title: Innate lymphoid cells activated by the cytokine TL1A link colitis to emergency granulopoiesis and the recruitment of tumor-promoting neutrophils

first: Silvia

last: Pires

address: 413E 69th st

institute: Weill Cornell Medicine

summary: The incidence of colorectal cancer (CRC) is increased in patients with ulcerative colitis (UC) and accounts for up to 15% annual mortality in patients with inflammatory bowel disease (IBD). Variants in TNFSF15, the gene that encodes TL1A, are associated with more aggressive IBD and advanced CRC. Here, we show that TL1A signaling is required for colitis-associated tumorigenesis and sufficient to promote CRC in mouse models. TL1A signaling in group 3 innate lymphoid cells (ILC3) promotes GM-CSF dependent activation of colonic neutrophils and colitis-associated tumors in mouse models. TL1A-mediated, ILC3-dependent tumor-associated neutrophil (TAN) signatures were evident in mouse models and reduced in subjects with UC treated with anti-TL1A therapy. Furthermore, TL1A promoted ILC-dependent emergency granulopoiesis, which is similarly evident in IBD subjects with TNFSF15 risk variants. These results reveal a new mechanism by which TL1A signaling in tissue resident ILCs shape TANs and emergency granulopoiesis with the potential to guide emerging anti-TL1A therapies for IBD.

overall_design: To determine the impact of TL1A-dependent inflammation on neutrophils, we performed RNA-sequencing of bone marrow-derived neutrophils cultured with supernatants from TL1A- unstimulated or stimulated ILC3s. For RNA-sequencing of bone marrow derived neutrophils 1x105 cells were stimulated for 18h with ILC3s supernatants, and 2×103 of sort-purified intestinal ILC3s were unstimulated or stimulated for 18h with TL1A


title: Effect of TIMP1 depletion on gene expression in MIA PaCa-2 cell line by CRISPR/Cas9-based targeting of exon 4

status: Public on Nov 25 2025

city: Munich

first: Julian

last: Frädrich

address: Ismaninger Strasse 22

department: Institute of Experimental Oncology & Therapy Research

country: Germany

institute: TUM School of Medicine and Health

type: Expression profiling by high throughput sequencing

summary: This is a bulk RNA sequencing dataset of MIA PaCa-2 cells with or without genetic manipulation of the TIMP1 gene. A two-guide RNA system was used and designed to target two sites of exon 4, introducing a 64-bp deletion, leading to a frameshift and premature stop-codon. This led to the generation of two TIMP1 KO cell lines, as well as a CRISPR control cell line that acquired only a silent point mutation (g.64C>T) without altering the amino acid sequence. To measure the impact of TIMP1 on MIA PaCa-2 gene expression, bulk RNAseq was performed for all four cell lines (WT, CRISPR Control, KO 1, and KO 2) in triplicates.

overall_design: All four cell lines were culltured to 70% confluency. Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) and RNAseq was performed on a NovaSeq X Plus platform (Illumina).

first: Achim

last: Krüger


title: Transcriptomic changes upon doxorubicin treatment in hCMEC/D3

status: Public on Nov 21 2025

city: New Brunswick

first: Chadni

last: Patel

state: NJ

address: 195 Little Albany Street

country: USA

institute: Rutgers Cancer Institute

summary: Current chemotherapy regimens have significantly improved overall survival for children with cancer. However, these curative treatments are associated with detrimental side effects such as chemotherapy-induced cognitive impairment (CICI), or “chemobrain.” Measurable deficits in cognitive function may persist years after chemotherapy treatments, significantly reducing quality of life. Specifically, doxorubicin (DOXO), a commonly used chemotherapeutic agent in curative regimens for children with cancer, plays a pivotal role in the development of CICI, even though it does not cross the blood brain barrier (BBB). We propose to address the poorly understood mechanism of DOXO-related CICI by studying changes induced by DOXO in BBB integrity in vitro, using human cerebral microvascular endothelial cells (hCMEC/D3). Our findings provide critical insights on how DOXO impacts the BBB and builds a foundation for developing preventative measures and therapeutic interventions that may improve the quality of life for patients.

overall_design: RNA-sequencing was performed to gain insights regarding the gene expression changes induced by doxorubicin (DOXO) treatment in human cerebral microvascular endothelial cells (hCMEC/D3). The hCMEC/D3 were treated 500 nM of doxorubicin (DOXO) or PBS, for 24 hours.

first: Peter

middle: D

last: Cole


title: Bulk RNA-Seq  of head and neck squamous cell carcinomas

status: Public on Nov 20 2025

city: Houston

first: Yu

middle: Leo

last: Lei

state: TX

address: 1901 East Rd

department: Head and Neck Surgery

institute: The University of Texas M.D. Anderson Cancer Center

summary: To substantiate the physiological relevance of the glutamine-BATF2 pathway, we performed bulk RNA-Seq on 15 HNSCC specimens. Then, we performed a correlation analysis between BATF2-IFN-I pathway genes and glutamine metabolism markers.

overall_design:
Bulk RNA-seq was performed on fresh tumor tissues from 15 oral cancer patients, with duplicate samples sequenced for each patient. Here are total 30 samples and  samples 31 is the replacement of samples 10. >>>Raw data for human samples not available due to patient privacy concerns<<<

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

middle: L

first: James

middle: J

last: Moon

first: Steven

middle: B

last: Chinn

first: Greg

middle: T

last: Wolf

first: Yuying

last: Xie

first: Arash

last: Yunesi

first: Xingwu

last: Zhou

first: Wang

last: Gong


title: A tumor-associated macrophage-targeted immunocytokine leveraging T and NK cell synergy for potent cancer immunotherapy

status: Public on Nov 19 2025

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: ATAC-seq and RNA-seq analysis of Eriocheir sinensis muscle in inter-molt stage

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

country: China

institute: College of Life Sciences, Tianjin Normal University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The chromatin accessibility and gene expression of muscle in E. sinensis in inter-molt (C) stage were sequenced by Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) and RNA-seq, respectively. The data was used to analysis the differentially expressed genes (DEGs) in muscle from post-molt to inter-molt by combining ATAC-seq and RNA-seq.

overall_design: Muscle of healthy crabs in inter-molt (C stages) were collected and used for ATAC-seq and RNA-seq analysis. In each stages, three muscle samples were collected as the experimental replications. ATAC-seq was performed with Illumina Hiseq platform with E. sinensis genome (accession number PRJNA555707) as the reference genome. RNA-seq was performed with Illumina novaseq platform with E. sinensis genome (accession number PRJNA555707) as the reference genome.

first: Jingjing

last: Li

first: Jinsheng

last: Sun


title: WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity [ChIP-seq]

city: Shanghai

first: jiaying

last: xie

address: Dongfang Road

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

summary: Stem cell pluripotency relies on a finely tuned interplay between transcription factors and epigenetic regulators. Here, we identify a direct interaction between NANOG, a master pluripotency transcription factor, and WDR5, a core component of the SET1/MLL complex that is essential for maintaining stem cell identity. Mechanistically, WDR5 reshapes the prion-like structures of NANOG into dynamic, liquid-liquid phase-separated (LLPS) condensates, facilitating its recruitment to pluripotency-associated promoters and activating target gene expression. X-ray crystallography and NMR spectroscopy reveal that the NANOG homeodomain engages WDR5 through an extensive structural interface distinct from previously characterized short linear motifs. The NANOGR153A mutation disrupts its interaction with WDR5, leading to impaired LLPS formation, reduced chromatin co-occupancy, and diminished levels of active histone marks (H3K4me3 and H4K16ac), ultimately compromising the pluripotency of embryonic stem cells. Furthermore, pharmacological inhibition of the WDR5-NANOG interaction using a WIN motif inhibitor robustly suppresses leukemia stem cell expansion in vivo, highlighting its therapeutic potential. Collectively, this study uncovers an LLPS-mediated regulatory mechanism whereby WDR5 modulates NANOG condensate dynamics to sustain stem cell identity in both physiological and pathological contexts.

overall_design: Chromatin immunoprecipitation followed by sequencing (ChIP–seq) for H3K4me3/H4K16ac/Nanog/Wdr5 in mouse embryonic stem cells

first: Xianle

last: Shi

first: Yanjing


title: WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity [Nanog_WT_R153A_RNAseq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mESCs in Nanog WT and Nanog R153A mutant cells


title: DDX6 undergoes phase separation to modulate metabolic plasticity and drug resistance in AML [CRISPR Screen]

city: Duarte

first: Rui

last: Su

state: CA

address: 1500 E Duarte Rd

institute: City of Hope

summary: Chemoresistance in acute myeloid leukemia (AML) is a major cause of poor prognosis and frequent relapse among patients. Under stress conditions such as chemotherapy or radiotherapy, processing bodies (PBs) and stress granules (SGs) can sequester essential mRNAs and proteins to modulate leukemia cell survival. However, the precise role(s) of PBs and SGs in AML pathogenesis and chemotherapy response remains unclear. To systematically identify PB/SG-associated genes that are critical for AML survival, we selected 101 genes encoding RNA-binding proteins that are localized within PBs and SGs, and constructed a customized CRISPR library targeting these genes for both in vitro and in vivo CRISPR screening with AML cell line (Mono-Mac-6) and patient-derived xenograft (PDX) cells.

overall_design: In the pilot experiment, the infection efficiency of 2,084 gRNAs was maintained at 0.2–0.3. Subsequently, the CRISPR library (containing 2,084 gRNAs) was introduced into Cas9-expressing Mono-mac-6 AML monoclonal cells and patient-derived xenograft (PDX) AML cells via lentiviral transduction, ensuring an infection efficiency of 0.2–0.3. Transduced AML cells were then selected with blasticidin (10 μg/mL) and puromycin (Mono-mac-6: 0.5 μg/mL; PDX-1: 16 μg/mL) for 3–5 days to obtain positively transduced populations. Cells collected after selection were designated as day 0 (baseline) samples. For the in vitro screening, both Mono-mac-6 and PDX cells were used (three biological replicates, 2 × 10⁶ cells per replicate). For the in vivo screening, PDX cells were used (six biological replicates, 2 × 10⁶ cells per replicate). For the in vivo CRISPR screen, PDX cells were injected into immunodeficient mice. After 28 days, bone marrow cells were harvested, and human CD45⁺ PDX cells were isolated using magnetic bead sorting as endpoint samples for sequencing (six replicates, 2 × 10⁶ cells per replicate). For the in vitro CRISPR screen, both Mono-mac-6 and PDX cells were continuously cultured for 28 days (maintaining ≥10,000-fold total cell expansion), after which cells were collected as endpoint samples for sequencing (three replicates per group, 2 × 10⁶ cells per replicate).

first: Chun-Wei (David)

last: Chen

first: Hongjie

last: Bi

first: Anthony

last: Chan


title: A tumor-associated macrophage-targeted immunocytokine leveraging T and NK cell synergy for potent cancer immunotherapy [CITE-seq]

summary: Tumor-associated macrophages (TAMs) expressing the myeloid checkpoint TREM2 are key immunosuppressive cells in the tumor microenvironment (TME), driving tumor progression and contributing to poor prognosis in cancer patients. Due to their pivotal role, TAMs have emerged as a promising target for immunotherapies. However, current TAM-targeting monotherapies show limited efficacy, highlighting the need for strategies engaging multiple immune modalities. Here, we developed a new class of cancer immunotherapies: myeloid-targeted immunocytokines and NK-T cell enhancers (MiTEs). MiTEs are trans-acting immunocytokines with tumor-specific activation, allowing dual targeting of TAMs and lymphocytes by TREM2 antagonism and cytotoxic effector cell activation through IL-2. To avoid off-target toxicities, MiTEs contain an IL-2 masking moiety, which is cleaved by a TAM-specific protease. MiTEs demonstrate high efficacy in preclinical tumor models through extensive immune reprogramming spanning TAM, T and NK cell compartments. MiTEs show transformative potential for treating solid-cancers by inducing potent multi-arm anti-tumor immunity and minimizing toxicities.

overall_design:
Fresh tumor samples were obtained from discarded surgical resection specimens collected from consented patients under a Cooperative Human Tissue Network-CHTN IRB approved protocol.  Tumor samples were cut into 1-2mm3 Patient-Derived Tumor Fragments (PDTFs) and cryopreserved in 1ml CryoStor CS10).
Cryopreserved PDTFs from five distinct renal cell carcinoma patient tumors were rapidly thawed in a 37°C water bath and immediately placed in RPMI 1640 medium supplemented with 5% fetal bovine serum (FBS). Following thawing, individual tumor fragments were cultured for 48 hours as previously detailed73. For each donor, a total of 16 fragments per treatment condition were allocated to each of the four experimental arms: Isotype Control: anti-Respiratory Syncytial Virus (RSV) IgG1 (10 nM) and anti-Hen Egg Lysozyme (HEL) IgG4 (10 µg/mL), anti-PD-1 Monotherapy: anti-PD-1 (10 µg/mL; Cat: SIM0010) and anti-RSV-IgG1 (10 nM), MiTE144 Monotherapy: MITE144 (1 0nM) and anti-HEL-IgG4 (10 µg/mL), Combination Therapy: MITE144 (10 nM) and anti-PD-1 (10 µg/mL).
Upon completion of the 48-hour culture period, 90ul of supernatants were collected and frozen for secreted protein analysis. Next, all fragments from the same donor and treatment arm were pooled and digested into single cell suspensions. Immune cells were enriched from the digested fragments using CD45 magnetic-activated cell sorting (MACS). The resulting CD45-enriched cell fractions were subsequently stained with a custom Immunai CITE-seq antibody panel (see STAR methods) and subjected to fluorescence-activated cell sorting (FACS) to isolate viable CD45 cells.
Single-cell gene expression (GEX) and feature (CITE-seq) libraries were prepared from the sorted cells using the 10x Genomics Chromium Next GEM Single Cell 5' Kit v2. Libraries were sequenced on a Novaseq X Plus sequencer using a 300 cycle kit.

first: Michelle

last: von Locquenghien

first: Pascale

last: Zwicky

first: Ken

first: Diego

last: Jaitin

first: Fadi

last: Sheban

first: Florian

last: Uhlitz

first: Chamutal

last: Gur

first: Reut

last: Sharet Eshed

first: Eyal

last: David

first: Kfir

last: Mazuz

first: Jahan

last: Adeeb Rahman

first: Noam

last: Solomon

first: Roberto

last: Avellino

first: Assaf

last: Weiner


title: Type I Interferon Induced Apoptosis Drives Chronic Wounds in ISG15 deficiency

city: New York

first: Dusan

last: Bogunovic

state: NY

institute: Columbia Univesity

summary: Chronic exposure to IFN-I in ISG15 deficiency drives impaired wound healing, improper macrophage activation and enhanced Epithelial-to-Mesenchymal transition, likely causing fibrosis in multiple organ systems.

overall_design: This is a cross-sectional study involving the accrual of 3-4-mm skin punch biopsy samples from one healthy control and biologic naïve ISG15 deficient patients with skin lesions. The samples were then subjected to the protocols entailed by spatial transcriptomics platform.

first: Christos

last: Sazeides

first: Ikjot

last: Sidhu


title: WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity

first: jiaying

last: xie

overall_design: To elucidate the mechanisms underlying the enhanced self-renewal capacity of AE9a hematopoietic stem and progenitor cells (HSPCs), potentially mediated through elevated NANOG expression and its functional interplay with WDR5, we conducted transcriptome-wide RNA sequencing (RNA-seq) analyses to systematically characterize transcriptomic alterations in both wild-type and AE9a murine HSPCs following pharmacological inhibition of WDR5 and MLL1.

first: Duo

last: Wang

first: Xianle

last: Shi

first: Jiaying

last: Xie

first: Lijie

last: Zhao

first: Bin

last: Wu

first: Yanjing

last: Li


title: Identification of lncRNA PRNCR1/miR-642a-5p/SSTR3 ceRNA network as novel biomarkers in detection of type 2 diabetes mellitus

status: Public on Nov 18 2025

city: Fuzhou

first: Jinyan

last: Chen

address: No.7 Wusi Road

institute: Fufian Academy of Medical Sciences

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
Microarray analysis and RNA sequencing were performed in strictly grouped sample of peripheral blood mononuclear cells (PBMCs) from T2DM cases and healthy controls. In total, 328 upregulated and 203 downregulated lncRNAs companied with 173 upregulated and 155 downregulated mRNAs, and 24 upregulated and 18 downregulated miRNAs were identified in T2DM under a fold change filter of > 1.5 and P value < 0.05. Functional enrichment (KEGG and GO) analysis showed that differentially expressed mRNAs were mainly related to biological processes, such as cell response to endogenous stimulus, intracellular signal transduction, cGMP-PKG signaling pathway, and pancreatic secretion. Signiﬁcant downregulation of lncRNA PRNCR1, IRAIN, together with miR-1268b and SSTR3, and upregulation of   lncRNA AC021491.4, miR-30c-2-3p, miR-642a-5p and TNFRSF10B were validated by quantitative real-time PCR (qRT-PCR) in T2DM compared with matched controls.
PRNCR1 was localized in the cytoplasm, and AGO2 RIP and dual luciferase reporter assays indicated that PRNCR1 directly sponges miR-642a-5p to downregulate the expression of SSTR3. The receiver operating characteristic (ROC) curves showed that PRNCR1 had a high diagnostic accuracy for differentiating T2DM from healthy controls.

overall_design: The experiment is divided into two groups: the healthy control group and T2DM cases. Then perform lncRNAs chips by Arraystar Human lncRNAs chip (Arraystar).

first: Shushu

last: Long


title: A tumor-associated macrophage-targeted immunocytokine leveraging T and NK cell synergy for potent cancer immunotherapy [scRNA-seq]

first: Ido

last: Amit

summary: Tumor-associated macrophages (TAMs) expressing the myeloid checkpoint TREM2 are key immunosuppressive cells in the tumor microenvironment (TME), driving tumor progression and contributing to poor prognosis in cancer patients. Due to their pivotal role, TAMs have emerged as a promising target for immunotherapies. However, current TAM-targeting monotherapies show only modest efficacy in clinical trials in solid tumors . Here, we have developed a new class of cancer immunotherapies: myeloid-targeted immunocytokines and NK-T cell enhancers (MiTEs). MiTEs are trans-acting immunocytokines with tumor-specific activation, allowing dual targeting of TAMs and lymphocytes by TREM2 antagonism and cytotoxic effector cell activation through IL-2. To avoid off-target toxicities, MiTEs contain an IL-2 masking moiety, which is cleaved by a TAM-specific protease. MiTEs demonstrate high efficacy in preclinical tumor models through extensive immune reprogramming spanning TAM, T and NK cell compartments. MiTEs show transformative potential for treating solid-cancers by inducing potent multi-arm anti-tumor immunity and minimizing toxicities.

overall_design: hTREM2 mice were s.c. injected with 1M MC38 tumor cells (day 0). Mice were intravenously treated with 200 µg per dose of anti-RSV, anti-TREM2, anti-PD-1, anti-TREM2 + anti-PD1, anti-CTLA-4, anti-TREM2 + anti-CTLA-4, MiTE-144, MiTE-144 + anti-PD1, or MiTE-144 + anti-CTLA-4 on days 8 and 10 (n = 5). Immune cells were isolated on day 11, FACS sorted (total CD45+ and T/NK cell enrichment) and underwent scRNAseq employing SPID-seq resulting in a total of 45,505 high-quality cells from 45 mice.

first: Michelle

last: von Locquenghien

first: Pascale

last: Zwicky

first: Ken

first: Diego

last: Jaitin

first: Fadi

last: Sheban

first: Florian

last: Uhlitz

first: Chamutal

last: Gur

first: Reut

last: Sharet Eshed

first: Eyal

last: David

first: Kfir

last: Mazuz


title: lncRNA CISTR-ACT regulates cell size in human and mouse by guiding FOSL2  [ChIP-seq]

city: Toronto

first: Philipp

last: Maass

state: Ontario

address: 686 Bay St

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

summary: Organisms regulate cell size and shape to function efficiently. Aberrant cell morphogenesis is commonly associated with disease, yet gene-regulatory mechanisms remain unknown. CISTR-ACT was the first lncRNA involved in inter-chromosomal contacts and Mendelian disease, and is associated with mean corpuscular volume (red blood cell size). Here, functional dissection of CISTR-ACT’s DNA- and RNA-encoded mechanisms by in vitro and in vivo perturbations reveal that CISTR-ACT regulates cell size across cell types and species. CISTR-ACT’s locus is embedded in a stable inter-chromosomal environment which contains cell size genes that are regulated by CISTR-ACT in trans. CISTR-ACT’s RNA also has function and directly interacts with transcription factor FOSL2 to guide its regulation of cell morphogenesis and cell-cell adhesion genes. In the absence of CISTR-ACT, the FOSL2-chromatin binding is perturbed. Our study exemplifies how a functionally conserved lncRNA regulates cell size with multiple modes of action and ultimately   contributes to clinically relevant phenotypes.

overall_design: FOSL2 ChIPseq in RPMI 2650 cells.

first: Katerina

last: Kiriakopulos

first: Katty

last: Soleimanpour

first: Brandon

last: McMurray

first: Benjamin-Israel

last: Moke

first: Jordan

last: Chalmers

first: Jeremy

last: Newton

first: Milad

last: Mokhtaridoost

first: Taylor

last: De Young

first: Kate

last: Delfosse

first: Mai

last: Ahmed

first: Cassandra

last: Wong

first: Sigmar

last: Stricker

first: Yun

first: Brian

last: Nieman

first: Anne-Claude

last: Gingras

first: Monica

last: Justice

first: Julie

last: Lefebvre

middle: G


title: LncRNA CISTR-ACT regulates cell size in human and mouse by guiding FOSL2 [RNA-Seq]

first: Philipp

last: Maass

summary: Organisms regulate cell size and shape to function efficiently. Aberrant cell morphogenesis is commonly associated with disease, yet gene-regulatory mechanisms remain unknown. CISTR-ACT was the first lncRNA involved in inter-chromosomal contacts and Mendelian disease, and is associated with mean corpuscular volume (red blood cell size). Here, functional dissection of CISTR-ACT’s DNA- and RNA-encoded mechanisms by in vitro and in vivo perturbations reveal that CISTR-ACT regulates cell size across cell types and species. CISTR-ACT’s locus is embedded in a stable inter-chromosomal environment which contains cell size genes that are regulated by CISTR-ACT in trans. CISTR-ACT’s RNA also has function and directly interacts with transcription factor FOSL2 to guide its regulation of cell morphogenesis and cell-cell adhesion genes. In the absence of CISTR-ACT, the FOSL2-chromatin binding is perturbed. Our study exemplifies how a functionally conserved lncRNA regulates cell size with multiple modes of action and ultimately contributes to clinically relevant phenotypes.

overall_design: RNAseq from CRISPR techniques (Cas9, CasRx, CRISPR-Display) to modulate CISTR-ACT in C-28/I2, RPMI 2650, K562, and iPSC-derived neural progenitor cells. RNAseq from Cistr knockout mouse tissue (blood, bone marrow, cerebellum, cerebral cortex, hippocampus, hypothalamus).

first: Katerina

last: Li


title: Circular RNA PTPN4 Contributes to Blood-Brain Barrier Disruption During Early Epileptogenesis

city: nanjing

first: jiurong

last: yang

institute: 东南大学

summary: Circular RNAs (circRNAs) are crucial regulators of gene expression, exhibiting dynamic expression patterns during both normal brain development and diverse pathological states. In this study, we report the elevated expression of CircPTPN4 in the brain tissue and plasma during early epileptogenesis in a murine temporal lobe epilepsy model. Overexpression of CircPTPN4 disrupts the tight junctions of brain microvascular endothelial cells (BMECs), compromising blood-brain barrier (BBB) integrity. Mechanistically, CircPTPN4 functions as a competitive endogenous RNA by sequestering miR-145a-5p, thereby upregulating endothelin-converting enzyme-1 (ECE-1). Subsequent ECE-1-mediated endothelin-1 (ET-1) production activates the p38/MAPK pathway, downregulating tight junction protein expression. Knockdown of CircPTPN4 attenuated tight junction disruption and BBB impairment during acute epileptogenesis while reducing spontaneous seizure frequency in chronic epilepsy. These findings establish the CircPTPN4/miR-145a-5p/ECE-1 axis as both a diagnostic biomarker and therapeutic target for BBB preservation in early-stage epilepsy.

overall_design: This study employed a mice model of temporal lobe epilepsy (TLE) and an in vitro epileptic discharged neuron model to investigate the integrity of the BBB and the tight junctions of brain microvascular endothelial cells (BMECs) under epileptic conditions.To identify dysregulated circRNAs in the brains of epileptic mice, we performed circRNA sequencing analysis on cortical tissue 24 hours after status epilepticus. Furthermore, circRNA-miRNA interactions and miRNA-target gene associations were examined through biotinylated RNA pull-down assays, fluorescence in situ hybridization (FISH), and luciferase assays. In vivo viral interventions were utilized to modulate gene expression, including the knockdown and overexpression of circPTPN4 and endothelin-converting enzyme-1 (ECE-1), while miR-145a-5p mimics and inhibitors were applied in vitro to evaluate their functional effects.

first: Jiurong

last: Yang


title: The Drosophila OSC Genome: A Resource for Studies of Transposon and piRNA Biology [smallRNA-Seq]

status: Public on Nov 17 2025

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Accurate genome assemblies are critical for understanding small RNA-mediated genome defense. In animals, the PIWI-interacting RNA (piRNA) pathway protects genome integrity by silencing transposable elements. Studying how piRNAs are generated and how they guide heterochromatin formation requires complete reconstruction of genomic piRNA source loci and detailed transposon maps. Here, we present a high-quality de novo genome assembly of Drosophila melanogaster ovarian somatic cells (OSCs), a widely used cell line that recapitulates nuclear piRNA biology. The OSC genome differs substantially from the reference genome, with major differences in transposon content and piRNA cluster composition. Our assembly resolves the 700 kb flamenco locus, the primary piRNA cluster in OSCs, and provides a genome-wide transposon map. Using this resource, we characterize piRNA source loci, reveal how piRNA cluster composition determines transposon-derived piRNA profiles, and clarify the widespread impact of the nuclear piRNA pathway on heterochromatin. Finally, we provide an open platform for integrating user-generated datasets with the OSC genome, creating a community resource for studying transposon control and piRNA biology.

overall_design: Sequencing of Argonaut bound small RNAs from wildtype and Armitage depleted cells. In addition small RNA data of an experiment where flamenco transcription is reduced by promoter proximal tethering of silencing domains.

first: Julius

last: Brennecke


title: Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression [Hi-C]

city: Los Alamos

first: Eric

middle: M

last: Small

state: New Mexico

address: Bikini Atoll Rd.

department: Earth and Environmental Sciences Division

institute: Los Alamos National Laboratory

summary: Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states such as cancer. Therapies focused on epigenetic modulation alter gene expression to correct dysfunction, though the mechanisms and perpetuation of these states is unknown. Here, we use integrated epigenomics and three-dimensional chromatin structure-function analyses after acute histone deacetylase inhibitor cancer drug treatment (suberoylanilide hydroxamic acid in lung cancer cells). Treatment induced substantial (13%) genomic rearrangement that rebounds despite persistent gene expression changes and spreading of acetylation. The chromatin functional landscape (accessibility, active transcription modification, and gene expression) is controlled and locus-specific, while chromatin contacts are globally altered resulting in a moderate weakening of topologically associating domains. Chromatin states are more dynamic at transcriptionally active loci while genes with reduced expression are epigenetically stable suggesting chromatin architectural turnover and nucleosome remodeling is locus-specific and underlies the bidirectional expression changes. Thus, local 3D chromatin and genome structural dynamics is integral for loci regulation in response to epigenomic perturbation. The partial persistence of these altered features may have larger implications for efficacy of epigenetic drugs in amelioration of disease states.

overall_design: We performed multi-omic assessments of human lung carcinoma (A549) cells with and without HDACi drug treatment to identify genome-wide transcriptional, epigenomic, and chromatin structural responses. A concentration of 10 µM SAHA was chosen for subsequent experiments as this treatment considerably altered acetylation on lysine 27 of histone 3 (H3K27ac) while still retaining viable cells at 48 hours post treatment for chromatin structure-function characterization. Time course experiments were conducted in triplicate; control (mock-treated) and treated (10 µM SAHA) A549 cells were collected at 24 and 48 hpt. Genome-wide assays for control and treated paired cells included ChIP-seq (H3ac, H3K27ac, H3K4me3) and RNA-seq, each with three biological replicates, and Hi-C with two biological replicates. ATAC-seq samples from three biological replicates per condition were generated from a separate repeated experiment.

first: Vrinda

last: Venu

first: Cullen

last: Roth

first: Samantha

middle: H

last: Adikari

first: Anna

last: Vlot

first: Kyle

middle: A

last: Sullivan

first: Chanaka

last: Abeyratne

first: Daniel

last: Jacobson

first: Shawn

middle: R

last: Starkenburg

first: Karissa

middle: Y

last: Sanbonmatsu

first: Christina

last: Steadman


title: Deciphering Precursor Cell Dynamics in Esophageal Preneoplasia via Genetic Barcoding and Single-Cell Transcriptomics

first: Jinho

last: Jang

state: Texas

address: 1755 Wyndale Street

institute: MD Anderson Cancer Center

summary: Cancer cell lineage plasticity complicates tumor initiation and progression. Using genetic barcoding and single-cell RNA sequencing (scRNA-seq), we mapped esophageal preneoplastic cell lineages and developed the eXamined Ridge (XR) score to identify high-plasticity cells. We discovered preneoplastic precursor cells (PNPCs) as key progenitors and identified Nfib and Qk as conserved markers, highlighting potential biomarkers for early cancer detection and intervention.

overall_design: For scRNA-seq analysis, esophageal organoids were derived from Trp53^floxed/floxed mice, with Ad-Cre-EGFP introducing Trp53 knockout, followed by CRISPR/Cas9-mediated Cdkn2a or Notch1 knockout to generate PC and PCN organoids. Organoid cells were dissociated, cultured in DMEM + 10% FBS with Y-27632, and maintained without Y-27632 after three passages before single-cell analysis.

first: Kyung-Pil

last: Ko

first: Jie

last: Zhang

first: Sohee

last: Jun

first: Jae-Il

last: Park


title: Dietary sulfur amino acid restriction elicits a cold-like transcriptional response in inguinal but not epididymal white adipose tissue of male mice

city: Ithaca

first: Philip

last: Ruppert

address: 244 Garden Avenue

department: Division of Nutritional Sciences

institute: Cornell University

summary: Introduction: About 1 billion people are living with obesity worldwide. GLP-1-based drugs have massively transformed care, but long-term consequences are unclear in part due to reductions in energy expenditure with ongoing use. Diet-induced thermogenesis (DIT) and cold exposure (CE) raise EE via brown adipose tissue (BAT) activation and beiging of white adipose tissue (WAT). Methionine restriction (MetR) is a candidate DIT stimulus, but its EE effect has not been benchmarked against CE, nor have their tissue-level interactions been defined. Objective & Methods: In a 2×2 design (Control vs. MetR; room temperature, RT: 22 °C vs. CE: 4 °C for 24 h), we used male C57BL/6N mice to benchmark MetR-induced thermogenesis against CE and mapped how diet and temperature interact across tissues. Bulk RNA-seq profiled liver, iBAT, iWAT, and eWAT. Differential expression was modeled with main effects and a diet×temperature interaction. KEGG GSEA was used to assess pathway-level enrichment. Results: MetR increased EE at RT and shifted fuel use towards lipid oxidation, supporting MetR as a bona fide DIT stimulus. CE elevated EE across diets and blunted diet differences. Transcriptomic responses were tissue-specific: in liver, CE dominated gene induction while MetR and CE cooperatively repressed genes. The combination enriched glucagon/AMPK-linked and core metabolic pathways. In iBAT, CE dominated thermogenic and lipid-oxidation programs with minimal MetR contribution. In iWAT, MetR and CE acted largely additively with high concordance, enhancing fatty-acid degradation, PPAR signaling, thermogenesis, and TCA cycle pathways. In eWAT, robust co-dependent and synergistic differential expression emerged only with MetR+CE. Conclusion: MetR is a genuine DIT stimulus that remodels metabolism in a tissue-specific manner. Our study provides a tissue-resolved transcriptomic resource that benchmarks diet-induced (MetR) against cold-induced thermogenesis and maps their interactions across liver, iBAT, iWAT, and eWAT.

overall_design: RNA-seq profiling of Liver, iWAT, iBAT and eWAT from C57BL/6N mice (Taconic) exposed to Sulfur amino acid restriction (0.12% Methionine, 0% Cysteine) or Control diets (0.86% Methionine, 0% Cysteine) (Research diets cat no. A11051301B and A11051302B) for 7 days +/- 24h of Cold exposure (22°C to 4°C).

first: Philip M

first: Aylin

middle: S

last: Güller

first: Marcus

last: Rosendal

first: Natasa

last: Stanic

first: Jan-Wilhelm

last: Kornfeld


title: Limb-on-a-Chip: An All-Hydrogel Platform for Scalable and Reproducible Engineering of Neuromuscular Tissues

city: Cambridge

first: Ritu

last: Raman

state: MA

address: 77 Massachusetts Avenue

department: Mechanical Engineering

institute: Massachusetts Institute of Technology

summary: Disease or damage that impacts neuromuscular tissues thus has a severe negative impact on health, mobility, and quality-of-life, motivating the development of tissue engineered models of the motor control system. Here we present a 1-step fabrication method for manufacturing an all-hydrogel organ-on-a-chip with a spinal cord-inspired design, enabling reproducible patterning of multiple independent motor units.

overall_design: C2C12 myoblasts, wild type(WT) and genetically encoded calcium indicator line(RGECO), grown on a methacrylated gelatin hydrogel and differentiated for 14 days before RNA extraction.

first: Angel

last: Bu

first: Laura

last: Schwendeman

first: Sonika

last: Kohli

first: Tamara

last: Rossy


title: Age and cell type specific specific effects of histone variant H2BE in the brain [Cortex_CUT&Tag]

status: Public on Nov 13 2025

city: Philadelphia

first: Sean

last: Louzon

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Transcription is regulated in part through histone proteins that complex with DNA and control access to genes. Histones can be replaced with variant forms that are particularly critical in the brain and accumulate throughout lifespan. Recently, we defined the first broadly expressed H2B variant, H2BE, and demonstrated that it regulates chromatin structure, neuronal transcription, and mouse behavior. However, the role of H2BE in other cell types and its role throughout lifespan remain unknown. Here, we discovered that H2BE is highly expressed in astrocytes as well as neurons and accumulates with age in both cell types. Using single-nucleus RNA-sequencing, we demonstrate that loss of H2BE robustly affects gene expression in both astrocytes and neurons, with divergent effects in young and aging brains. Interestingly, loss of H2BE in young brains causes similar gene expression changes as aging and some effects of aging are reversed with H2BE loss. Lastly, behavioral testing demonstrates that H2BE loss disrupts long-term memory but improves working memory in aging mice. Together, these data provide novel links between histone variants, aging-related gene expression changes in both astrocytes and neurons, and memory.

overall_design: Cortex tissue was isolated from male mice at 3, 12, and 18 months of age and then underwent Cut&Tag-sequencing with H2BE (Millipore ABE1384) or IgG antibody (Sino Biological CR1). 2 H2BE biological replicates per age, 1 IgG biological replicate per age.


title: Age and cell type specific specific effects of histone variant H2BE in the brain [E2F_CUT&Tag]

overall_design: Cortical astrocytes were isolated from WT P1 mouse pups. They were cultured for 7 days before collection for control samples. Passaged samples were split after 7 days in culture and then grew for an additional 12 days before collection for Cut&Tag-sequencing. (n = 3 biological replicates)


title: Integrated Multiomics Profiling Uncovers miRNA-Guided Regulatory Networks After Spinal Cord Injury in Rats [mRNA-seq]

city: Vestec

first: Ruslan

last: Klassen

address: Průmyslová 595

department: Institute of Biotechnology

country: Czech Republic

institute: Czech Academy of Science

summary: Spinal cord injury (SCI) is a debilitating condition with no effective treatment. The injury triggers a complex cascade of molecular and cellular events that drive both damage and repair processes. To explore these mechanisms, we performed a comprehensive multiomics analysis in a rat compression model of SCI, focusing on the acute phase. Transcriptomic profiling revealed extensive gene dysregulation, highlighting early inflammation, neuronal death, and synaptic dysfunction, followed by the initiation of reparative processes. Cell type composition analysis showed a rapid infiltration of peripheral immune cells, activation of microglia, and loss of neurons, astrocytes, and oligodendrocytes. miRNA profiling uncovered a highly dysregulated miRNA landscape, with the miR-17~92 cluster emerging as a key regulator of neurogenesis, synaptic activity, and cell survival. Integrative miRNA-mRNA-protein analysis identified potential therapeutic targets, including miR-20a, whose inhibition in vitro supported neurogenesis and reduced apoptosis under oxidative stress. Our findings provide new insights into the molecular mechanisms of SCI and highlight miRNAs as potential targets for therapeutic intervention.

overall_design: Adult male Wistar rats (n=64) were used as an experimental model. The rats were obtained from the facility's breeding center (Physiological Institute of the Academy of Sciences of the Czech Republic, Prague, Czech Republic). Animals undergoing surgery weighed 300 ± 30 g and were 10 weeks old. Animals were maintained on a 12-h light/dark cycle with ad libitum access to food and water. Rats were randomly divided into experimental groups: SCI 3 hpi (n=4), 12 hpi (n=4), 24 hpi (n=4), 3 dpi (n=4), 7 dpi (n=4), time- corresponding shame-operated groups (n=4 for each group) and an intact control group (n=4), also 8 animals were used for behavioral tests and 12 animals were used for immunohistochemical analysis.

first: Sarka

last: Chytilova

first: Ivan

last: Arzhanov

first: Daniel

last: Zucha

first: Eva

last: Rohlova

first: Peter

last: Androvic

first: Pavel

last: Abaffy

first: Lucia

last: Urdzikova-Machova

first: Mikael

last: Kubista

first: Nataliya

last: Romanyuk

first: Lukas

last: Valihrach


title: Integrated Multiomics Profiling Uncovers miRNA-Guided Regulatory Networks After Spinal Cord Injury in Rats [miRNA-seq]


title: Modified loop2 epegRNA improve prime editing efficiency.

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

summary: Prime editor (PE) has wide application prospects in disease treatment due to its diversity of editing outcomes. However, the editing efficiency of PE still needs to be further improved for therapeutic applications. Here, we increase the probability of hybridization of the pegRNA primer binding site (PBS) to single-stranded DNA flap by adding additional PBS sequence and reverse transcription template (RTT) to the loop region of pegRNA. The selection of loop and the design of loop length are optimized. The resulting modified loop2 epegRNA (ML-epegRNA) showed higher prime editing efficiency than that of the epegRNA in HEK293T cells. In addition, we used ML-epegRNA for PE editing of multiple editing types in multiple cell lines, and the results showed a general improvement in editing efficiency. Overall, the ML-epegRNA expands the capabilities of genome editing tools.

overall_design:
After the plasmid with PE protein components and designed pegRNA was transferred into the cells, the positive cells were separated by flow sorting and the genome was extracted. Use site-specific primers with second-generation sequencing adapters to amplify target sites via PCR for library construction. High-throughput sequencing by Illumina NovaSeq6000.

Please note that the records have been updated with additional samples (GSM9556967-GSM9557028) and new processed data file (processed_data20251206.xlsx) on Mar 3, 2026.

first: Bailun

last: Li

first: Zhike

last: Lu

first: Ting

last: Zhou

first: Huilin

last: Mou

first: Zhilin

last: Zou

first: Wenyu


title: RNA-seq analysis of YUMM1.7 mouse melanoma cells treated with ADAR1i-124 or 5-AZA-CdR to study their effects on RNA editing

first: Haoran

last: Zhang

state: Pennsylvania

address: 415 Curie Boulevard

summary: ADAR1i-124 is a small-molecule RNA editing inhibitor that can block the editase domain of ADAR1 and robustly suppress the A-to-I RNA editing on double-stranded RNAs (dsRNAs). 5-AZA-CdR is an FDA-approved DNA methyltransferase inhibitor (DNMTi) that can increase the transcription of transposable elements and thus induce more dsRNAs. To determine the efficacy of ADAR1i-124 and test whether it has overlapping targets or synergistic effects with 5-AZA-CdR, total RNA-seq analysis was performed on YUMM1.7 cells treated with 5-AZA-CdR (1 uM, 72 h), ADAR1i-124 (10 uM, 12 h) or combination of two treatments , using 0.1% DMSO as control. Immunoprecipitation (IP) with the J2 or Z22 antibodies was also adopted to enrich the dsRNA species and investigate how drugs affect the dsRNA forms and IP enrichment.

overall_design: Total RNA-seq profiling of YUMM1.7 mouse melanoma cells treated with DMSO, ADAR1i-124_10uM_12h, 5-AZA-CdR_1uM_72h or two drug combination. Besides, the RNA pools were also enriched for dsRNA species by IP_J2 or IP_Z22 and then subjected to RIP-seq.

first: Moeko

last: Minakuchi

first: Qin

first: Kazuko

last: Nishikura


title: Age and cell type specific specific effects of histone variant H2BE in the brain [snRNA-seq]

first: Sean

last: Louzon

overall_design: Nuclei were isolated from cortices of 2-4 month old (young) and 18 month old (old) WT and H2BE-KO mice. Nuclei capture and library preparation were performed using single-nucleus Drop-seq (n=3 biological replicates per genotype for young and n=2 biological replicates per genotype for old)


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783_batchE

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

summary: This study aimed to identify transcript expression induced by digestion-related herbal medicines (DHM) and modes of action (MOA) of DHM in SW1783 cell line. For the production of THM-induced transcripts, digestion herbal medicines water extract (THW) and digestion herbal medicines ethanol extract (THE) were used.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin, LY294002, and thioridazine 10uM, respectively), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively.


title: GFP Reporter System Reveals Cell-to-Cell Variability in Aquaporin-2 Expression

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary: Vasopressin regulates transcription of the aquaporin-2 gene (Aqp2) in collecting duct principal cells. To investigate regulatory mechanisms in Aqp2 gene transcription, we engineered an Aqp2 reporter cell line using CRISPR/Cas9 to insert a green fluorescent protein (GFP) cassette at the endogenous Aqp2 gene locus in mpkCCD cells. In the absence of dDAVP, a vasopressin analog, these cells exhibited low or undetectable GFP and Aqp2 expression in all cells. dDAVP stimulation (1nM dDAVP for 48hrs) markedly increased both GFP and Aqp2 expression together with reversal upon dDAVP removal. These observations demonstrate that GFP faithfully tracks Aqp2 expression. Interestingly, fewer than 50% of cells express GFP and Aqp2 after dDAVP or forskolin, indicating significant variability even though they were clonally-derived. We flow-sorted  the GFP- cells (Aqp2-) and GFP+ cells (Aqp2+), regrew them, and restimulated them separately with dDAVP.  Cells originating from GFP- cells gave rise to both GFP- cells and GFP+ cells, and GFP+ cells similarly regenerated both GFP- and GFP+ populations in the same proportion. Flow cytometry analysis of the DNA content showed variability in cell cycle phases, with most GFP+ cells in G0/G1, and more GFP- cells in G2/S. RNA-seq analysis of the GFP- and GFP+ cells revealed increased abundance of cell-cycle related transcripts in the GFP- cells. We conclude that: 1) heterogeneity in Aqp2 expression is related to cell cycle state; and 2) the newly generated reporter cell line will likely serve as a useful tool to study Aqp2 transcriptional regulation.

overall_design: To provide a surrogate marker for Aqp2 expression and to investigate the mechanisms of vasopressin-mediated heterogeneity, we developed an Aqp2-GFP reporter cell line using CRISPR/Cas9-mediated gene editing—a technique that has revolutionized genetic engineering. By tagging the endogenous Aqp2 gene with GFP in mouse collecting duct cells (mpkCCD), we were able to directly visualize and quantify Aqp2 expression in living cells. Here, we show that GFP faithfully tracks the Aqp2 expression and could servers as a reporter for Aqp2 transcriptional regulation. We further investigate the heterogeneity of Aqp2 expression using RNA-seq and FACS analysis and show that the heterogeneity is partially driven by the cell cycle. Finaly, our reporter cell line could provide as a powerful tool for studying Aqp2 transcriptional regulation in future studies screening for both positive and negative regulators.

first: Mark

last: Knepper


title: Age and cell type specific specific effects of histone variant H2BE in the brain [Cut&Tag]

overall_design: Cortical astrocytes were isolated from WT P1 mouse pups. They were cultured for 7 days before collection for Cut&Tag-sequencing. (n = 3 biological replicates)


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID. [ChIP-seq]

city: Montréal

first: Javier

last: Di Noia

state: QC

address: 110 Pine Avenue West

institute: Institut de recherches cliniques de Montréal (IRCM)

summary: Activation-induced deaminase (AID) initiates class switch recombination (CSR) and somatic hypermutation of immunoglobulin genes, which are required for efficient antibody responses. Collaterally, AID can also mutate a set of off-target genes with oncogenic consequences. The mechanisms that make such loci susceptible to AID are not fully understood. We find that the H3K79 histone methyltransferase DOT1L is located close to AID in the nucleus. Not only does DOT1L activity facilitate CSR, but it also facilitates AID off-target activity, including Igh-cMyc translocations. Genes mutated by AID display high DOT1L activity. DOT1L deficiency causes mostly increased nascent transcription, accompanied by a modest reduction in RNAPII occupancy. By integrating different genomic approaches, we discovered that DOT1L restricts the velocity of transcription elongation proportionally to the level of higher order H3K79 methylation (H3K79me2/3) and favors RNAPII pausing. These transcriptional conditions enhance AID occupancy and, consequently, its activity. Our data indicate a role for DOT1L and H3K79me2/3 in limiting transcription and highlight stronger RNAPII pausing and attenuated RNAPII elongation velocity as critical steps for productive AID association and mutagenesis at target loci. Furthermore, increased transcription elongation velocity could explain both upregulation and downregulation of genes in DOT1L-deficient cells.

overall_design: Quantitative ChIP-seq for RNAPII, S2P-RNAPII, S5P-RNAPII, Rad21 and Nipbl in WT and Dot1l-/- CH12F3-G cells; and ChIP-seq for H3K79me2 and H3K79me3 in WT CH12F3-G cells.

first: Poorani Ganesh

last: Subramani

first: Noé

last: Seija

first: Jana

last: Ridani

first: Jonathan

last: Boulais

first: Paul

last: Donnelly

first: Mélanie

last: Provencher

first: Halil

last: Bagci

first: Christian

last: Poitras

first: Jean-François

last: Côté

first: François

last: Robert


title: Age and cell type specific specific effects of histone variant H2BE in the brain [RNASeq]

overall_design: Cortical astrocytes were isolated from WT P1 mouse pups. They were cultured for 7 days before RNA collection for sequencing. (n = 3 biological replicates)


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783_batchC


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_A549_batchE

summary: This study aimed to identify transcript expression induced by digestion-related herbal medicines (DHM) and modes of action (MOA) of DHM in A549 cell line. For the production of THM-induced transcripts, digestion herbal medicines water extract (THW) and digestion herbal medicines ethanol extract (THE) were used.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin 10uM), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively.
Please note that the processed data 'RCM_digestion_A549.txt' contains the data from all batchA-batchE datasets.


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_A549_batchD


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID. [TT(chem)-seq]

overall_design:
To investigate changes in nascent transcription upon Dot1l depletion, CH12F3-G Dot1l knockout cells were generated by CRIPSR.
We then perform paired-end TT(chem)-seq of unstimulated WT and Dot1l-/- CH12F3 cells, using S. cerevisiae (strain BY4741) cells as spike-in controls.


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_A549_batchA


title: Age and cell type specific specific effects of histone variant H2BE in the brain [Intact_RNAseq]

overall_design: Cortical nuclei were isolated from P0, P14, and P28 male mouse pups. Mice were heterozygous for the CAG-Sun1/sfGFP nuclear marker and NEX-cre. Cre-expressing cortical nuclei were isolated using isolation of nuclei tagged in specific cells type (INTACT) immunpurification method. (n = 4 biological replicates per age)


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783_batchA


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HT29_batchE

summary: This study aimed to identify transcript expression induced by digestion-related herbal medicines (DHM) and modes of action (MOA) of DHM in HT29 cell line. For the production of THM-induced transcripts, digestion herbal medicines water extract (THW) and digestion herbal medicines ethanol extract (THE) were used.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin 10uM), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively. As a result of RNA sequencing analysis, outlier values that did not produce results due to low RNA concentration were excluded from the sample.


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_A549_batchB


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HT29_batchD


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HT29_batchB


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_A549_batchC


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HT29_batchC


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2_batchE

summary: This study aimed to identify transcript expression induced by tonifying herbal medicines (THM) and modes of action (MOA) of THM in A549 cell line. For the production of THM-induced transcripts, digestion herbal medicines water extract (THW) and digestion herbal medicines ethanol extract (THE) were used.


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783_batchD


title: Age and cell type specific specific effects of histone variant H2BE in the brain [ATACSeq]

overall_design: Cortical astrocytes were isolated from WT P1 mouse pups. They were cultured for 7 days before collection for ATAC-sequencing. (n = 3 biological replicates merged)


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2_batchD


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HT29_batchA


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2_batchB


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID. [RNA-Seq]

overall_design:
To investige gene expression changes upon Dot1l depletion, CH12F3-G Dot1l knockout cells were generated by CRIPSR.
We then perform paired-end RNA-seq of unstimulated WT and Dot1l-/- CH12F3 cells, using Kc167 cells as spike-in controls.
Differential gene expression for WT vs Dot1l-/- CH12F3-G cells. Normalized counts, log2 fold changes and DESeq2 padj values are in the supplementary file "norm_counts.txt".

first: Poorani


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID. [CUT&RUN]

overall_design: CUT&RUN for Rpb1 and CTCF in WT and Dot1l-/- CH12F3-G cells; and CUT&RUN for H3K27me3 in WT CH12F3-G cells.


title: The effects of IL-16 deficience on gene expression after 24 week high-fat diet in mice

status: Public on Nov 12 2025

city: Gui'an

first: Hailong

last: Ou

state: Guizhou

address: No.6 Ankang Avenue

institute: Guizhou Medical University

summary: IL16-/-ApoE-/- mice and ApoE-/- mice were fed with high-fat diet for 24 weeks. The aortas from the two group mice were isolated for RNA-sequencing. Results showed that IL16-/- deletion caused a total of 1201 genes was altered, of which 943 genes were upregulated and 258 genes were downregulated in mice. Genes encoding membrane and extracellular components were remarkably enriched by Gene Ontology (GO) analysis, such as Collagen I α1 (ColIα1), ColIα2, Elastin, Filamin-α (Flnα), integrin beta 1 (Itgb1) and TIMP-3.

overall_design: We generated double-mutant mice (IL-16-/-ApoE-/-). The mice and ApoE-/- mice were treated with high-fat diet for 24 weeks at the age of 8-week. Then, the aorta were isolated for RNA-sequencing.


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID

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

overall_design: Refer to individual Series


title: Oligodendroglial hypothesis of autism: the primary role of master regulator gene Baf155 [ChIP-Seq]

status: Public on Nov 11 2025

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

summary: Autism spectrum disorders (ASD) are polyetiological neurodevelopmental disorders associated with both genetic and non-genetic risk factors with complex and heterogeneous clinical manifestations. A single susceptibility gene usually fails in triggering an intricate array of autistic symptoms, suggesting a primary mechanism may be required to integrate multiple susceptibility genes in casing the disease. Recent evidence highlights the role of myeline disruption in pathogenesis of ASD. However, neither the mechanisms of impaired myelination nor its contribution to ASD symptomatology are fully characterized. We demonstrate the loss of Baf155, a newly recognized autistic susceptibility gene that encodes a core member of the chromatin remodeling complex, affects oligodendroglial differentiation and myelination. BAF155 targets multiple synapse-related genes in oligodendrocyte precursor cells (OPCs), these genes being responsible for regulating the synaptic communication between OPCs and neurons. Heterogeneous target genes affected by BAF155 deficiency in OPCs across various brain regions leads to significant impairments in myelination which may contribute to the diverse manifestations observed ASD patients. Taken together, our findings reveal a primary mechanism that orchestrates multiple ASD susceptibility genes in instigating the disease.

overall_design: ChIP-seq technology is used to determine BAF155 binding sites in primary oligodendrocyte precursor cell (OPC) culture on day 1 and day 5 during differentiation.

first: Jianqin

last: Niu

first: Lan

last: Xiao

first: Xiaorui

last: Wang

first: Qi


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2_batchC

first: Musun

last: Park


title: Oligodendroglial hypothesis of autism: the primary role of master regulator gene Baf155 [RNA-Seq]

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: To investigate whether BAF155 modulates the responses of OPCs to neuronal inputs in distinct brain regions, we assessed the differentially expressed genes in acutely isolated OPCs from mPFC and hippocampus of Baf155 knockout mice and their non-Cre littermates by RNA-seq . In line with that, we analyzed the variability of OPCs from mPFC and hippocampus response to different neurotransmitters(Glutamate/GABA) by RNA-seq.


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783_batchB


title: RNA-seq analysis of perichondral tissues obtained from rabbit

city: Shanghai

first: Hai

last: Tang

address: 507 Zhengmin Road, Yangpu District, Shanghai, China

institute: Shanghai Pulmonary Hospital affiliated to Tongji University

summary: RNA sequencing for 6 samples

overall_design: Examing 2 conditions, each with 3 replicates

first: Chang

last: Chen


title: Gene expression profile at single cell level of Tendon at neonate or adult sample with or without injury

city: 北京市

first: 美莲

last: 蔡

state: 北京市

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

summary: We used single cell RNA sequencing (scRNA-seg) to analyze the  diversity of tendon cells at different ages with or without injury. W

overall_design: We compared the gene expression profiles of cells isolated from control and injury tendon tissues both in neonatal period (postnatal day 3, P3) and adult (6-8 weeks).

first: Liujing

first: Meilian

last: Cai

first: Shuai

last: Lin

first: Ruili

last: Yang


title: Comparative Single-Cell Transcriptomics of Immune Profiles in LADA Versus Type 1 Diabetes

status: Public on Nov 09 2025

city: Moscow

first: Vadim

last: Chechekhin

address: Leninskie gory 1

country: Russia

institute: Lomonosov Moscow State University

summary: Autoimmune diabetes encompasses rapidly progressive type 1 diabetes mellitus (T1D) and indolent latent autoimmune diabetes in adults (LADA), yet the immunological drivers of this kinetic divergence remain unresolved. We performed single-cell RNA sequencing with paired T and B cell receptor profiling on over 400,000 peripheral blood mononuclear cells (PBMCs) from patients with LADA, newly diagnosed T1D, and healthy controls. PBMC composition was comparable across cohorts, indicating that qualitative rather than quantitative immune differences underlie disease heterogeneity. In T1D, pan-lineage activation of NF-kB, EGFR, MAPK, and hypoxia pathways, coupled with a TNF-centered communication hub, enhanced MHC signaling, and disrupted adhesion, promoted systemic inflammation. LADA, by contrast, exhibited global suppression of NF-kB/EGFR activity, retention of moderate JAK/STAT tone, reinforced natural killer cell inhibitory checkpoints via HLA-C-KIR2DL3/3DL1 interaction, and stabilized CD8+ T cell synapses through HLA-C-CD8 binding, collectively restraining effector activation. Single-cell V(D)J analysis revealed polyclonal, patient-unique adaptive repertoires, emphasizing the primacy of signaling context over receptor convergence. These findings define LADA and T1D as endpoints on an inflammatory-inhibitory spectrum and identify the NF-kB/EGFR-JAK/STAT gradient and HLA-C-KIR axis as potential therapeutic targets for preserving residual beta-cell function in autoimmune diabetes.

overall_design: scRNA-seq of PBMCs from patients with type 1 diabetes, latent autoimmune diabetes in adults, and healthy controls


title: gene expression profiles of Col1α1+Vldlr+ and Col1α1+Vldlr- TSPCs

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

summary: We here report Reln-VLDLR receptor-ligand interactions are the primary mechanism for communication between lymphatic endothelial cells (LECs) and tendon stem/progenitor cells (TSPCs). The depletion of Vldlr results in impaired tendon regeneration.Specifically, lymphoangiocrine Reelin interacts with Col1α1+Vldlr+TSPCs to activate Notch1-Srebf2 mediated cholesterol metabolism loop, maintaining TSPC stemness and enhancing tendon regeneration.

overall_design: To explore the role of Vldlr+ cells in tendon regeneration, we sorted Col1α1+Vldlr+ and Col1α1+Vldlr- TSPCs by flow cytometry.We then comparare gene expression profiling analysis of RNA-seq data for Vldlr+ and Vldlr- TSPCs.


title: Pulsed 980 nm Near-Infrared Photobiomodulation Attenuates OVA-Induced Allergic Asthma by Modulating Th2 Cytokine Responses and Inflammatory Cell Infiltration

status: Public on Nov 06 2025

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary: Photobiomodulation (PBM) is a non-invasive therapeutic strategy that uses specific light wavelengths to stimulate cellular processes that promote tissue repair, reduce inflammation, and alleviate pain. In this study, we evaluated the efficacy of a high-intensity 980 nm near-infrared (NIR) pulsed laser in a murine model of ovalbumin (OVA)-induced allergic asthma. In OVA-sensitized mice, typical allergic features were noted, including airway wall thickening, significant peribronchial and perivascular inflammatory cell infiltration, and compressed alveolar spaces. NIR PBM treatment markedly attenuated these histological changes. At the molecular level, PBM significantly downregulated type 2 cytokine gene expression, including IL-4, IL-5 and IL-13, in the lung tissue. Flow cytometry analyses further revealed that PBM reduced the infiltration of pulmonary eosinophils and inflammatory monocytes. Transcriptomic profiling coupled with gene set enrichment analysis (GSEA) indicated that PBM suppressed NF-κB-mediated inflammatory signaling while modulating Th2-related responses. Collectively, our findings demonstrate that high-intensity 980 nm NIR PBM effectively mitigates key features of allergic asthma in a murine model, supporting its potential as a non-pharmacological, non-invasive adjunct therapy for asthma management.

first: Zhengyi

last: Wu

first: Shih-Chin

last: Cheng


title: PAD4⁺ Neutrophils Promote Hepatic Stellate Cell Activation and Accelerate MASH Fibrosis Progression via NETs-DNA/TAOK1/MAPK Pathways

status: Public on Nov 07 2025

city: Nangjing

first: Jiajia

last: shen

address: No.300,guangzhou Road

institute: nanjing medical university

summary: Neutrophils play a pivotal role in the progression of metabolic-associated steatohepatitis (MASH) by mediating inflammatory responses. However, the heterogeneity of neutrophil subsets in MASH and their specific contributions to disease progression remain unclear. In this study, analysis of liver biopsies from 265 patients revealed a strong association between elevated neutrophil counts and MASH severity, particularly fibrosis. Five distinct neutrophil subsets were identified in human liver tissue, with PAD4⁺ neutrophils serving as key drivers in MASH progression. Mechanistically, PAD4⁺ neutrophils generate neutrophil extracellular traps (NETs) and activate hepatic stellate cells via the TAOK1-dependent MAPK signaling pathway. Inhibition of PAD4⁺ neutrophils in vivo attenuated the progression of liver fibrosis without exacerbating liver injury. Collectively, these findings elucidate the pivotal involvement of PAD4⁺ neutrophils in MASH progression and identify them as promising therapeutic targets for mitigating fibrosis and inflammation.

overall_design: RNA-seq dataset of neutrophis and lneutrophil extracellular trapping network intervening in human liver stellate cell LX-2


title: Rat-specific Expression of Placental MATE1 Contributes to Species Difference in Fetal Transfer of Metformin and 1-Methyl-4-phenylpyridinium

status: Public on Nov 04 2025

city: Tokyo

first: Pharmaceutics

last: Keio

address: 1-5-30 Shibakoen, Minato-ku

department: Pharmacy

country: Japan

institute: Keio University

summary: Metformin readily crosses the human placenta. However, the fetal-to-maternal plasma concentration ratio (F/M ratio) of metformin has been reported to be as low as 0.057 in rats. This study investigated the underlying mechanisms of these interspecies differences by examining the expression and function of candidate transporters, organic cation transporter 3 (OCT3/SLC22A3) and multidrug and toxin extrusion protein 1 (MATE1/SLC47A1), in the placenta across species. Expression analysis at gene and protein levels using RNA-sequencing and absolute quantification by LC-MS/MS revealed minimal species differences in placental OCT3 expression (less than 4-fold for mRNA and protein). In contrast, MATE1 showed almost exclusive expression in the rat placental labyrinth but minimal or undetectable levels were observed in samples prepared from human placental villi and mouse placental labyrinth. To evaluate the function of the placental MATE1, we compared the placental transfer of two MATE1/OCT3 substrates, metformin and 1-methyl-4-phenylpyridinium (MPP+), in pregnant rats and mice in the presence and absence of pyrimethamine, a MATE1 inhibitor. The pyrimethamine was dosed to reach the plasma concentration which specifically inhibits MATE1 based on the measured IC50 of pyrimethamine to rat Mate1 and Oct3, which were 0.015 μM and 100 μM, respectively. The F/M ratios of metformin and MPP+ in the absence of pyrimethamine were half or less in rats compared to mice. Notably, pre-administration of pyrimethamine increased the F/M ratios of metformin and MPP+ by approximately 50% in rats but not mice. These findings demonstrate that functional placental MATE1 expression is specific to rats, which, in part, contributes to the low fetal transfer of cationic compounds compared to other species. This is of significant concern, as it suggests that nonclinical developmental and reproductive toxicity studies of MATE1 substrate drugs in rats may underestimate fetal exposure and toxicity when extrapolated to humans.

overall_design: RNA-seq profiling of placental labyrinth of gestational day (GD) 17.5 C57BL/6J mice and GD 20.5 SD rats.

first: Ashukan

last: Suzuki

first: Saki

last: Noguchi

first: Toshiaki

last: Tsuchitani

first: Takuro

last: Ishinabe

first: Masatoshi

last: Tomi


title: Spatiotemporal transcriptomic and metabolomic landscapes of wild soybean seed development reveal regulatory mechanisms of nutrient accumulation [scRNA-Seq]

status: Public on Nov 02 2025

city: Harbin

first: Peiyan

last: Liu

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: Seed development is pivotal in soybean’s lifecycle, directly determining yield and nutritional quality related to oil and protein contents. However, spatiotemporally resolved mechanisms underlying cell differentiation and nutrient accumulation during seed growth remain elusive, especially in wild soybean (Glycine soja Sieb. et Zucc.), which harbors rich genetic diversity for quality traits. Here, spatial transcriptomics and metabolomics were combined to dissect their dynamics in G. soja seeds at the mid-maturity stage. Differential expression analysis characterized the distinct accumulation patterns between adaxial and abaxial embryo parenchyma cells, revealing abaxial cells are enriched in protein metabolism pathways while adaxial cells focus on lipid metabolism pathways, which is consistent with previous studies reporting spatial nutrient accumulation in G. soja seeds. Meanwhile, pseudotemporal trajectory analyses briefly supported a sequential transcriptional regulation pattern for these differences. Cell-cell communication analysis further uncovered potential signaling interactions mediating cell-type-specific differences across seed cells. Key genetic regulators and differential metabolites were identified through spatial transcriptomics and metabolomics co-expression analysis, with GsMAPK23-4 screened as a core candidate linked to cotyledon nutrient metabolism. Functional validation confirmed GsMAPK23-4 modulates seed quality: knockout mutants had significantly higher amino acids and proteins. These findings elucidate the cellular characteristics and differentiation processes in G. soja seeds at the mid-maturity stage, providing a molecular basis for understanding this phase and generating targets to improve soybean yield and quality.

overall_design: two samples from soybean seeds


title: Location and etiology modulate fibroblast activation in the failing human heart

status: Public on Nov 08 2025

city: Leuven

first: Hywel

middle: Llewelyn

last: Roderick

address: Gasthuisberg

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

summary: Cardiac fibrosis is a major contributor to heart failure (HF), yet its therapeutic targeting remains limited due to the complexity of fibrosis types and distributions. This study investigates fibroblast heterogeneity and spatial organization in the left ventricle of human hearts from non-failing donors and HF patients with ischemic or dilated cardiomyopathy. Using single-nucleus RNA sequencing and spatial transcriptomics, distinct fibroblast subpopulations were identified, with resident fibroblasts being depleted in HF and replaced by disease-associated states. Differences in activation ligands, transcriptional trajectories, and spatial localization revealed divergent fibroblast transitions between scar and interstitial fibrosis, and between HF subtypes. These results provide insight into fibroblast dynamics and offer potential targets to modulate fibrosis in heart failure.

overall_design: Nuclei from snap frozen human cardiac tissue was sequenced using 10x technology in 3 batches. 4 non-failing samples included (each 2 in one 10x lane). 6 samples from DCM, 5 samples from ICM (non-scar), and 5 samples form ICM-scar were included.

first: Mohamad

last: Youness

first: Samaneh

last: Ekhteraei-Tousi

first: Rosa

last: Doñate Puertas

first: Chandan

middle: K

last: Nagaraju

first: Karin

last: Sipido


title: CTNNB1 mutations have diverse effects on signalling in Embryonic Stem Cells

city: Leiden

first: Karamjit

middle: Singh

last: Dolt

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

summary: Bulk 3' RNA-Seq was performed on Embronic Stem Cells (E14) to explore the diverse effect of CTNNB1 mutation alongside GSK3β inhibition via CHIR99021 serving as a positive control.

overall_design: Genomewide expression profile in E14 ESCs with targetted CTNNB1 mutations and GSK3β inhibition via CHIR99021 for 48 hours. The sequncing libraries contained Read 1 (R1) and Read2(R2) for each sample. Read 1 contained the cDNA information and read 2 only the UMI and sample barcodes. R1 and R2 were combined to build R4 reads file that was alingned to mouse genome build mm10 to calculate the read counts per sample for comparision.

last: S. Dolt

first: Peter

last: Hohenstein


title: Effect of Hhex and AR deletion on mouse adrenal gene expression

status: Public on Nov 10 2025

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

summary: Glucocorticoids are cholesterol-derived steroid hormones produced by the adrenal gland and widely known for maintaining glucose homeostasis, modulating the immune system, and orchestrating the circadian rhythm. In this study, we defined HHEX as a key regulator of adrenocortical cell function. By using multiple transgenic mouse models, we demonstrate that HHEX shapes AR-dependent sexual dimorphism in the zF following the onset of puberty. HHEX protects lipid droplets integrity from lipid catabolism induced by AR signaling and its absence results in glucocorticoid insufficiency in males. Additionally, in both sexes, HHEX supports the inner zF transcriptome, including the expression of Abcb1b, a critical regulator of steroids and xenobiotics cellular levels.

overall_design: RNAseq profiling of wildtype (WT) mouse adrenal and conditional deletion of the transcription factor HHEX and androgen receptor AR in the adrenal gland

first: Typhanie

last: Dumontet


title: scRNA-seq of mouse prostate 2D and 3D organoids

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

institute: Helmholtz Institute for RNA-based Infection Research

summary: scRNA-seq of mouse prostate 2D,  3D organoids and ex-vivo prostate units

overall_design: We performed single-cell RNA-seq analysis of organoids and organoid-derived monolayers of mouse prostates treated with 5α-DHT and Ctrl.

first: Carmen

last: Aguilar

first: Antoine-Emmanuel

last: Saliba

first: Maria

last: Guedes

first: Alexander M.


title: Intracellular Delivery of Bone Nanoparticles to Mitigate Irradiation-Induced Damage in Bone Marrow Mesenchymal Stem Cells

status: Public on Nov 01 2025

city: Milwaukee

first: Bo

last: Wang

state: WI

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

summary: This study evaluated the therapeutic potential of intracellularly delivered bone-derived nanoparticles (BPs) in mitigating Ionizing radiation (IR)-induced BMSCs damage. We found that IR exposure caused significant BMSCs dysfunction, including reduced proliferation, increased apoptosis, persistent DNA damage, and a shift toward adipogenic differentiation. Treatment with BPs led to efficient intracellular uptake, improved cell morphology, enhanced proliferation, reduced apoptosis, and preservation of balanced differentiation capacity. Transcriptomic analysis via RNA sequencing revealed that BPs restored key molecular pathways disrupted by IR, particularly those involved in cell cycle regulation, extracellular matrix (ECM) remodeling, and apoptosis. By reversing these transcriptional impairments, BPs supported genomic stability and the regenerative function of BMSCs.

overall_design: The third passage BMSCs were seeded at a density of 1 × 105 cells per well in 12-well plates and divided into three experimental groups: Control group: BMSCs without IR exposure or BP co-culture. IR group: BMSCs exposed to IR treatment. IR&BP group: BMSCs exposed to IR followed by BP co-culture.After 7 days of culture, total RNA was extracted from all groups (n=3 per group) using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions. RNA concentration was measured using the Nanodrop ND-1000, and quality was assessed via capillary electrophoresis (Agilent Technologies). RNA sequencing (RNA-Seq) was performed by Novogene Corporation Inc.

first: Wang

last: Bo

first: Ma

last: Xiaolong

first: Nguyen

last: Christopher

first: Stellpflug

last: Austin

first: Li

last: Siqi

first: Han

last: Lu

first: Frei

last: Anne

first: Himburg

last: Heather

first: Gu

last: Linxia

first: Dong

last: Pengfei

last: Shue

first: Mak

last: Michael

first: Wu

last: Rongxue


title: Fluoxetine promotes recovery from noise-induced Hippocampus  degeneration

city: Seongnam

first: Hyun-Ju

last: An

state: --- Select One ---

address: Seongnam-si, 13496

institute: CHA university

summary: Fluoxetine treatment after noise exposure restored hippocampus synaptic expression of brevican and decreased low-frequency hearing thresholds. In cochlear nuclei, fluoxetine treatment decreased the expression of PNN and was predicted to upregulate the neuropeptide signaling pathway

first: Hyunju


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2_batchA

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

institute: Korean Institute of Oriental Medicine

summary: This study aimed to identify transcript expression induced by tonifying herbal medicines (THM) and modes of action (MOA) of THM in A549 cell line. For the production of THM-induced transcripts, digestion herbal medicines water extract (THW) and digestion herbal medicines ethanol extract (THE) were used.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin 10uM), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively. As a result of RNA sequencing analysis, outlier values that did not produce results due to low RNA concentration were excluded from the sample.


title: Remodeling of 3D Gene Architecture in Myocardium from Embryonic Development to Early Aging [snRNA-Seq]

city: Chengdu

first: Yuwei

last: Gou

address: No. 211, Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

summary: Heart-related diseases are increasingly attacking the younger population, and getting more prevalent as the population ages. Better understanding of heart development and aging could help decipher the mechanism of associated heart diseases.  In this study, we reported the application of a typical miniature swine -- Tibetan pig, as human heart model, and illustrated the changes in higher-order chromatin structure and transcription regulation from fetal to sexual maturity and early senescence, as well as the role they play in physiological development and aging. We observed altered multi-scale structures of the 3D genome from territories and A/B compartments to TADs and loops/PEIs. Changes in territories and A/B compartments indicate high plasticity and disorganization of chromatin structure for the fetal and senescent stages, respectively, compared to the more ordered conformation for the young adult stage, embodied by Von Neumann Entropy (VNE) and compartmentalization strength indexes. From such coarse scale, we also observed that heterochromatin gradually stacked and relaxed during development and senescence, supported by evidence of change in intensity of B-B interactions and correlation between sequence features and A/B compartment switches, across the three critical stages. A finer examination of TAD and loops/PEIs showed that young adults tend to have more accurate transcription regulation through finer control of chromatin structure dynamics, supported by higher correlation of gene expression and TAD connectivity, more space between dynamic boundaries and their targeted genes, and stronger ‘loop skew’ towards A compartments. Another observation of monotonic increase in long-range interactions and decrease in short-range interactions throughout the development and senescent process indicates the gradual loss of plasticity for chromatin conformation.

overall_design: To investigate the changes in the three-dimensional conformation of chromatin during development and aging, as well as the relationship between its trend and transcriptional expression

first: Qianzi

last: Tang


title: Ex vivo lung-organoid model for aberrant basaloid cell induction and activation

city: Kashiwa

first: BIN

last: WU

state: Chiba

address: #304, 6-6-2, Kashiwanoha

department: Research

institute: ImmunoGeneTeqs

summary: Lung epithelial cell injury contributes to various lung diseases, impacting lung function and overall human health. Bleomycin (BLM)-induced murine models of pulmonary fibrosis (PF) are commonly utilized to study lung epithelial cell injury. However, the complex microenvironments in inflamed lungs hinder clear causal relationships between cell-to-cell, molecules interaction. To address this limitation, we aimed to establish an ex vivo organoid model of BLM-induced lung injury recapitulating the cellular and molecular responses of BLM-induced lung epithelial injury in vivo.

overall_design: Lung organoids were generated by co-culturing primary murine CD326 positive lung epithelial cells and CD140a positive lung fibroblasts. To clarify transcriptomic changes of BLM-injured lung organoids at single-cell level, we stimulated lung organoids with bleomycin (0.3 ug/ml) in a culture media from day 8 to day 10 post co-cultured. After that, bleomycin was removed from the culture media and the lung organoids were further cultured until day 14 post co-cultured. scRNA-seq analysis was performed at day 14 post co-cultured.

first: Bin

last: Wu

first: Shigeyuki

last: Shichino

first: Satoshi

last: Ueha

first: Rina

last: Matsukiyo

first: Yu

last: Ishimura

first: Haru

last: Ogiwara

first: Masaki

last: Takasu

first: Shotaro

last: Yamano

first: Yumi

last: Umeda

first: Kouji

last: Matsushima


title: The transcription factor HHEX and the Androgen receptor (AR) drive the mouse adrenal sexual dimorphism

first: Antonio

last: Lerario

summary: Glucocorticoids are cholesterol-derived steroid hormones produced by the adrenal gland and widely known for maintaining glucose homeostasis, modulating the immune system, and orchestrating the circadian rhythm. In this study, we defined HHEX as a key regulator of adrenocortical cell function. By using multiple transgenic mouse models, we demonstrate that HHEX shapes AR-dependent sexual dimorphism in the zF following the onset of puberty. HHEX protects lipid droplets integrity from lipophagy induced by AR signaling and its absence results in glucocorticoid insufficiency in males.

overall_design: CUT&Tag of the histone modification H3K27ac and AR in the male mouse adrenal gland. A total of 6 male mouse adrenals was dissociated and 280 000 nuclei were used per Cut&Tag reaction using the kit CUT&Tag-IT (Active motifi, #53170) and AMPure XP reagent (Beckman Coulter, A63880)

first: Typhanie

last: Dumontet


title: Dissecting the epigenome dynamics in human immune cells upon viral and chemical exposure by multimodal single-cell profiling

city: Saarbrucken

first: Irem

middle: Begüm

last: Gündüz

state: Saarland

address: Building A2.4

department: Bioinformatics

institute: Saarland University

summary: Pathogen and chemical exposures lead to profound remodeling of the gene-regulatory landscape across human immune cell populations. Here, we present a single-nucleus chromatin accessibility atlas of human immune cells of individuals exposed to HIV-1, COVID-19, Influenza virus, organophosphates as well as healthy controls that provides insights into gene regulation driven by these cell-extrinsic stimuli. This atlas comprises 271,299 cells and 319,420 candidate regulatory elements that exhibited dynamic accessibility associated with gene expression across immune cell states. Our longitudinal HIV cohort revealed epigenetic signatures of T cell exhaustion, manifested in changes in the accessibility of binding sites for the FOXP family transcription factors. We further identified changes in the accessibility of candidate regulatory elements in CD14 monocytes upon SARS-CoV-2 exposure that are associated with a switch in NF-κB to AP-1-based regulation of cytokine networks. By integrating single-cell profiles of DNA methylation from matched samples we create a multimodal epigenome atlas of human immune cells across exposure states using the accessibility-derived candidate regulatory elements. Both modalities exhibit complementary epigenetic signatures at transcription factor binding sites associated with cell state, as exemplified in the process of memory formation in T-cells. Finally, by linking potentially regulatory DNA methylation signatures to changes in chromatin accessibility in monocytes, we identify AP1 motifs exhibiting epigenetic dynamics, indicating selective remodeling in TF networks in severe cases of COVID-19.

overall_design:
Single-cell ATAC-seq was performed on PBMCs from three human cohorts: (i) four HIV-infected individuals sampled longitudinally at pre-infection, acute, and chronic stages with ART administered between acute and chronic phases; (ii) five individuals challenged with live influenza virus and sampled at baseline (day -2), and 3, 6, and 28 days post-challenge; (iii) individuals with varying organophosphate exposure grouped by urinary TCPY levels (low: n=9, medium: n=6, high: n=20). Nuclei were processed using the 10x Genomics Chromium platform and sequenced on an Illumina NovaSeq 6000.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

last: Gunduz

first: Bei

last: Wei

first: Aaron

last: Wilk

first: Madeline

last: Lee

first: Catherine

last: Blish

first: Fabian

last: Muller

first: William

last: Greenleaf


title: Remodeling of 3D Gene Architecture in Myocardium from Embryonic Development to Early Aging [Hi-C]

first: Yuwei

last: Gou

summary:
Heart-related diseases are increasingly attacking the younger population, and getting more prevalent as the population ages. Better understanding of heart development and aging could help decipher the mechanism of associated heart diseases.
In this study, we reported the application of a typical miniature swine -- Tibetan pig, as human heart model, and illustrated the changes in higher-order chromatin structure and transcription regulation from fetal to sexual maturity and early senescence, as well as the role they play in physiological development and aging.
We observed altered multi-scale structures of the 3D genome from territories and A/B compartments to TADs and loops/PEIs. Changes in territories and A/B compartments indicate high plasticity and disorganization of chromatin structure for the fetal and senescent stages, respectively, compared to the more ordered conformation for the young adult stage, embodied by Von Neumann Entropy (VNE) and compartmentalization strength indexes. From such coarse scale, we also observed that heterochromatin gradually stacked and relaxed during development and senescence, supported by evidence of change in intensity of B-B interactions and correlation between sequence features and A/B compartment switches, across the three critical stages. A finer examination of TAD and loops/PEIs showed that young adults tend to have more accurate transcription regulation through finer control of chromatin structure dynamics, supported by higher correlation of gene expression and TAD connectivity, more space between dynamic boundaries and their targeted genes, and stronger ‘loop skew’ towards A compartments. Another observation of monotonic increase in long-range interactions and decrease in short-range interactions throughout the development and senescent process indicates the gradual loss of plasticity for chromatin conformation.

first: Qianzi

last: Tang


title: Influenza A virus modulation of Streptococcus pneumoniae infection using ex vivo transcriptomics in a human primary lung epithelial cell

status: Public on Oct 31 2025

city: Baltimore

first: Adonis

last: D'Mello

state: Maryland

address: Health Science Facility III, 670 W Baltimore St 3rd floor

institute: IGS- University of Maryland Baltimore

summary: Nanostring validation of deep sequencing of cDNA from Streptococcus pneumoniae EF3030 bacteria and normalized human broncial epithelial cells (nHBEC), together, and after coincubation with Influenza A virus pH1N1. (Accession:GSE225108)

sample_organism:
Streptococcus pneumoniae
Homo sapiens
Influenza A virus

overall_design: Cross platform validation of specific Streptococcus pneumoniae EF3030 genes from deep RNAseq samples (Accession:GSE225108). [HB indicates Human+Bacteria, HIB indicates Human+Influenza+Bacteria]

first: Hervé

last: Tettelin


title: Remodeling of 3D Gene Architecture in Myocardium from Embryonic Development to Early Aging

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

overall_design: Refer to individual Series


title: Age and cell type specific specific effects of histone variant H2BE in the brain

city: Philadelphia

first: Sean

last: Louzon

address: 3400 Civic Center Blvd

institute: University of Pennsylvania


title: Spatiotemporal transcriptomic and metabolomic landscapes of wild soybean seed development reveal regulatory mechanisms of nutrient accumulation [Spatial Transcriptomics]

first: Peiyan

last: Liu


title: Bulk RNAseq profiling of Streptococcus pneumoniae EF3030 and Influenza A virus (A/California/07/2009(H1N1))    mono/coinfection in the mouse lungs.

summary: To investigate the host-pathogen interactions of Streptococcus pneumoniae EF3030 (NZ_CP035897) and Influenza A virus (A/California/07/2009(H1N1))    in the mouse lung. We generated monoinfections and coinfections of C57BL/6 mice, as well as mock infection controls, and harvested whole mouse lung homogenates.

overall_design: We performed gene expression profiling analysis using bulk RNA-seq. K-means clustering of normalized gene expression values was used to identify true mock/coinfected cohorts of samples (mock infected, EF3030 infected, pH1N1 infected, and EF3030+pH1N1 coinfected), as some mice cleared infections over time. As such, with a focus on EF3030 infected and EF3030+pH1N1 coinfected groups, samples that did not fit into these 2 group clusters were labeled "inconclusive_infection".

first: Jessica

last: Lane

first: Carlos

last: Orihuela


title: A Novel Microprotein, MUCP1, Mediates Succinate Transport and Promotes Colorectal Cancer Progression by Modulating Glutamine Metabolism

first: Junjie

last: Nie

address: 4119 Powelton Avenue

institute: university of Pennsylvania

summary: Metabolic reprogramming is a hallmark of colorectal cancer (CRC) progression, yet the molecular mechanisms governing this process remain largely unresolved. And the translational roles of numerous long non-coding RNAs (lncRNAs) have been largely overlooked, despite their protein products being essential in cancer progression. This study identifies MUCP1, the microprotein encoded by lncRNA MUC20-OT1, as a central regulator of metabolic processes in CRC. Positioned on the mitochondrial outer membrane, MUCP1 is vital for the export of succinate, a key oncometabolite. Acute depletion of MUCP1 causes succinate accumulation, Tricarboxylic acid cycle (TCA) instability, and disruptions in glutamine metabolism. Cancer cells lacking MUCP1 show decreased H3K4me3 modifications on genes crucial for glutamine metabolism, driving further metabolic imbalance.  Sustained MUCP1 deficiency ultimately triggers metabolic reprogramming, emphasizing the role of this microprotein in linking mitochondrial metabolism to epigenetic regulation and presenting it as a promising therapeutic target in CRC.

overall_design: This RNA-seq dataset examines the transcriptomic impact of MUCP1 overexpression in SW480 colorectal cancer cells. The experiment includes two groups: control (LV-NC) and MUCP1-FLAG overexpression. RNA was extracted from biological replicates of both groups for sequencing, with the aim of identifying differentially expressed genes influenced by elevated MUCP1 levels. Comparative gene expression analysis and pathway enrichment studies were conducted to assess changes, particularly in metabolic and signaling pathways.

first: Shukui

last: Wang