candidate driver(s) by multi-omics approaches on human iPSC- derived neural progenitor cells (NPC) and cerebral organoids (CO). Results: We modeled duplication of the 1q21.1 region by overexpressing the 8 genes in the region in zebrafish. We found that only overexpression of CHD1L led to macrocephaly and increased larval body length. Conversely, deletion of the CHD1L zebrafish ortholog resulted in microcephaly and decreased larval body length. These mirror phenotypes are also observed when Chd1l expression is modulated in a mammalian model, notably with a variation in the number of mature Tbr1-positive neurons in the mouse embryo. NPCs derived from control and CHD1L Knock-out isogenic hiPSCs were subjected to transcriptomic and chromatin accessibility analyses. These approaches revealed that CHD1L regulates the expression levels and accessibility of genes involved in neuronal differentiation and synaptogenesis, including autism susceptibility genes such as UNC5D and DPP6. Strikingly, absence of CHD1L shifts the cellular identity from forebrain to retinal fate in CO. Finally, pathogenic missense and truncating variants of CHD1L were found in individuals with autism and/or height defects. Conclusion: CHD1L is a major contributor of the 1q21.1 duplication/deletion-associated microcephaly and growth defects. CHD1L dosage is required during human brain regionalization.

overall_design: Human Neural Progenictor Cells derived from hiPSC were subjected to CUT&RUN analysis targeting the proteins CHD1L and H3K4me2.

first: Marianne

last: Lemée

last: Ye

first: Christelle

last: Golzio


title: The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome [RNA-seq]

overall_design: Human Neural Progenictor Cells derived from hiPSC controls and mutant for the gene CHD1L were subjected to ATAC-seq analysis, includes fours replicates per cell line (one control and 2 isogenic mutants).

first: Maria-Nicla

last: Loviglio

first: Céline

last: Keime


title: Peanut Allergy Oral Immunotherapy Drives Single-Cell Multi-omic Changes in Peanut-reactive T cells Associated with Sustained Unresponsiveness

city: Palo Alto

first: Xiaorui

last: Han

state: CA

address: 240 Pasteur Dr. BMI

country: USA

institute: Stanford University School of Medicine

summary: Oral immunotherapy (OIT) is the only FDA-approved treatment for peanut allergy (PA). Peanut-reactive (pr) CD4+ T cells are pivotal in PA pathogenesis as well as OIT-induced desensitization (DS). However, the underlying pr CD4+ T cell immune mechanisms leading to sustained unresponsiveness (SU) after OIT discontinuation remain largely unknown. We analyzed single-cell RNA and protein immunophenotypes and TCR repertoires of pr CD4+ T cells from a phase 2 peanut OIT trial cohort. We identify increased cytotoxicity-related phenotypes and Th1 CTL (cytotoxic T lymphocytes)-like cell clonal expansion during OIT in pr T effector memory cells, while Th2-related phenotypes and Th2a-like cell clonal expansion decreased. OIT participants who achieved SU had lower baseline Th2-related phenotypes, elevated cytotoxicity-related gene signatures in pr Teff cells post-OIT and higher CD39 expression in pr Tregs (T regulatory cells) after OIT withdrawal. These findings clarify OIT-induced CD4+ T cell tolerance mechanisms and can guide effective allergen-specific OIT strategies.

overall_design: To comprehensively characterize the heterogeneous pr CD4+ T cell, including pr Teff CD4+ T cells (CD4+CD154+) and pr Treg CD4+ T cells (CD4+CD137+CD154-), and their longitudinal responses in OIT, we used peripheral blood mononuclear cells (PBMC) from 31 POISED (Our phase 2 randomized, controlled peanut OIT trial: Peanut Oral Immunotherapy: Safety, Efficacy, Discovery; NCT 02103270) participants: 23 active participants who underwent OIT and passed DBPCFC at week 104 (14 peanut-0 participants, of whom 7 passed (SU) and 7 failed (DS) at week 117, and 9 peanut-300 participants, of whom 5 passed and 4 failed DBPCFC at week 117); 8 placebo participants; and 5 age- and gender-matched non-peanut allergic controls. We stimulated PBMCs with peanut solution for 18 hours, and sorted pr CD4+ T cells (CD4+CD137+ and/or CD4+CD154+) and non-reactive (nr) CD4+ T cells (CD4+CD154-CD137-). Sorted cells were processed using the BD Rhapsody™ platform for single cell RNA-sequencing (scRNA-seq) with a focus on 432 immune-relevant target transcripts (399 commercially pre-defined target panel complemented with 33 targets of interest), and 42 immune-relevant Ab-seq markers for protein level detection as well as single-cell paired TCRαβ sequencing.

first: Xuhuai

last: Ji

first: Kari

middle: C

last: Nadeau


title: The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome [scMultiome]

overall_design: 60 days in vitro-old cerebral organoïds derived from hiPSC control or isogenic mutant for the gene CHD1L were subjected to single-nucléi 10X multiome analysis (10X Genomics) for Gene expression and ATAC-seq analysis.


title: The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome.

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Reprogramming SREBP1-dependent lipogenesis and inflammation in high-risk breast with licochalcone A: a novel path to cancer prevention

status: Public on Sep 24 2025

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

summary: Anti-estrogens have had a limited impact on breast cancer (BC) prevention. Novel agents with better tolerability, and efficacy beyond estrogen receptor (ER) positive BC are needed. We studied licochalcone A (LicA) for ER-agnostic BC prevention. We demonstrated that LicA significantly reduced proliferation in seven human breast cell lines and suppressed ER+ and ER- xenograft tumors in mice. We confirmed these observations ex vivo in contralateral unaffected breast (CUB) of women with unilateral sporadic BC, and breast cancer cell lines using RNA sequencing, metabolism flux modeling, confirmatory NanoString metabolic pathway panel analysis in independent sets of specimens, proteomics, and western blots. We found that LicA targets sterol regulatory element binding protein 1 (SREBP1) with subsequent metabolic-inflammatory changes, lowering spatiotemporally resolved cholesterol levels inside malignant cells to the levels in normal mammary cells. Mechanistically, in CUBs we observed that LicA downregulated PI3K-AKT-SREBP1-dependent lipogenesis, NF-kB-dependent inflammation, and de novo nucleotide biosynthesis, stalling proliferation. Studies in cell lines showed suppression of PI3K and AKT phosphorylation, SREBP1 protein expression, and the SREBP1-dependent enzymes such as ACAT2, ACLY, FASN, SCD, consistent with reduced NEDD8 required for SREBP1 stabilization. We found significant reduction in NF-kB expression, its nuclear translocation mediator karyopherin β1, and prostaglandin E2 synthesis. We demonstrated a reduction in PRPS1-catalyzed de novo nucleotide biosynthesis, and downregulation of proliferative markers MKI67, RRM2, and the survival marker BCL2.  LicA reduces pro-tumorigenic aberrations in lipid homeostasis and inflammation through SREBP1. It is a promising non-endocrine candidate for BC prevention. Future studies in immunocompetent BC prevention models are warranted.

overall_design: Surgical tissues of the contralateral unaffected breast of women with unilateral breast cancer was processed to microstructures and treated with LicA (5 uM) or DMSO for 24 h. RNA was extracted. It was quantified by Qubit and qualified by Bioanalyzer, prior to library preparation and RNa sequencing.

first: Atieh

last: Hajirahimkhan

middle: T

first: Carolina

middle: H

last: Chung

first: Xingyu

last: Guo

first: Kyli

last: Berkley

first: Raymond

last: Moellering

first: Oukseub

last: Lee

first: Ruohui

last: Chen

first: Wonhwa

last: Cho

first: Sriram

last: Chandrasekaran

first: Susan

middle: E

last: Clare

first: Seema

middle: A

last: Khan


title: Kdm6b-mediated epigenetic coordination of temporal precision during motor neuron differentiation [RNA-seq]

city: hefei

first: wenxian

last: wang

address: No. 81, Meishan Road, Shushan District, Hefei City, Anhui Province

institute: Anhui Medical University

summary: Histone modifiers are crucial for instructing multiple-stage cellular differentiation, yet the mechanisms underlying their temporal precision remain enigmatic. Here, we demonstrate that the H3K27 demethylase Kdm6b acts as an epigenetic regulator, coordinating stepwise motor neuron (MN) differentiation through sequential partnerships with stage-specific transcription factors (TFs). Genome-wide profiling reveals a progressive gain in Kdm6b occupancy, especially at distal regulatory elements, as differentiation proceeds. Kdm6b dynamically shapes chromatin landscapes by coordinating H3K27me3 removal with H3K27ac and H3K4me1 acquisition, thereby enabling timed gene activation from MN specification to maturation. Stage-specific inhibition of Kdm6b compromised the ordered expression of developmental genes. Mechanistically, Kdm6b interacts with temporal TFs over time to ensure precise transcriptional control and MN differentiation. Our work elucidates how a single epigenetic regulator achieves temporal fidelity in driving stepwise MN development, and exemplifies a mechanistic insight into epigenetic regulation in determining developmental timing, with broad implications for understanding neurodevelopment and related diseases.dynamic epigenetic choreography to precisely regulate MN developmental programs from early MN fate specification, intermediate cell differentiation and growth to later maturation. The ordered expression of developmental genes was compromised by stage-specific Kdm6b inhibition. Our work resolves how a single epigenetic regulator achieves temporal precision in driving stepwise MN development, with broad implications for neurodevelopment and diseases.

overall_design: RNA-seq profiling within in vitro differentiated motor neurons from mouse embryonic stem cells at stages D4, D4H8, D5 and D6.

first: Wenxian

last: Wang

first: Haihan

last: Ren

first: Bing

last: Pan

first: Jun-Ma

last: Yu


title: The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome [ATAC-seq]

first: Tao

last: YE

first: Marianne

last: Lemée

last: Ye

first: Christelle

last: Golzio


title: GCN5-ADA2 Recruits ATP-Citrate Lyase (ACL) and Forms Condensates to Modulate Acetylation at H3K9 for Functional Genes in Rice Meristem

status: Public on Sep 23 2025

city: Wuhan

first: Xiaoyuan

last: Guo

state: Hubei

address: No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: The SAGA complex is a highly conserved histone acetyltransferase (HAT) complex in eukaryotes, playing crucial role in regulating gene transcription throughout organismal development. The complex consists of two core components: GCN5, the HAT subunit, and ADA2, which primarily functions as an adaptor, facilitating interactions between GCN5 and other proteins and enhancing the complex’s accessibility to nucleosomes. Beyond its well-established roles, we discovered that, in rice, ADA2 possesses an evolutionary conserved intrinsically disordered region (IDR) that directs the SAGA complex to form nuclear condensates. Moreover, we identified a physical interaction between ADA2 and ATP-citrate lyase subunit A2 (ACLA2), leading to the formation of a GCN5-ADA2-ACLA2 (GAA) complex. Both GCN5 and ACLA2 exhibit phase separation in vivo, a process that is dependent on ADA2. Within these condensates, ACL contributes to the production and enrichment of acetyl-CoA, thereby promoting histone acetylation. Genetic evidence showed that knock-out or suppression of the three indicated genes collectively resulted in diminished meristem zones at both root tips and inflorescences, accompanied by a significant reduction in genomic H3K9 acetylation and transcriptional attenuation of essential genes for meristem function. In summary, our findings unveiled a novel mechanism for HAT in modulating gene transcription and plant development, in which the GAA complex phase separates and enriches acetyl-CoA metabolites within the nuclear puncta to facilitate the acetylation of histones at target genes.

overall_design: Transcriptome detection by RNA-seq for rice root tips and inflorescence meristems in wild type and the three indicated mutants/RNAi backgrounds. Genomic binding detection for the three components of GAA complex via CUT&Tag. Genomic histone H3 K9 acetylation detection of root tips for wild type and the three indicated mutants/RNAi backgrounds.

first: Tingting

last: Lu

first: Shaoli

last: Zhou


title: Kdm6b-mediated epigenetic coordination of temporal precision during motor neuron differentiation [CutRun_CutTag]

summary: Histone modifiers are crucial for instructing multiple-stage cellular differentiation, yet the mechanisms underlying their temporal precision remain enigmatic. Here, we demonstrate that the H3K27 demethylase Kdm6b acts as an epigenetic regulator, coordinating stepwise motor neuron (MN) differentiation through sequential partnerships with stage-specific transcription factors (TFs). Genome-wide profiling reveals a progressive gain in Kdm6b occupancy, especially at distal regulatory elements, as differentiation proceeds. Kdm6b dynamically shapes chromatin landscapes by coordinating H3K27me3 removal with H3K27ac and H3K4me1 acquisition, thereby enabling timed gene activation from MN specification to maturation. Stage-specific inhibition of Kdm6b compromised the ordered expression of developmental genes. Mechanistically, Kdm6b interacts with temporal TFs over time to ensure precise transcriptional control and MN differentiation. Our work elucidates how a single epigenetic regulator achieves temporal fidelity in driving stepwise MN development, and exemplifies a mechanistic insight into epigenetic regulation in determining developmental timing, with broad implications for understanding neurodevelopment and related diseases.

overall_design: Cut&Run-seq of Kdm6b, Neurod1 and Cux1/2, and Cut&Tag-seq of H3K27me3, H3K27ac, H3K4me1 and H3K4me3 within in vitro differentiated motor neurons from mouse embryonic stem cells at stages D4, D4H8, D5 and D6.

first: Qicheng

last: Liu

first: Bingqian

last: Li


title: PRMT5/WDR77 moonlights as an RNA-binding complex and shapes T cell function and anti-tumor immunity via post-transcriptional regulation of PDCD1

status: Public on Sep 27 2025

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

summary: To reveal the potential RNA targets of PRMT5 in  jurkat cells, we performed Flag Immunoprecipitation sequencing (RIP-seq) in PRMT5-Flag overexpression (OE) jurkat  cells after  stimulated with polyhydroxyalkanoates (PHA) for 48 hours.

overall_design: Jurkat cells lysate was Immunoprecipitation by Flag, then subjected to RNA-sequencing analysis

first: Yinmin

last: Gu


title: Genomic and Epigenomic Coordination Maintains  Subgenome Transcriptional Balance in Allotetraploid Brassica napus [WGBS]

status: Public on Sep 22 2025

first: Jie

address: 1 Lion Rock Street

type: Methylation profiling by high throughput sequencing

summary: Allopolyploidization-induced "genome shock" poses severe challenges to subgenome stability. However, the mechanisms by which subgenomes achieve functional homeostasis through genomic and epigenomic regulation remain poorly understood. This study integrates multi-omics data from Brassica napus and its putative diploid progenitors to reveal that coordinated convergence of genomic and epigenomic plays a central role in maintaining subgenome functional homeostasis within allopolyploids. Here, we present the first comprehensive, high-quality epigenomic maps to date for the diploid Brassica rapa and Brassica oleracea. Comparative genomic analyses revealed that epigenomic reprogramming in A and C subgenomes of the allotetraploid drives convergent chromatin states, which substantially diminished expression divergence between homoeologous gene pairs. Notably, compared to the A subgenome, the C subgenome in the allotetraploid exhibits more pronounced sequence conservation of regulatory elements and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) influenced by genomic variation in the A subgenome demonstrate convergent evolutionary patterns toward the C subgenome. This study provides novel insights into the coordinated convergence of genomic and epigenomic regulation between subgenomes in allotetraploid Brassica napus, demonstrating that allopolyploids resolve subgenomic conflicts through multi-layered regulatory networks. These findings establish a novel paradigm for elucidating the molecular basis of polyploidy advantages in crops and for enabling rational design of synthetic polyploids.

sample_organism:
Brassica napus
Brassica rapa
Brassica oleracea

overall_design: Whole-genome bisulfite sequencing (WGBS) for young leaves of B. rapa and B. oleracea.


title: Kdm6b-mediated epigenetic coordination of temporal precision during motor neuron differentiation

summary:
This SuperSeries is composed of the SubSeries listed below.
GSE305831 and GSE305767.


title: Genomic and Epigenomic Coordination Maintains  Subgenome Transcriptional Balance in Allotetraploid Brassica napus [ATAC-seq]

platform_organism:
Brassica napus
Brassica rapa
Brassica oleracea

overall_design: Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) for young leaves of B. rapa and B. oleracea.


title: Broad H3K4me3 domains support oocyte genome silencing and maturation but are dispensable for repression in early embryos

status: Public on Oct 01 2025

city: Oslo

first: Gareth

last: Greggains

address: Boks 1072 Blindern

country: Norway

institute: University of Oslo (UiO)

summary: To investigate whether demethylation of broad histone H3 lysine 4 trimethyl (H3K4me3) domains is sufficient to trigger premature embryonic genome activation (EGA), we overexpressed the H3K4me3 demethylase KDM5B in mouse zygotes and early 2-cell (2C) embryos via mRNA injection. We performed single-cell RNA sequencing (scRNA-seq) using the SMART-Seq Stranded Kit (Takara Bio) on individual Kdm5b-yfp–injected and water-injected control zygotes and 2C embryos. Differential expression analysis revealed minimal transcriptional changes, and developmental stage, rather than KDM5B overexpression, accounted for most gene expression variance. Our findings demonstrate that wide-scale removal of H3K4me3 in zygotes or early 2C embryos is not sufficient to induce premature EGA, suggesting that genome silencing at these stages does not depend on broad H3K4me3 domains.

overall_design: S-phase zygotes or both blastomeres of G1-phase 2C embryos were microinjected with Kdm5b-yfp mRNA; water-injected zygotes or 2C embryos served as controls. The C-terminal YFP tag enabled live-cell confirmation of KDM5B expression. Samples were collected for scRNA-seq ~5–6 h post-injection (late zygotes: 17 h after ovulation, corresponding to late S/G2 phase; early 2C embryos: 5.5–8 h after division, corresponding to late S phase). During collection, 10 single zygotes from each group (Kdm5b-yfp-injected and control) were transferred into separate tubes. For 2C embryos, we included both single intact embryos and pooled blastomeres from partially lysed embryos to maximise sample use (lysed blastomeres were excluded during zona pellucida removal). In the control 2C group, 9 samples were collected: 6 single embryos with both blastomeres intact, one pool of two embryos with only one blastomere intact, and two pools of three such embryos. In the Kdm5b 2C group, 6 samples were collected: 5 single embryos with both blastomeres intact, and one pool of three embryos with only one blastomere intact.

first: Trine

last: Skuland

first: Madeleine

last: Fosslie

first: Sherif

last: Khodeer

first: Endalkachew

last: Ashenafi Alemu

first: Jens

last: Vilstrup Johansen

first: Yanjiao

first: Mads

last: Lerdrup

first: John Arne

last: Dahl

middle: D


title: Genomic and Epigenomic Coordination Maintains  Subgenome Transcriptional Balance in Allotetraploid Brassica napus


title: Genomic and Epigenomic Coordination Maintains Subgenome Transcriptional Balance in Allotetraploid Brassica napus [ChIP-seq]

overall_design: Chromatin Immunoprecipitation followed by seqencing (ChIP-seq) for histone modifications (H3K4me3, H3K4me1, H3K27me3 and H3K9me2) in young leaves of B. rapa and B. oleracea.


title: Resilience to Endoplasmic Reticulum Stress Mitigates Calcium-Dependent Membrane Hyperexcitability Underlying Late Disease Onset in Spinocerebellar Ataxia Type 6

city: Dallas

first: Jane

last: Johnson

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

summary: An enduring puzzle in many inherited neurological disorders is the late onset of symptoms despite expression of function-impairing mutant protein early in life. We examined the basis for onset of impairment in Spinocerebellar ataxia type 6 (SCA6), a polyglutamine ataxia with late-onset cerebellar neurodegeneration. In a mouse model of SCA6, we identified a homeostatic response that engages the unfolded protein response early in disease. This protective response provided insight into endoplasmic reticulum (ER) stress-mediated cerebellar Purkinje neuron membrane hyperexcitability as a driver of disease. Age-dependent impairment of chaperone-mediated compensation for ER stress increased calcium-dependent Purkinje neuron membrane excitability. Redundant pathways of the unfolded protein response mediate this resilience to ER stress. ER stress-related decompensation applies also to other late-onset human cerebellar ataxia. These studies elucidate a mechanism of resilience connecting aberrant proteostasis and calcium-dependent intrinsic membrane hyperexcitability to explain delayed disease onset more widely in age-dependent neurodegenerative disease.

overall_design: mRNA sequencing was performed on a NovaSeq instrument (Illumina, Inc.) with ~155 million reads and 150 bp paired-end reads. 5 cerebellum samples from each genotype from each age were used. Samples were prepared individually and pooled together to reduce batch effects. The samples were then demultiplexed into fastq files and statistics were collected using FastQC (Babraham Bioinformatics). The fastq files were trimmed using Trimmomatic (Bolger et al., 2014). 150 bp reads were aligned using STAR (Dobin et al., 2013), and the percent of unique reads were calculated. Raw read counts per gene per sample were calculated using HTSeq (Anders et al., 2015). Outliers were removed based on principal component analysis and hierarchical clustering. Differential gene expression analysis was performed using DESeq2 (Love et al., 2014).

first: Vikram

last: Shakkottai


title: Genomic and Epigenomic Coordination Maintains  Subgenome Transcriptional Balance in Allotetraploid Brassica napus [RNA-seq]

overall_design: RNA-seq for young leaves of B. rapa and B. oleracea.


title: Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections [RNA-Seq 1]

status: Public on Sep 19 2025

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

institute: CIML

summary: Plasmacytoid dendritic cells (pDCs) are major producers of type I/III interferons. Since these cytokines are crucial for antiviral defense, it is assumed to be also the case for pDCs. However, robust evidence supporting this dogma is scarce. Genetic mutations or pharmacological manipulations causing pDC loss or disrupting their interferon production affect other immune cells, which could confound interpretation. To overcome this bottleneck, we engineered pDC-less mice, specifically and constitutively devoid of pDCs because expressing diphteria toxin under coordinated control by the Siglech and Pacsin1 genes co-expressed only in pDCs. pDC-less mice mounted protective intrinsic and innate immune responses against systemic infection with mouse cytomegalovirus, and were more resistant to intranasal infection with influenza virus and SARS-CoV2. Thus, contrary to dogma, pDCs and their interferon production proved dispensable or deleterious during systemic or respiratory viral infections. pDC-less mice will enable rigorously revisiting the roles of pDCs in health and disease.

overall_design: Lungs were isolated from K18-hACE mice unifected (D0) or at day 1 (D1), day 2 (D2), day 4 5D4) or 6 (D6) after intranasal SARS-CoV2 infection. RNA extracted from lungs was used to prepare libraries for RNA-seq. 3 replicates at D0 and D1, 5 at D2 and  D4 and 2 at D6.

first: Clemence

last: Ngo

first: Khalissa

last: Rahmani

first: Michael

last: Valente

first: Marc

last: Dalod

first: Elena

last: Tomasello


title: Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo IV

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

summary: The colorectal epithelium is a rapidly renewing tissue, with a remarkable capacity to regenerate following injury. In colorectal cancer (CRC), this regenerative capacity can be co-opted to drive epithelial plasticity. Activation of oncogenic MAPK signalling in CRC is common, with mutations frequently found in both KRAS (40-50%) and BRAF (10%), alongside other mechanisms of EGFR pathway upregulation. Nonetheless, inhibition of this pathway is often linked to rapid therapeutic resistance in patients. Given the recent development of KRAS inhibitors and the licensing of BRAF+EGFR inhibitor combinations we have investigated mechanisms of resistance to these agents in complex mouse models of CRC. Here we show that MAPK signalling supports the regenerative/revival stem cell phenotype in vivo, while its inhibition leads to rapid remodelling of both Kras and Braf mutant mouse models to a high Wnt activity canonical stem cell phenotype marked by expression of Lgr5. This results in acute therapeutic resistance in Kras driven, and delayed resistance in Braf driven models. Importantly, where therapeutic MAPK targeting is applied in the presence of a single regenerative epithelial population, such as early metastatic disease, or where plasticity is restrained, for example through Wnt pathway restriction, a marked impact on tumourigenesis is observed. Modelling of an BRAF and RNF43-mutant patient population, clinically super-responders to BRAF/EGFR inhibitor therapy, demonstrates excellent response to therapy due to restricted epithelial plasticity, highlighting the criticality of cellular plasticity in therapeutic response. Together, our data provide clear insight into the mechanisms underpinning resistance to targeting oncogenic MAPK signalling in CRC. Moreover, we demonstrate that strategies that aim to restrict epithelial plasticity or corral into or intervene when tumours are in a regenerative cell fate may improve efficacy of MAPK targeting agents in CRC.

overall_design: Following treatment with either EGFR inhibitor or vehicle control, mouse colonic tumours with loss of Apc were sequenced by Gem-X flex single cell sequencing.

first: Mark

last: White

first: Megan

last: Mills

first: Laura

last: Millett

first: Owen

last: Sansom


title: Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo II

overall_design: Mice were induced with a single 70uL injection of 100uM 4-OH tamoxifen into the colonic submucosa. When an established tumour was identified on colonoscope (beginning weekly two weeks post injection), mice were placed on a treatment regime. Mice were treated once  daily with AZD4625 (OG 100uL 100mg/kg) or vehicle (0.5% HPMC 0.1% Tween 80) for 4 days and sampled two hours post dose on the fourth day.


title: Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo III

overall_design: Organoids derived from either small intestinal tumours or liver metastasis, from mice with mutations in either Kras/P53/Notch1 or Apc/Kras/P53/Tgfbr1, were sequenced using Gem-X flex single cell technology.


title: Transcriptomic changes in response to inducible CTNNB1 activation in murine B-ALL cells

city: New Haven

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

summary: As part of canonical WNT signaling, TCF7/β-catenin-complexes promote MYC-dependent proliferation. Compared to solid tumors, we found that B-cell acute lymphoblastic leukemia (B-ALL) cells, express β-catenin protein at 80- to 200-fold lower levels and critically depend on its efficient degradation: β-catenin protein was constitutively phosphorylated by GSK3B and poised for proteasomal degradation. Lesions of the β-catenin-protein degradation machinery are common oncogenic drivers, however, B-ALL cells lacked these mutations and critically depend on unencumbered β-catenin-protein degradation. Instead of TCF7/β-catenin-complexes to activate MYC, β-catenin paired with B-lymphoid Ikaros factors, resulting in MYC-repression and acute cell death. To leverage β-catenin-protein degradation as previously unrecognized vulnerability in B-ALL, we validated GSK3B-inhibition in patient-derived xenograft models in vivo. CRISPR/Cas9 chemogenomic screens confirmed β-catenin protein degradation as central mechanistic target of established GSK3B-inhibitors. Based on favorable safety profiles in clinical trials, our results provide a rationale for repurposing existing GSK3B-inhibitors for patients with refractory B-cell malignancies.

overall_design: RNAseq in BCR-ABL1+ transformed murine pre-B with or without induction of beta-catenin activation using a CTNNB1 exon3 floxed model

first: Kadriye Nehir

last: Cosgun

first: Markus

last: Muschen


title: PRDM16 Regulates Prostate Cancer Cell Dormancy and Prevents Bone Metastatic Outgrowth

status: Public on Sep 17 2025

city: Tampa

first: Conor

last: Lynch

state: Florida

address: 12902 USF Magnolia Drive

institute: H.Lee MOFFITT Cancer Center

summary: Understanding dormancy in prostate cancer (PCa) is challenging due to model availability. Here, using murine and human PCa cell lines, we generated a stress-induced model of dormancy in vitro and demonstrated that the phenotype could be sustained upon intrailiac artery delivery into the bone marrow microenvironment. RNA-Seq analysis revealed that the transcription factor PR domain containing 16 (PRDM16) was commonly upregulated in dormant PCa cells compared to controls. Further, bone marrow disseminated tumor PCa cells from primary orthotopic tumors were largely positive for PRDM16. Genetic ablation and forced ectopic expression supported a role for PRDM16 in maintaining PCa dormancy in vitro and in vivo. Clinically, PRDM16 negatively correlated with disease recurrence, and PRDM16 negatively correlated with the E2F cell cycle program in disseminated tumor cells derived from PCa patient bone marrow. Gene enrichment and characterization studies implicated PRDM16 as a regulator of metabolic and cell cycle pathways. ChIP-qPCR further revealed that PRDM16 binds upstream of the promoter of RB1, a potent repressor of E2F activity. Overall, this study developed a straightforward method for inducing cancer cell dormancy and applied this approach to find that PRDM16 governs an intrinsic dormancy program in PCa.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNASeq analysis of different PCa cell lines in active, dormant, and reawakened conditions after short in vitro culture 48 hours in dormancy and 24 hours in reawakened conditions.

first: Mostafa

middle: M

last: Nasr


title: Global transcriptome analysis of early and terminal erythropoiesis in newly diagnosed with multiple myeloma patients associated anemia

status: Public on Sep 18 2025

city: Zhengzhou

first: Shihui

last: Wang

state: Henan

address: No. 7 Weiwu Road, Zhengzhou, Henan, China

department: Institute of Hematology

institute: Henan Provincial People’s Hospital

summary: In NDMM anemia patients, erythroid progenitors show downregulation of growth factor response pathways (e.g., SPHK1), while terminal erythroblasts have upregulation of mitochondrial oxidative phosphorylation and p53-related genes, with increased cellular ROS levels. Mechanistically, genes like COX6C, UQCRB, UQCRH, PMAIP1, and MYCT1 are up-regulated in terminal erythroblasts.

overall_design: RNA was extracted from sorted BM erythroid progenitors and terminal erythroblasts, followed by Illumina NovaSeq 6000 sequencing. After quality control, reads were aligned to hg38 using kallisto, with differential expression analysis performed by DESeq2. PCA and GO enrichment analyses were conducted.

first: Huizhi

last: Zhao


title: Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo

overall_design: Following treatment with either vehicle or a combination of Braf and EGFR inhibition, tumours in mice with mutations in Braf, P53 and Rnf43 were sequenced by Gem-X flex single cell sequencing after 1 or 3 days.


title: Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections [RNA-Seq 2]

first: Bertrand

last: Escaliere

overall_design: Lungs were isolated from control and pDC-less mice unifected (D0) or at day 3 (D3) or 6 (D6) after intranasal IAV infection. RNA extracted from lungs was used to prepare libraries for RNA-seq. For each mouse strain 3 replicates at D0, 4 at D3 and D6.

last: Ngo


title: Extensive Crosstalk between BMP and Notch Signaling Pathways in Activated Adult Muscle Stem Cells [RNA-seq II]

city: Berlin

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

summary: Muscle stem cells (MuSC) are the cellular source for generation and regeneration of skeletal muscle. To ensure correct muscle growth, MuSC self-renewal and differentiation need to be tightly regulated. Several signaling systems have been implicated in the control of MuSCs, among them Bone Morphogenetic Proteins (BMPs) and Notch, both of which promote MuSC proliferation and suppress differentiation. To better understand the mechanisms of function and the target genes regulated by BMP signaling in myogenesis, we investigated the transcriptional responses of adult mouse MuSCs to BMP6/4 using RNA-sequencing. BMP6/4-stimulation of freshly isolated MuSCs for one hour rapidly increased the expression of classical BMP target genes like Id1 and strongly induced expression of genes of the Notch pathway (Hes1, Hey1, Lfng, Snai1). In parallel, using Cleavage Under Targets and Tagmentation (CUT&Tag), we generated whole-genome binding profiles for the BMP pathway effectors pSMAD1/5/9 and SMAD4 and detected binding in promoters and potential regulatory elements of BMP targets and Notch pathway genes (Hes1, Hey1, Lfng, Snai1) indicating that BMP signaling directly influences Notch and that crosstalk between the two pathways regulates myogenesis.

overall_design:
RNA-seq of BMP6-stimulated and control adult mouse muscle stem cells, two biological replicates

UPDATE: [Mar-06-2026] The Sample titles were updated. The old titles are in the Sample description field.

first: Birthe

middle: K

last: Lange


title: CXCR4-modification boosts CAR-T cell efficacy by improving tumor tracking and bone marrow homing in B cell malignancies [In vivo]

city: chengdu

first: pei

last: shu

address: guoxue lane

institute: west chia hospital, sichuan university

summary: Hematological malignancies of B-cell origin are characterized by frequent expressions of CXCR4 and CXCL12. The CXCR4-CXCL12 axis facilitates the metastasis of B-cell lymphoma and multiple myeloma (MM). It is also a pivotal regulator in the migration and bone marrow homing of T-cells. Herein, we hypothesized that engineering CAR-T cells to overexpress CXCR4 could utilize CXCR4-CXCL12 axis to enhance their therapeutic efficacy by increasing tumor tracking and bone marrow accumulation.

overall_design: In this study, we found that lentiviral transduction caused significant CXCR4 downregulation on T-cells, leading to impaired migration to CXCL12. The CXCR4 receptor-overexpressed (CXCR4hi) CD19 CAR-T and BCMA CAR-T cells showed superior tumor tracking and clearance capacities in localized and systemically disseminated models of B-cell lymphoma and MM, respectively. Notably, CXCR4-modification facilitated homing of CAR-T cells and accumulation in bone marrow, which further promoted memory T-cell differentiation, persistence and prolonged anti-tumor activity. Building on these findings, an investigator-initiated clinical trial (IIT) evaluating CXCR4hi CD19 CAR-T cells in patients with relapsed/refractory B-cell malignancies (NCT04684472) achieved encouraging efficacy: the low-dose cohort yielded 3 complete responses (CR) and 1 partial response (PR) within one-month post-infusion. These findings support CXCR4 modification as a strategy to improve CAR-T cell efficacy in hematologic B-cell malignancies, warranting further clinical investigation.

first: yongsheng

last: wang

first: dan

last: li

first: fuchun

last: guo

first: diyuan

last: qin

first: liqun

last: zou


title: Extensive Crosstalk between BMP and Notch Signaling Pathways in Activated Adult Muscle Stem Cells [CUT&Tag]

overall_design:
CUT&Tag-seq for pSMAD1/5/9, SMAD4, and H3K27ac on BMP6-stimulated and control adult mouse muscle stem cells, two biological replicates

UPDATE: [Mar-06-2026] The Sample titles were updated. The old titles are in the Sample description field.

first: Viktoriia

last: Huryn


title: CXCR4-modification boosts CAR-T cell efficacy by improving tumor tracking and bone marrow homing in B cell malignancies [In vitro]


title: Effect of Fak1/Ptk2 knockout in a mouse model of NF2-related schwannomatosis

city: Indianapolis

first: Steven

middle: P

last: Angus

state: IN

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University School of Medicine

summary: NF2-related schwannomatosis (NF2-SWN) is a cancer predisposition syndrome characterized by the development of bilateral vestibular (VS) and spinal schwannomas. While benign, these tumors can cause significant morbidity and effective pharmacological treatments remain limited. Here we demonstrate that genetic ablation of focal adhesion kinase 1 (FAK1/PTK2) impairs tumor formation and preserves hearing in a murine model of NF2. Mechanistically, we show that Fak1 deletion decreases macrophage infiltration, attenuates NLRP3 inflammasome activation and suppresses the HGF-MET axis. Pharmacological inhibition of FAK with single agent VS-4718 did not significantly reduce macroscopic tumor volume, however, its use in combination with the MEK inhibitor selumetinib resulted in both a significant reduction tumor volume and the preservation of dorsal root ganglion (DRG) architecture. Our findings establish a critical role for FAK in schwannoma development and provide rationale for evaluation of combination FAK plus MEK inhibition in future clinical trials for NF2-associated schwannomas.

overall_design: Dorsal root ganglia (8 per mouse) tissue was microdissected from 10-month old euthanized Postn-Cre(+);Nf2 flox/flox animals (n=6, 3 male, 3 female) and from Postn-Cre(+);Nf2 flox/flox;Fak1 flox/flox (double knockout, DKO) animals(n=6, 3 male, 3 female), flash frozen and sent to Azenta/GenWiz for mRNA sequencing.

first: Dana

last: Mitchell


title: Transcriptome response to FAK1 (PTK2) targeting in a murine Nf2 null schwannoma cell line model

overall_design: An immortalized Schwann cell line derived from the Nf2 flox/flox mouse model was previously infected with Cre to generate the Nf2-/- MS03 cell line. The MS03 cell line was treated with DMSO, 1 micromolar defactinib, 1 micromolar VS4718, 1 micromolar GSK2256098, 1 micromolar IN10018, or the PROTAC FAK degraders: 1 micromolar PROTAC FAK degrader 1 (PROTAC-3, HY-119932), 0.1 micromolar GSK-215, or 0.1 micromolar BSJ-04-146 for 24 hours. Cells were harvested, RNA extracted for RNA sequencing.


title: LKB1 regulates adipose tissue ILC2 function through regulating mitochonrial

city: Shanghai

first: Youqin

last: Zhang

address: No. 280, Chongqing South Road

institute: NewsMORE+  Shanghai Institute of Immunology

summary: Our study represents LKB1 defects lead to the loss and dysfunction of adipose tissue ILC2s.And we found that LKB1 regulate ILC2s homeostasis and cytokines function in a cell-intrinsic manner.In high-diet-fed mice,LKB1 in ILC2s protects against metabolic disturbances and fat fibrosis.LKB1 deficient in ILC2 impaired the oxidative phosphorylation and led to mitochondria loss though more mitophagy.

overall_design: mRNA profiles of VAT ILC2s  from 14-week old wild-type male mice fed with normal diet(ND) or high-fat-diet(HFD) for 8 weeks starting at 6 weeks old

first: Lei

last: Shen

first: Jiping

last: Sun


title: Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo [RNA-Seq]

status: Public on Sep 16 2025

first: Kathryn

last: Gilroy

overall_design: Bulk RNAseq expression data from treated and untreated mouse small intestine and colon tumours, with genetic modifications in combinations of the genes Apc, Kras, Braf, p53, Alk5, Notch1, Bcl9, Bcl9l and Rnf43.

first: Mark

last: White

first: Megan

middle: L

last: Mills

first: Laura

last: Millett

first: Rosalin

last: Simpson

first: Andrew

last: Campbell

first: Owen

middle: J

last: Sansom


title: Effect of latent tuberculosis on individuals compared with healthy controls

city: Karachi

first: Asghar

last: Nasir

state: Sindh

address: Stadium Road

department: Pathology and Laboratory Medicine

country: Pakistan

institute: Aga Khan University

summary: Blood transcriptomes were analyzed in individuals with and without latent tuberculosis infection (LTBI) using the Clariom S RNA microarray assay (Affymetrix).

overall_design: Participants were recruited with and without diabetes and subsequently tested for latent tuberculosis infection (LTBI), resulting in four groups. Blood transcriptomes from all four groups were analyzed using the Clariom S RNA microarray assay (Affymetrix Inc.).

first: Maliha

last: Yameen

first: Kiran

last: Iqbal

first: Javaria

last: Ashraf

first: Zahra

last: Hasan


title: Transposable elements as catalysts of genome evolution in Drosophila virilis

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Transposable elements (TEs) drive genomic innovation, but their dynamics in non-model species remain unclear. Herein, we integrated multiomics data to explore TE dynamics in Drosophila virilis, an important model for repetitive DNA research. By combining computational predictions with manual curation, we identified 100 TE families and delineated three temporal waves of TE mobilisation: recent activity, speciation-associated divergence, and ancient invasions. TEs in D. virilis dynamically colonise euchromatin and heterochromatin, contradicting the idea that heterochromatin is just a passive dump for degenerate repeats. Most TE families are prevalent across all analyzed D. virilis strains, while certain DNA transposons and retroelements exhibit strain-specific expansion, suggesting different TE activity and silencing across populations. Nonetheless, there is substantial evidence for extensive horizontal transfer of TEs among close relatives, demonstrating that the D. virilis species group function effectively as TE “ecosystem”. Epigenetic profiling revealed H3K9me3 spreading from TEs represses adjacent genes in a distance-dependent manner, influenced by insertion length and genomic context, affecting developmental and metabolic genes. We also discovered the first polymorphic inversion in D. virilis, likely linked to retrotransposons. Our findings illuminate TEs as catalysts of genomic innovation, influencing gene regulation and evolutionary trajectories, providing a framework for studying TE dynamics across species.

overall_design: RNA-seq, ChIP-seq and long-read genomic sequences of various strains of Drosophila virilis

first: Sergei

middle: Y

last: Funikov


title: Notch coordinates self-organization of germ layers and axial polarity in cnidarian gastruloids

status: Public on Sep 15 2025

city: Vienna

first: Juan

middle: Daniel

last: Montenegro

state: Vienna

address: Djerassiplatz 1

department: Department of neurobiology and developmental biology

country: Austria

institute: University of Vienna

summary: Dissociation and reaggregation experiments in several animal systems have revealed the stunning capacity of self-organization. Reaggregated early gastrula cells (here called gastruloids) of the sea anemone Nematostella vectensis are able to regenerate with only little delay whole organisms that are virtually indistinguishable from normal developing polyps. However, the molecular control underlying the restoration of body axis and germ layers remains largely unknown. To address this, we established a standardized protocol, which reproducibly generates gastruloids developing into polys with a single body axis. Here, we show that committed mesodermal and endodermal cells are sorted out  to the surface of the aggregate, where  mesodermal cells form clusters of about 30 cells. At a critical time point, one mesodermal cluster immigrates, along with peripherally attached endodermal cells. Thereby, the inner germ layer and the oral-aboral axis is established in one and the same process. Functional studies demonstrated that this polarization of the endodermal cells requires a feedback loop of Notch and Wnt signaling. The dissociation of the early embryo disrupts Notch signaling in the endodermal cells, which leads to transient adoption of an endomesodermal profile, marked by the expression of the mesodermal cadherin1 until the boundaries between the germ layer identities are re-established. Our results highlight distinct morphogenetic behaviors of mesodermal and endodermal cells and the hitherto unknown role of Notch signaling in germ layer boundary formation in self-organizing gastruloids. Conservation of Notch-mediated boundary formation between endoderm and mesoderm mirrors bilaterian mechanisms, demonstrating how adoption of ancestral regulatory networks governing morphogenesis likely enabled the diversification of metazoan body plans.

overall_design: (1) DMSO treated library: Embryos were raised until 24hpf and then treated from 24hpf to 48hpf with 50uM DMSO as control and then samples were collected for sequencing; (2) LY treated library: Embryos were raised until 24hpf and then treated from 24hpf to 48hpf with 50uM LY411575 as treatment and then samples were collected for sequencing; (3) Gastrula.ACME library: Embryos were raised until 24hpf and then samples were collected for sequencing; (4) 4, 12, 24 and 48 hpa Embryos were raised until 24h and then dissociated, reaggregated and allowed to develop until the specified time when samples were collected.

first: Ulrich

last: Technau

first: Narayanaswamy

last: Sanjay

first: Franziska

last: Haas

first: Emmanuel

last: Haillot

first: Elly

last: Tanaka


title: Non-remnant triglyceride-rich lipoproteins due to lipoprotein lipase deficiency increase atherosclerosis in mice

city: New York

first: Ira

last: Goldberg

state: NY

address: 435 E. 30th St, Science Building, 617

department: Division of Endocrinology, Diabetes and Metabolism

institute: New York University Grossman School  of Medicine

summary: Although hypertriglyceridemia and postprandial lipemia associate with greater atherosclerosis, partially metabolized triglyceride-rich lipoproteins termed remnants rather than nascent lipoproteins have been implicated as the culprits. Whether chylomicrons are inherently atherogenic remains unclear. To test whether increased levels of nascent triglyceride-rich lipoproteins (TRLs)  in the absence of markedly reduced LDL-C levels contribute to atherosclerosis, we created mice with induced whole-body lipoprotein lipase (LpL) deficiency combined with LDL receptor (LDLR) deficiency. On an atherogenic Western-type diet (WD), male and female mice with induced global LpL deficiency (iLpl-/-) and LDLR knockdown (Ldlrkd) developed hypertriglyceridemia and elevated cholesterol levels; all the increased cholesterol was in chylomicrons or large VLDL. After 12 weeks on a WD, atherosclerotic lesions both in the brachiocephalic artery and the aortic root were more severe in iLpl-/-/Ldlrkd mice than control Ldlrkd mice. Aorta from hypertriglyceridemic mice had changes in the transcriptomes of endothelial cells, macrophages, and smooth muscle cells indicating vascular inflammation. Our data show that intact TRLs contribute to atherosclerosis, explain the association of postprandial lipemia and vascular disease, and prove that non-remnant TRLs are not benign.

overall_design: We induced LpL deficiency in LDL receptor knockout mice to assess the contribution of unhydrolyzed triglyceride-rich lipoproteins to atherosclerosis. LDLR KO mice with or without concomitant LpL deficiency were fed a western diet for 12 weeks, after which their aortic roots and brachiocephalic arteries were isolated for assessment of atherosclerotic lessions. In addition, we performed single cell RNA sequencing analysis of aortic arches from LDLR KO with or without concomitant LpL deficiency.

first: Ainara G

last: Cabodevilla

first: Maria Concepcion

last: Izquierdo

first: Debapriya

last: Basu

first: Waqas

last: Younis

first: Munichandra B

last: Tirumalasetty

first: Qing Robert

last: Miao

first: Dimitris

last: Nasias

first: Jenny E

last: Kanter

first: Tse Wing

last: Ho

first: Jana

last: Gjini

first: Edward A

last: Fisher

first: Jeffrey

last: Kim

first: Warren L

last: Lee

first: Karin E

last: Bornfeldt

first: Ira J.


title: Thimerosal Inhibits Tumor Malignant Progression Through Direct Action and Enhancing the Efficacy of PD-1-Based Immunotherapy

city: GuangZhou

first: Zeng

last: Jun Xiang

address: No. 1023–1063 South Shatai Road, Baiyun District

institute: The Southern of Medical University

summary: Background: Thimerosal is a mercury-containing preservative widely used in vaccines.. This study aimed to investigate its potential antitumor effects and mechanisms in solid malignancies, particularly colorectal cancer and melanoma. Methods: A combination of in vitro and in vivo approaches was employed. Cell proliferation, apoptosis, migration, and invasion were assessed using Cell Counting Kit-8 (CCK-8), colony for-mation, ATP viability, Western blotting, flow cytometry, wound-healing and transwell assays. Sub-cutaneous, lung metastases, and Azoxymethane/Dextran Sulfate Sodium Salt (AOM/DSS)-induced colitis-associated colorectal cancer (CRC) models were established to examine antitumor efficacy and safety. The functional role of mercury ions was validated using structural analogues. Mechanistic studies included RNA sequencing, Western blot, and immunohistochemical analysis of CD8+ T cell infiltration. The synergistic effect with programmed cell death protein 1 (PD-1) antibodies therapy was also evaluated. Results: Thimerosal potently inhibited tumor growth (with IC50 values ranging from 0.1 to 1 µM in vitro) and significantly prolonged survival without overt toxicity in vivo. Mechanistically, mercury ions were critical functional sites mediating Thimerosal’s antitumor effects. Specifically, Thimerosal inhibited the phosphorylation of Janus kinase 1(JAK1) and signal transducer and activator of tran-scription 3(STAT3). Furthermore, Thimerosal enhanced the infiltration of CD8+ T cells into the tumor microenvironment and synergistically augmented the efficacy of PD-1 antibody therapy. Conclusion: Thimerosal exerts dual antitumor roles by direct JAK1/STAT3 inhibition and immune modulation via CD8+ T cell recruitment. It represents a promising repurposed drug and immuno-therapeutic adjuvant for CRC and melanoma.

overall_design: Based on the provided background, the experimental design was structured to comprehensively evaluate thimerosal's antitumor potential. It utilized a combination of in vitro assays (CCK-8, colony formation, flow cytometry, wound-healing, transwell) on cancer cell lines and in vivo models (subcutaneous, lung metastasis, and AOM/DSS-induced CRC) in mice to assess efficacy and safety. The role of mercury ions was specifically tested using structural analogs. Mechanistic studies involved RNA sequencing, western blotting to analyze the JAK1/STAT3 pathway, and immunohistochemistry to quantify CD8+ T cell infiltration. Finally, the synergistic effect of thimerosal with anti-PD-1 therapy was investigated.

first: Ping

last: Wang

first: Yan-Han

last: Chen

first: Ze-Tao

last: Zhan

first: Jun-Xiang

last: Zeng

first: Yu

first: Yuan

last: Lin

first: Tao

first: Wei-Jie

last: Zhou


title: Progressive neuroinflammation and deficits in motor function in a mouse model with an Epg5 pathogenic variant of Vici syndrome

status: Public on Sep 11 2025

city: Kansas City

first: Jay

last: Vivian

state: MO

address: 2401 Gillham Road

department: Clinical Genetics

institute: Children's Mercy Hospital

summary: Transcriptomic profiling was performed on CNS tissues of 7 month old sibling control or homozygous mutant mice carrying a genetically engineered truncating W860X mutation recapitulating a pathogenic variant of Vici Syndrome. Analysis revealed robust neuroinflammatory signatures, implicating the activation of both microglia and astrocytes. Notably, the molecular profiles of Epg5-deficient mice share features with disease-associated microglia observed in other models of neurological disease and injury.

overall_design: Total RNA isolated from anterior spinal cord or cerebellum of 7 month old wildtype control or W860X homozygous mutant mice (four mice each; two male, two female) was used in an Illumina-based bulk RNA sequencing for whole transcriptomic analyses.


title: Identification of cells exhibiting elevated ERBB network activity in KRas/ Myc-driven lung tumours

first: Robin

last: Shaw

address: Switchback Road

summary: Our lab has identified a completely unexpected requirement for ERBB signalling in KRAS‐driven Lung Adenocarcinoma (LuAd). We have shown that this requirement is present from the very outset of lung tumour initiation, and, crucially, we have found a pronounced increase in ERBB signalling during progression from low grade adenocarcinoma to locally invasive disease. We hypothesize that this increased activity, which manifests as strongly elevated expression of multiple EGF/ERBB-family ligands, such as Amphiregulin (AREG), and paracrine activation of ERBB2 on infiltrating macrophages, may be exploited for early detection of KRAS‐ driven malignancy. Alongside a more general increase in AREG expression as tumours progress to higher grade disease, we find individual cells that express extremely high levels of AREG mRNA. We refer to these cells as AREG super-expressers and their lineage identity is unknown. Cell morphology suggests they maybe epithelial, however, unlike the bulk of tumours, these cells fail to express the lung epithelial marker SPC and staining for cytokeratins is inconclusive. Their detection at and adjacent to the tumour:normal interface suggests that they maybe disseminating tumour cells undergoing EMT. Alternatively, they may belong to another lung-resident or infiltrating population, induced to express AREG through direct contact with tumour cells. Immediately adjacent to progressing tumours we find large numbers of F4/80-positive macrophages that stain strongly for tyrosine phosphorylated ERBB2 (p-Tyr-ERBB2), suggesting paracrine activation in response to local production of ERBB ligands. The aim of this part of the work is to identify the cell lineage of the AREG superexpressers and to investigate the effect of ERBB-inhibition using the multi-ERBB inhibitor Neratinib.

overall_design: scRNA-seq was performed on whole-tumour cell suspensions from lungs of SPC-Cre+ KrasG12D+/-;MYC+/+ (KM) genetically engineered mice 8-9 weeks after transgene induction. Three days prior to culling, mice received daily (3 doses total) intraperitoneal injections of neratinib in peanut oil (80mg/kg), peanut oil, or were left untreated (n=3 per group).

first: Bjorn

last: Kruspig

first: Sarah

last: Laing

first: Ximena L.

last: Raffo-Iraolagoitia

first: Ann

last: Hedley

first: Ya-Ching

last: Hsieh

first: Kristina

last: Kirschner

first: Crispin

last: Miller

first: Daniel J.

last: Murphy


title: Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo [scRNA-Seq]

first: Kathryn

last: Gilroy

overall_design:
Mice were induced with a single 70uL injection of 100uM 4-OH tamoxifen into the colonic submucosa. When an established tumour was identified on colonoscope (beginning weekly two weeks post injection), mice were placed on a treatment regime. Mice were treated twice daily with MRTX1133 IP AM and PM (MRTX1133 100uL 7.5mg/kg) or vehicle (100uL10% hydroxpropyl beta cyclodextrin in 50mM citrate buffer ph5) for 4 days and sampled two hours post AM dose on the fourth day.

Single cell RNAseq data from colon and SI tumours (submitted previously in GSE280631 & GSE293737 as detailed in GSE307774_reanalysis_samples.xlsx), from mice expressing mutations in combinations of Apc, Braf, Kras, p53 and Rnf43. Genetic alterations were induced with intraperitoneal tamoxifen and tumours were homogenised and digested for sequencing using a Mcllwain Tissue Chopper and the GentleMACS Octo Dissociator in combination with the mouse tumour dissociation kit. Sequencing libraries were prepared using reagents from the 10x Chromium Single-Cell 3′ v3 Gel Bead Kit and Library (10x Genomics) according to the manufacturer’s protocol and then sequenced on an Illumina Novaseq 6000. Sequence alignment of single-cell data to the mm10 genome was performed using the count tool from the Cell Ranger package version 6.1.2 according to the developer’s instructions, generating barcodes, features and matrix output files for each sample.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Mark

last: White

first: Megan

last: Mills

first: Laura

last: Millett

first: Andrew

last: Campbell

first: Owen

last: Sansom


title: G-Quadruplex DNA suppresses Transcription during DNA Replication [CUT&Tag]

status: Public on Sep 10 2025

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

summary: G-quadruplex DNA (G4-DNA) structures play crucial but incompletely understood roles in coordinating DNA replication and transcription. Here, we investigate the dynamics of G4-DNA during DNA replication and its functional interplay with transcription machinery in synchronized tumor cells. Using a double-thymidine block to arrest cells in early S phase, we profile G4-DNA structures and associated transcription factors through CUT&Tag, while monitoring transcriptional changes via PRO-seq. To mechanistically dissect these relationships, we perturb the system by overexpressing G4-DNA helicases (DHX36 and BRIP1), treating with the G4-destabilizing agent PhpC, and knocking down the novel G4-binding protein RFC3. Our integrated analysis reveals how G4-DNA spatially and temporally regulates replication-transcription coupling, with important implications for understanding genome stability in cancer. These findings provide new insights into the role of G4-DNA as a regulatory nexus between DNA replication and gene expression.

overall_design: This study investigates the role of G4-DNA in regulating DNA replication-coupled transcription by combining cell cycle synchronization, genetic perturbations, and multi-omics profiling in HCCLM3 hepatocellular carcinoma cells. Using a double-thymidine block, we synchronize cells to Early S phase to examine phase-specific dynamics of G4-DNA structures and their interplay with transcription machinery. To dissect mechanistic relationships, we (1) overexpress G4-DNA helicases (DHX36/BRIP1), (2) treat with the G4-destabilizing agent PhpC, and (3) knockdown the novel G4-binding protein RFC3 in synchronized cells. These perturbations are analyzed through CUT&Tag (profiling transcription-associated proteins like RNA Pol II-S2P/S5P and NELF complex) and PRO-seq (quantifying transcriptional output). Our integrated approach will delineate how G4-DNA modulates replication-transcription crosstalk, with implications for understanding genome stability in cancer.

first: Xuedan

last: Sun

first: Shixiang

last: Pan

last: Zhang

first: Bo

last: Chu

first: Lianxin

last: Liu


title: Dog aortic endothelial cells as a model for studying the effects of nanoplastics

status: Public on Sep 08 2025

city: Brescia

first: Martina

last: Tambassi

state: Italy

address: Via Bianchi, 9

department: Risk Analysis and Genomic Epidemiology Unit

country: Italy

institute: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, VAT IT00284840170

summary: A growing concern regards plastic fragments mainly nanoplastics (NP). The present study was set up on aortic endothelial cells (CnAEOC) since dog is a model for translational medicine. Through fluorescence microscopy, we observed an interaction between NP and cells, demonstrating a localization at the cytoplasmic level. Furthermore, the data collected show a disruption of both cell proliferation and metabolic activity. The results also show the induction of oxidative stress. In detail, NP caused an increase in the levels of ROS production and an inhibition of enzymatic defense systems. On the contrary, there was no alteration of the non-enzymatic defense mechanism. The analysis conducted to evaluate a possible induction of autophagy, a survival mechanism implemented by cells, following exposure to NP reported the absence of autophagy involvement in the model analyzed. Finally, investigations were conducted regarding the involvement of NP in gene expression processes. Both RNA-seq and RT-PCR did not highlight differentially expressed genes in treated cells.

overall_design: RNA-seq profiles of dog aortic endothelial cells treated with polystyrene nanoplastics 25 µM for 48 hours and untreated

first: Giuseppina

last: Basini

first: Simona

last: Bussolati

first: Francesca

last: Grasselli

first: Anna

last: Scalori

first: Erika

last: Scaltriti

first: Stefano

last: Grolli

first: Roberto

last: Ramoni

first: Melissa

last: Berni


title: Masculinizing Testosterone Therapy Reduces the Incidence of PIK3CA-Mutant/ER⁺ Breast Cancer but Not BRCA1-Associated Triple-Negative Breast Cancer

city: Boston

first: Jan

last: Heng

state: MA

address: 330 Brookline Ave, Dana 517B

department: Pathology

institute: Beth Israel Deaconess Medical Center

summary: The effects of gender-affirming testosterone therapy (TT) on breast cancer (BC) risk in the general trans masculine population and among BRCA1/2mut carriers are unclear. We found that TT reduced the size but not the number of terminal duct lobular units, increased stromal expression of estrogen receptor (ER), progesterone receptor, and Ki67, and had an immunosuppressive effect. We leveraged preclinical models to assess TT’s effect on BC incidence and biology. Consistent with the human data, TT reduced mouse mammary gland branching and the number of terminal end buds. TT decreased Pik3ca-related ER+ BC incidence by 81% compared to female controls (adj RR 0.19, 95% CI 0.08-0.45), but had no effect on Brca1-related triple negative BC incidence. Our findings clarify that TT modifies the risk for PIK3CA-related ER+ BC but not BRCA1-associated triple-negative BC, emphasizing the ongoing need for surveillance and individualized care in this population.

overall_design: RNASeq profiling of human breast (non cancer) tissue and mouse tumor, comparing samples exposed to testosterone therapy versus no testosterone.

first: Yu Jing Jan

first: Gerburg

last: Wulf


title: JAX Study 9- RNA-seq of male KOLF2.2J hiPSC-derived cortical brain organoids homozygous null for eight different transcription factors.

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

institute: EMBL-EBI

summary: This study aims to phenotype iPSC-derived cortical brain organoids that contain homozygous null alleles for transcription factors expressed in the early neuroectoderm. Null alleles were generated using insertion of a premature termination codon with frameshift (PTC+1). RNA-seq data was generated at the indicated day post initiation of differentiation from hiPSCs. The study included the homozygous null alleles for the following transcription factors: EMX2, FOXG1, POU3F2, SOX1, HES5, SOX21, POU3F1 and SP8. This analysis provided insight into the impact of loss of function for these transcription factors in cortical brain organoid differentiation.

overall_design: The study involved the generation of RNA-seq on 39 samples. Different time points of differentiation to cortical brain organoids were chosen according to the initiation of the transcription factor in wildtype cells within this differentiation scheme. Three biological replicates were run for gene. Additionally, three biological replicates were run of wildtype KOLF2.2J cells (the parental male cell line in which the KOs were generated) under the same differentiation conditions in the different time points. This comprehensive design allowed for a robust analysis of the effects of transcription factor manipulation on brain organoid formation.

first: Juliana

last: Diniz

first: Bill

last: Skarnes

first: Paul

last: Robson


title: An epigenetic repressor TRIM66 dictates monogenic olfactory receptor expression, neural activity, and olfactory behavior

first: Yalei

last: Kong

institute: Shanghai Jiao Tong University

summary: Olfactory receptor gene choice is an intricate example of monogenic and monoallelic expression, where one out of over 1000 receptor genes is tran- scribed in each olfactory sensory neuron. This process involves expression of multiple olfactory receptor genes in immature neurons, followed by silencing of all but one receptor genes during maturation. However, the molecular identity of the repressors remains mysterious. Here, we discover TRIM66 as a key repressor. Multiple receptor genes are retained at low levels in most single mature OSNs after deletion of Trim66, leading to decreased expression of the vast majority of olfactory receptor genes. Mechanistically, TRIM66 can bind to, assembly, and repress olfactory receptor enhancers, thereby silencing extra olfactory receptor genes. Functionally, deletion of Trim66 leads to severe defects in the olfactory information processing and innate olfactory behaviors. Our study provides the missing link in understanding the transition from polygenic to monogenic olfactory receptor expression.

overall_design:
To examine the potential role of Trim66 in olfactory receptor (OR) expression, we generated KO and cKO mouse lines and assessed changes in receptor expression following Trim66 deletion (For bulk RNA-seq and scRNA-seq data).
To investigate the mechanisms of OR gene regulation by Trim66, we performed ChIP-seq in the MOE of WT mice using antibodies against TRIM66, ATF5, EZH2, and YY1 (For ChIP-seq data).
To evaluate changes in chromatin accessibility, We further performed ATAC-seq in the MOE of Trim66 knockout mice (For ATAC-seq data).
We further performed Hi-C in Trim66 knockout mice to investigate 3D genome organization (For Hi-C data).
Additionally, we carried out CUT&Tag experiments in Olfr1507-expressing OSNs isolated from Olfr1507-ires-tdTomato; Trim66 knockout mice using antibodies against H3K27ac and H3K27me3 to profile histone modifications (For H3K27ac, H3K4me1, H3K9me3, and H3K27me3 data).
To explore the mechanisms of olfactory receptor gene regulation by Trim66, We performed ATAC-seq for the Olfr1507 OSNs in the MOE of Olfr1507-ires-tdTomato; Trim66 knockout mouse (For Olfr1507 OSNs ATAC-seq data ).

first: Hongqiang

last: Bao

first: Qian

last: Li


title: Multi-step genomics on single cells and live cultures in sub-nanoliter capsules

status: Public on Sep 09 2025

first: Ignas

last: Mazelis

address: 210 Longwood Avenue

department: System Biology

institute: Harvard Medical School

summary: Single-cell genomics encompasses a set of methods whereby hundreds to millions of cells are individually subjected to multiplexed assays including sequencing DNA, chromatin accessibility or modification, RNA, or combinations thereof 1,2. These methods enable unbiased, systematic discovery of cellular phenotypes and their dynamics 1–3. Many functional genomic methods, however, require multiple steps that cannot be easily scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells, mRNA, and gDNA, while allowing free diffusion of media, enzymes and reagents. CAGEs enable carrying out high-throughput assays that require multiple steps, including combining genomics with live-cell assays. We establish methods for barcoding CAGE DNA and RNA libraries, and apply them to measure persistence of gene expression programs by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and extend them to live-cell assays.

sample_organism:
Escherichia coli
Homo sapiens
Mus musculus

overall_design:
RNA-seq data for the establishment of Capsule-based multi-step processing of single-cell in cultures. Data includes inC-RNAseq of fresh, frozen, and fixed cell lines, frozen PBMCs and cell lines cultured in CAGES. Washed cells were encapsulated into CAGEs, lyzed, washed, followed by mRNA capture via oligo-dT RT. cDNA was amplified in CAGEs, barcoded using split-pool implementation. Barcoded cDNA was used for 3’ end RNA-seq library preparation using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. Data also included single-cell inC-ATACseq data of cell lines, GFP-RFP gDNA amplicon sequencing of individual cells as well as plasmid barcoding test. Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - transcript; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1, RT/ATAC/PCR barcode and UMI [for RNAseq].

Plasmid_sequencing: Sequencing data for the establishment of Capsule-based multi-step processing of single-cell and cultures. Data includes inC-seq barcoding of plasmid DNA processed in CAGES. DNA containing CAGEs were washed and plasmid DNA were amplified in CAGEs, barcoded using split-pool barcode addition. Barcoded DNA amplicon were indexed and sequenced using Illumina
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - gDNA amplicon; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1 and CMV gDNA loci.

Fresh_Fixed: RNA-seq data for the establishment of Capsule-based multi-step processing of single-cells and live cultures. Data includes inC-RNAseq of fresh and PFA fixed K562 cells processed in CAGES. Washed cells were encapsulated into CAGEs, lyzed (decrosslinked in PFA case), washed, followed by mRNA capture via oligo-dT RT. cDNA was amplified in CAGEs, barcoded using split-pool implementation. Barcoded cDNA was used for 3? end RNA-seq library preparation using NEBNext® Ultra? II DNA Library Prep Kit for Illumina.
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - transcript; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1, RT/ATAC/PCR barcode and UMI [for RNAseq].

gDNA_Amplicons: Sequencing data for the establishment of Capsule-based multi-step processing of single-cell and cultures. Data includes inC-seq barcoding of GFP and RFP gDNA amplicon derived from a 1:1 mix of K562 and L1210 single-cells processed in CAGES. Washed cells were encapsulated into CAGEs, lyzed, washed, followed by mRNA capture via oligo-dT RT. gDNA targeted with CMV and RFP or GFP loci primers was amplified in CAGEs and barcoded using split-pool CAGE aproach. Barcoded gDNA amplicon were indexed and sequenced using Illumina
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - gDNA amplicon; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1 and CMV gDNA loci.

PBMCs: RNA-seq data for the establishment of Capsule-based multi-step processing of single-cells and live cultures. Data includes inC-RNAseq of cryopreserved PBMCs processed in CAGES. Thawed and washed cells were encapsulated into CAGEs, lyzed, washed, followed by mRNA capture via oligo-dT RT. cDNA was amplified in CAGEs and barcoded using inC-seq split-and-pool implementation. Barcoded cDNA was used for 3? end RNA-seq library preparation using NEBNext® Ultra? II DNA Library Prep Kit for Illumina.
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - transcript; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1, RT and UMI.

Cell_Culturing: RNA-seq data for the establishment of Capsule-based multi-step processing of single-cells and live cultures. Data includes inC-RNAseq of K562, L929 and induced pluripotent stems cells cultured in CAGES. After culturing, cells were lyzed followed by mRNA capture via oligo-dT RT. cDNA was purified, amplified and was used for 3? end RNA-seq library preparation using NEBNext® Ultra? II DNA Library Prep Kit for Illumina.
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - transcript; read2 - PCR barcode, read3 - index; read4 - UMI [no barcodes were used]

CAGE_Colonies: RNA-seq data for the establishment of Capsule-based multi-step processing of single-cells and live cultures. Data includes inC-RNAseq of mixed K562 and L1210 cells expanded into clones from single cells inside CAGEs in the presence of Decitabine, 5-Azacytidine or Vorinostat.  Cells were pretreated with drugs and encapsulated into CAGEs, followed culturing. Cells were lysed after 0, 2, 4, 6 days followed by oligo dT mRNA capture. cDNA was barcoded using split-pool inC-seq approach and Barcoded DNA was used for scRNA-seq library construction
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - transcript; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1, RT/ATAC/PCR barcode and UMI [for RNAseq].

[UPDATE] Please note that new .h5ad files have been added for GSM9228947 and GSM9228948 samples on Mar 26, 2026.

first: Haoxiang

last: sun

first: Arpita

last: Kulkarni

first: Theresa

last: Torre

first: Allon

last: Klein


title: Comparative single-cell multiomic analysis reveals evolutionarily conserved and species-specific cellular mechanisms mediating natural retinal aging [Mouse_Xenium]

status: Public on Sep 05 2025

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

summary: We performed integrated single-cell RNA- and ATAC-Seq analyses of the retina and retinal pigment epithelium (RPE) across the natural lifespan in zebrafish, mice, and humans. By profiling gene expression and chromatin accessibility, we identified extensive cell type- and species-specific aging-dependent changes, with a much smaller number of broadly expressed and conserved genes that include regulators of inflammation and autophagy. We constructed predictive aging clocks for retinal cell types and observed dynamic, reversible shifts in cellular age following acute injury. Spatial transcriptomic analysis revealed region-specific aging signatures and proximity effects, with Müller glia exhibiting pro-rejuvenative influences on neighboring neurons. Targeted Müller glia-specific induction of Yamanaka factors reduced molecular age in rod photoreceptors and bipolar cells without altering glial age. Our findings define conserved and divergent regulatory and signaling pathways mediating retinal aging, highlighting Müller glia as potential therapeutic targets for combating age-associated retinal degeneration.

overall_design: we generated mouse datasets by the Xenium 5k platform to analyze aging-dependent gene expression changes in the mouse retina in situ. This retina dataset consists of 4 ages of retina samples, at 5, 12, 55, and 112 weeks, and each age contains two sections (center and peripheral) from one male and one female. We directly tested whether constitutive, low level, Muller glia-specific expression of these factors resulted in rejuvenation of any retinal cell types, using the Muller glia-specific inducible Cre line GlastCreER 65 in conjunction with Cre-inducible rtTA and doxycycline-inducible Oct4, Sox2, Klf4, and mCherry. Doxycycline-treated retinas were analyzed using Xenium 5K spatial transcriptomics.

first: Isabella

last: Palazzo

first: Yang

last: Jin

first: Leah

last: Campbell

first: Clayton

last: Santiago

first: Rogger

last: Carmen-Orozco

first: Thanh

last: Hoang

first: Jared

last: Tangemen

first: Alexander

last: Park

first: Shawn

last: Yang

first: Jianming

last: Shao

first: Rui

last: Chen

first: David

last: Hyde

first: Jiang

last: Qian

first: Seth

last: Blackshaw


title: The multimodal transcriptional response of denervated skeletal muscle involves alterations in cholesterol homeostasis impacting muscle size

city: Cincinnati

first: Douglas

last: Millay

state: OH

address: 3333 Burnet Ave Cincinnati, OH 45229

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital and Medical Center

summary: The development and maintenance of the neuromuscular junction (NMJ) requires reciprocal signals between the nerve terminals and the multinucleate skeletal muscle fiber (myofiber). This interaction leads to highly specialized transcription in the sub-synaptic or NMJ myonuclei within mature myofibers leading to clustering of acetylcholine receptors  (AChRs). Here we utilized single-nucleus RNA sequencing (snRNA-seq) to delineate the transcriptional response of myonuclei to denervation. Through snRNA-seq on skeletal muscle from two independent mouse models of denervation, sciatic nerve transection and amyotrophic lateral sclerosis, we identify a multimodal transcriptional response of NMJ-enriched genes and an alteration in cholesterol homeostasis in both slow and fast myofibers. Gramd1, a family of genes involved in non-vesicular cholesterol transport, are enriched at the NMJ at baseline and upregulated in both models of denervation by the NMJ and extrasynaptic myonuclei In vivo gain and loss of function studies indicate that NMJ-enriched Gramd1 genes regulate myofiber sizes independent of an obvious impact on AChR clustering. We uncovered a dynamic transcriptional response of myonuclei to denervation and highlight a critical role for cholesterol transport to maintain myofiber sizes.

overall_design: Tibialis anterior (TA) muscles from SOD1G93A or C57BL/6 mice were harvested immediately following euthanasia, minced, and placed in homogenization buffer (0.25 M sucrose and 1% BSA in Mg2+-free, Ca2+-free, RNase-free 1x PBS). Nuclei isolation was done as previously described [20]. After filtration via a 40 μm strainer, nuclei were labeled with Hoechst dye and 0.2 U/μL Protector RNase inhibitor (Roche). All Hoechst stained myonuclei were purified using FACS (BD Aria, 70 μm nozzle) and gathered in sorting buffer containing Protector RNase inhibitor (0.2 U/μL). The nuclei were counted with a hemocytometer, and the concentration was fine-tuned as needed to reach the optimal range for the 10X Chromium chip. The 10X Chromium system was then used to load the nuclei using the Single Cell 3′ Reagent Kit v3.1, following the guidelines provided by the manufacturer. Around 12,000 nuclei were loaded for each operation. Sequencing was performed on an Illumina NovaSeq 6000 System.

first: Cristofer

last: Calvo

first: Casey

middle: O

last: Swoboda

first: Fabian

last: Morales

first: Siddhant

last: Nagar

first: Michael

last: Petrany

first: Chengyi

last: Sun

first: Hima

middle: B

last: Durumunla

first: Mattia

last: Quattrocelli


title: Critical opposing roles for TFEB andTFE3 in melanoma progression

status: Public on Sep 03 2025

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

summary: Unlike MITF-M, the melanocyte-specific isoform of MITF, TFEB, TFE3 and non-melanocyte MITF isoforms are regulated primarily by mTORC1-mediated phosphorylation at the lysosome that promotes their cytoplasmic retention. As low levels of glucose or amino acids trigger down-regulation of MITF, it is likely that on nutrient limitation some MITF functions are assumed by TFE3 and TFEB, enabling MITFLow melanoma cells to survive and proliferate. The role TFEB and TFE3 in melanoma biology and their impact on MITF-driven proliferation is poorly understood.

overall_design: TFEB and TFE3 KO of 501mel melanoma cell lines were generated using guides targetting TFE3 (GGTACTGTTTCACCTGCTGC) and TFEB (AGTACCTGTCCGAGACCTAT). KO cells were clonally isolated and validated prior to experiment.

first: Diogo

last: Dias

first: Colin

middle: R

last: Goding


title: Aberrant Hippo-YAP/TEAD signaling drives malignant transcriptional reprogramming in external auditory canal squamous cell carcinoma

city: La Jolla

first: Kuniaki

last: Sato

state: CA

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

institute: University of California San Diego

summary: External auditory canal squamous cell carcinoma (EACSCC) is an extremely rare malignancy. The molecular characteristics and evidence-based therapeutic strategies of EACSCC still remain to be elucidated. To elucidate the transcriptomic aberrations of EACSCC, RNA-seq was performed on non-cancerous ear skin tissues and EACSCC tissues.

overall_design: Library preparation from RNA extracted from cultured cells and RNA sequencing were performed using a DNBSEQ-G400 sequencer. The sequenced reads were aligned to the human reference genome GRCh38 using STAR v2.7.9a with Gencode v38 annotations. Gene count tables were generated with RSEM v1.3.1.

first: Noritaka

last: Komune

first: Mayumi

last: Ono

first: Takashi

last: Nakagawa


title: Tumor nutrient stress gives rise to a drug tolerant cell state in pancreatic cancer

city: Chicago

first: Alex

last: Muir

email: amuir@berkeley.edu, amuir@uchicago.edu

state: Illinois

department: Ben May Department for Cancer Research

institute: University of Chicago

summary: Cytotoxic chemotherapy remains the standard-of-care treatment for patients with pancreatic ductal adenocarcinoma (PDAC). However, chemotherapy only has modest effects at improving overall survival due to primary or rapidly acquired chemoresistance. The biological underpinnings of PDAC therapy resistance are incompletely defined, but the tumor microenvironment is known to be a major contributor to chemoresistance. We have found chemoresistance is imprinted on PDAC cells by the tumor microenvironment and persists for a period of days after PDAC cells are removed from tumors. However, PDAC chemoresistance is lost upon long term culture in standard laboratory conditions. Interestingly, culture of PDAC cells in Tumor Interstitial Fluid Medium (TIFM), a culture medium we developed to recapitulate the nutrient availability of the tumor microenvironment, maintains PDAC cells in a chemoresistant state even after long term culture ex vivo. These findings suggest that microenvironmental metabolic stress keeps PDAC cells in a physiologically relevant, therapy resistant cell state that standard culture models fail to maintain. Using TIFM culture, we sought to understand how PDAC cells in this state resist chemotherapeutic challenge. We found that chemotherapy drugs largely retain on-target activity within TIFM medium but fail to activate cell death, enabling a “chemotolerant” cell state, which is also observed in PDAC tumors. This chemotolerant state is driven by suppression of apoptotic priming and can be overcome by targeting the anti-apoptotic regulator BCL-xL. Taken together, these findings suggest that reprogramming of cell death mechanisms by the PDAC nutrient microenvironment is a key contributor to therapy resistance in this disease.

overall_design: Murine pancreatic cancer cells (mPDAC1) were grown in RPMI-1640 or in tumor interstitial fluid medium (TIFM). Cells in each medium were treated with either vehicle or 125nM gemcitabine for 24 hours. RNA was then extracted and sent for library prep and sequencing with the University of Chicago Genomics Core.

last: Sheehan


title: Myeloid Leukemia

status: Public on Sep 04 2025

city: Nanjing

first: feifei

last: yang

address: Changle Road 68

institute: Nanjing first hospital,Nanjing medical university

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Genome-wide profiling of TFE3 targets in melanoma

overall_design: 501mel melanoma cell lines engineered to express ectopic-doxycycline-inducible-HA-epitope-tag TFE3. Cells were then treated with either 250nM Torin1 or control for 6h. Samples were then processed as described below.


title: Autologous multiantigen-targeted T cell therapy for pancreatic ductal adenocarcinoma: results of a Phase I, three-arm, nonrandomized clinical trial (TACTOPS)

status: Public on Sep 12 2025

city: Houston

first: Shamika

last: Ketkar

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of edicine

summary: T-cell therapy has thus far proven ineffective for treating pancreatic ductal adenocarcinoma (PDAC), in part due to heterogeneous expression of tumor-associated antigens (TAAs). In a Phase I/II trial, autologous ex vivo expanded T-cells targeting five TAAs - PRAME, SSX2, MAGEA4, Survivin, and NY-ESO-1 - were prepared and administered (1x107 cells/m2/infusion) monthly to subjects with advanced PDAC responding (Arm A, n=13) or refractory to (Arm B, n=12) first-line chemotherapy, or to those with potentially resectable disease (Arm C, n=12). Primary endpoints were safety and feasibility of delivering 6 infusions; additional endpoints were clinical and immunologic response. Of 56 subjects procured, 37 were infused (median 3 doses), with only one treatment-related serious adverse event reported. Disease control rates in Arms A and B were 84.6% (95% CI: 54.6%-98.1%) and 25% (95% CI: 5.5%-57.2%), respectively; in Arm C, 2/9 resected subjects remain disease-free at 55 and 66 months. The infused cells persisted for up to 12 months post-infusion, and elevated levels of effector, tumor-directed T cells were detected both during dosing (p=0.027) and follow-up in “responders” (objective response in Arms A/B, no relapse in Arm C) compared to “non-responders” (progression in Arms A/B, relapse in Arm C).

overall_design:
Transcriptomic characteristics were explored in a subset of antigen-stimulated (vs unstimulated) mTAA T cell products (n=7) by single cell RNA sequencing (scRNAseq).
Please note that processed data files generated from both V(D)J and 5′ expression libraries are linked to the corresponding GEX sample records

first: Ann

last: Leen


title: Genome-wide profiling of TFEB targets in melanoma

overall_design: 501mel melanoma cell lines engineered to express ectopic-doxycycline-inducible-HA-epitope-tag TFEB. Cells were then treated with 5ng Dox overnight to attain expression of ectopic TFEB that was comparable to the endogeneous level. The following day cells were treated with 250nM Torin1 or control for 6h. Samples were then processed as described below.

first: Érica

last: Aparecida de Oliveira


title: Loss-of-function mutations in the melanocortin-2-receptor (mc2r) lead to skin hyperpigmentation in teleost fish

status: Public on Sep 02 2025

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

country: Spain

institute: CSIC

summary: Melanocortins regulate pigmentation via melanocortin receptors (MCRs), which exhibit high conservation across zebrafish and humans. MC2R is distinctive among melanocortin receptors in that it is activated exclusively by ACTH and requires Mrap1 for optimal functionality, in contrast to other receptors that possess the capacity to bind diverse ligands. Although the melanocortin 1 receptor (MC1R) is well characterised for its role in pigmentation, the function of MC2R remains largely unknown. This study examines the influence of MC2R on pigmentation by generating MC2R knockout zebrafish using the CRISPR/Cas9 system. The results demonstrated that the mc2rKO mutants exhibited pronounced hyperpigmentation, characterised by an elevated number of melanophores and xanthophores, while preserving the distinctive striped pattern and dorsoventral countershading. Gene expression analyses show an increase in the expression of genes involved in melanosome synthesis and melanin production, contributing to a darker phenotype, as well as genes associated with lipid metabolism and carotenoid accumulation, which result in enhanced yellow coloration. These results suggest that mc2r plays a role in modulating the development, distribution and metabolic activity of pigment cells.

overall_design: RNA-seq profiling of wild-type and mc2r gene knockout zebrafish

first: Elisa

last: Barreiro-Docío

last: Guerrero-Peña

first: Pryanka

last: Soni

first: Luis

last: Méndez-Martínez

first: Carolina

last: Costas-Prado

first: José

last: Vázquez

last: Cerdá-Reverter

first: Josep

last: Rotllant


title: CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias [ChIP-Seq]

first: Travis

last: Fleming

address: 1 Blackfan St

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: Acute myeloid leukemias (AMLs) have an overall poor prognosis and many high-risk cases co-opt stem cell gene regulatory programs, yet the mechanisms through which this occurs remain poorly understood. Increased expression of the stem cell transcription factor, MECOM, underlies one key driver mechanism in largely incurable AMLs. How MECOM results in such aggressive AML phenotypes remains unknown. To address existing experimental limitations, we engineered and applied targeted protein degradation with functional genomic readouts to demonstrate that MECOM promotes malignant stem cell-like states by directly repressing pro-differentiation gene regulatory programs. Remarkably and unexpectedly, a single node in this network, a MECOM-interacting regulatory element located 42 kb downstream of the myeloid differentiation regulator CEBPA is both necessary and sufficient for MECOM-driven leukemogenesis. Importantly, targeted activation of this regulatory element promotes differentiation of these aggressive AMLs and reduces leukemia burden in vivo, suggesting a broadly applicable differentiation-based approach for improving therapy.

overall_design: ChIP-seq profiling of MECOM and H3K27ac chromatin occupancy in a MECOM-FKBP12F36V cell line (MUTZ-3) treated with 500nM dTAGV-1 or DMSO for 6 hrs during in vitro culture.

first: Vijay

middle: G

last: Sankaran


title: CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias [PRO-Seq]

overall_design: Nascent RNA-seq (PRO-seq) profiling of a MECOM-FKBP12F36V cell line (MUTZ-3) treated with 500nM dTAGV-1 or DMSO for 1-4 hrs during in vitro culture.


title: JAX Study 11- RNA-seq of male KOLF2.2J hiPSC-derived cortical brain organoids during different time points.

status: Public on Sep 01 2025

first: MorPhiC

last: Consortium

summary: This study aims to gather information on iPSC-derived cortical brain organoids differentiated in six different time points. Bulk RNA sequencing (RNA-seq) was performed at days 3, 4, 5, 20, 25, and 32 post-initiation of differentiation. The resulting dataset provides a foundational control reference for assessing the roles of various transcription factors previously manipulated in cortical organoid models.

overall_design: RNA-seq was conducted on 18 samples representing six differentiation time points, with three biological replicates per condition. Wildtype KOLF2.2J hiPSC lines were differentiated under uniform conditions to generate cortical brain organoids. This comprehensive design allowed for a robust analysis of previously manipulated transcription factors on brain organoid formation.

first: Juliana

last: Diniz

first: Bill

last: Skarnes

first: Paul

last: Robson


title: CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias [ATAC-Seq]

overall_design: ATAC-seq profiling of MECOM-FKBP12F36V cell lines (MUTZ-3, UCSD-AML1, HNT-34, and OCI-AML4) treated with 500nM dTAGV-1 or DMSO during in vitro culture.


title: CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias [RNA-Seq]

overall_design: RNA-seq profiling of MECOM-FKBP12F36V cell lines (MUTZ-3, UCSD-AML1, HNT-34, and OCI-AML4) treated with 500nM dTAGV-1 or DMSO for 6-24 hrs during in vitro culture.