title: Gnai1+ stromal cells regulate intestinal goblet and Paneth cell differentiation through c-Jun signaling

status: Public on Sep 27 2025

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

summary: Combining single-cell and spatial transcriptomics for mapping different intestinal segments is still relatively absented, and the subtypes of intestinal stromal cells and their downstream signling also remain obscure. Our study provides a comprehensive view of 18 identified cell types across five mouse intestinal segments using single-cell RNA sequencing (scRNA-seq). Integrating scRNA-seq with spatial transcriptomics reveals gene profiles along both segmental and crypt-villus spatial dimensions, including cell characteristics, interactions, signaling networks, extracellular matrix contributions, and functional coordination. Not only the different subtypes of intestinal immune cells were analyzed, but also a subtype of Pdgfra-high stromal cells, Gnai1+ stromal cells, was identified. These cells can support intestinal morphology and regulate the activities of goblet cells, Paneth cells, and intestinal stem cells via the activation of c-Jun and Wnt signaling. Thus, we have compiled a publicly available single-cell and spatial transcriptomics resource covering five intestinal segments to facilitate further research, particularly on stromal cell populations and intestinal microenvironment homeostasis.

overall_design:
10x Genomics Visium spatial sequencing libraries were constructed from mouse small and large intestinal segments
Single-cell RNA sequencing libraries were constructed to profile cellular heterogeneity and gene expression across the duodenum, jejunum, ileum, colon, and rectum segments of the mouse intestine

first: Yalong

last: Wang

first: Wanlu

last: Song


title: Single-cell RNA sequencing reveals distinct senotypes and a quiescence-senescence continuum at the transcriptome level following chemotherapy

status: Public on Oct 30 2025

city: Boulder

first: Brianna

last: Fernandez

state: CO

address: 3415 Colorado Avenue

department: Biochemistry

country: USA

institute: University of Colorado Boulder

type: Expression profiling by high throughput sequencing

summary: Quiescence (reversible cell-cycle arrest) and senescence (irreversible arrest) are challenging to distinguish due to a lack of specific biomarkers, yet both arise simultaneously after chemotherapy. While senescence suppresses tumors by limiting proliferation and recruiting the immune system, quiescent cancer cells evade future therapies and may resume proliferation. Here, we pair time-lapse imaging of cell-cycle dynamics with single-cell RNA-sequencing after etoposide treatment to differentiate these states, linking heterogeneous cell-cycle phenotypes to the transcriptomic landscape. We identify diverse senescent types (senotypes) and link them to two arrest pathways – a gradual path arising after a standard mitosis-to-G0 transition, and a rarer but direct path driven by a mitotic slip. Using pseudotime trajectory analysis, we find that senescent phenotypes begin to manifest early and gradually along the first trajectory, even in shallow quiescent cells. These data support a model wherein, following chemotherapy, quiescence and senescence exist on a continuum of cell-cycle withdrawal at a transcriptome-wide level.

overall_design: MCF10A cells were treated with 2.5, 10, or 25μM etoposide for 24 h. Cells were then washed twice with PBS before being returned to full-growth media. Full-growth media was refreshed every 3d during the drug recovery period. Cells were sequenced on day 6 following etoposide washout.

first: Victor

last: Passanisi

first: Humza

middle: M

last: Ashraf

first: Sabrina

middle: L

last: Spencer


title: RNAPII and DNA supercoiling regulate cohesin engagement in neurons [ChIP-Seq]

status: Public on Nov 01 2025

city: Dallas

first: Ram

last: Madabhushi

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin looping by CTCF and cohesin is thought to be crucial for chromosome organization and gene transcription. Yet the precise relationships between CTCF, cohesin, and transcription in neurons are still poorly understood. To address this issue, we compared the occupancy of CTCF and the cohesin subunits, SMC1 and RAD21, relative to transcriptionally engaged RNAPII and as a function of stimulus-dependent transcription in cultured mouse cortical neurons. We show that CTCF and cohesin are enriched at transcription start sites (TSS) and that their levels increase with the level of transcriptionally engaged RNAPII, suggesting that RNAPII facilitates the engagement of CTCF and cohesin. Unexpectedly, while neuronal stimulation causes widespread transcriptional activation, it resulted in the rapid genome-wide loss of SMC1 and RAD21 signals, including at the TSS of genes, loop anchors, and TAD boundaries. Activity-dependent reductions in cohesin were independent of CTCF but were mimicked by inhibiting topoisomerase IIb (TOP2B), which resolves torsional stress from DNA supercoiling. We show that neuronal stimulation elevates DNA supercoiling and that increasing torsional stress triggers the dissociation of cohesin from chromatin. Overall, these results suggest that modulation of torsional stress could be a physiologically relevant mechanism of regulating cohesin engagement and chromatin architecture in neurons.

overall_design: ChIP-seq in mouse primary cortical neurons

first: Morgan

last: Crewe

first: Ilse

last: Delint-Ramirez

first: Lance

last: Heady


title: Apoptotic Cell Clearance Triggers Epithelial Fate Reprogramming During Prostate Regression [ChIP-seq]

status: Public on Dec 02 2025

city: Montreal

first: Luke

last: McCaffrey

state: Quebec

address: 1160 Pine Ave Ouest

department: Oncology

country: Canada

institute: McGill University

summary: Androgen deprivation induces extensive tissue remodeling in the prostate, characterized by epithelial cell attrition and acquisition of a progenitor-like state in residual luminal epithelial cells. The mechanisms driving differentiated epithelial cells toward a progenitor fate remain unclear. Here, we identify that prostate regression is mediated by the engulfment of apoptotic neighbors by epithelial cells and that efferocytosis promotes acquisition of a progenitor-like state.   We show that epithelial cells are the predominant phagocytes during regression, engaging in temporally coordinated waves of apoptotic cell clearance. This process is accompanied by marked metabolic reprogramming, including increased aerobic glycolysis and lactate production. This coincides with enhanced histone lysine-lactylation at promoters of genes involved in autophagy, apoptosis regulation, and luminal progenitor identity. Blockade of efferocytosis in vivo via epithelial-specific expression of the dominant negative phosphatidylserine binding protein MFGE8-D89E impaired prostate regression and compromised the induction of the luminal progenitor marker Tacstd2. These findings reveal that epithelial efferocytosis is an essential mechanism that couples cell clearance and epithelial plasticity. This work establishes epithelial efferocytosis as a determinant of cell state transitions in the prostate, with implications for a direct role in castration-resistant prostate cancer and other regenerative or remodeling processes.

overall_design: Genome binding/occupancy profiling by high throughput sequencing in mouse prostate

first: Adda-Lee

last: Graham-Paquin


title: Microarray analysis of glucose metabolism-related genes in human umbilical cord blood derived-mesenchymal stem cells treated with everolimus under high glucose conditions

status: Public on Sep 22 2025

city: Cheongju

first: Hyo Youn

last: Jo

address: 1, Chungdae-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do

department: Veterinary medicine

country: South Korea

institute: Chungbuk National University

summary: Umbilical cord blood-derived mesenchymal stem cells (UCB-MSCs) have attracted attention as a potential cell therapy due to their immunomodulatory properties, paracrine trophic effects, and differentiation capacity that promote tissue repair and functional recovery. However, exposure to diabetic conditions impairs mitochondrial function in UCB-MSCs, leading to reduced stem cell activity and increased cell death, ultimately compromising their therapeutic efficacy. Hyperglycemic stress abnormally activates mTOR signaling, driving dysregulated glucose metabolism and mitochondrial dysfunction. To assess whether everolimus, an mTOR inhibitor, can mitigate these effects, we examined glucose metabolism-related enzyme expression in UCB-MSCs exposed to high glucose with or without everolimus treatment. Microarray profiling targeted 84 glucose metabolism-related genes, including eight housekeeping genes, of which 64 genes were reliably detected. Comparison of high glucose (H) versus high glucose plus everolimus (HE) conditions (two replicates each) revealed limited transcriptional changes, with only a subset of genes showing differential expression between groups. Overall, these results indicate that everolimus does not significantly alter glucose metabolism gene expression in UCB-MSCs.

overall_design: UCB-MSCs were cultured until 70% confluency, then switched to serum-free medium for 24 hours to induce starvation. Cells were assigned to two experimental groups. In the high glucose group (H), UCB-MSCs were exposed to 25 mM D-glucose for 72 h. In the everolimus plus high glucose group (HE), UCB-MSCs were pretreated with 100 nM everolimus for 30 min, followed by the addition of 25 mM D-glucose and incubation for 72 h. Each group included two biological replicates (H1, H2, HE1, HE2).

first: Hyo

middle: Y

first: Hyun

middle: J

last: Lee


title: Characterization of non-NF2 related schwannomatosis

status: Public on Jan 30 2026

city: Boston

first: Sonu

last: Subudhi

state: MA

address: 100 Blossom St, Cox 7

department: Radiation Oncology

institute: Massachusetts General Hospital

summary: The goal of the study is to profile the transcriptome of non-NF2 related schwannomatosis

overall_design: We compared RNASeq data between 3 patient samples vs. 3 normal nerve RNAs.

first: Xu

last: Lei

first: Subudhi

last: Sonu


title: RNA sequencing of aggressive variant prostate cancer biopsies

status: Public on Jan 31 2026

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: Aggressive variant prostate cancer is characterized by poor clinical outcomes and profound molecular heterogeneity. In this study, we performed integrative genomic analyses of AVPC to identify potential drug sensitivities and molecular features associated with platinum response.

overall_design:
RNA sequencing of biopsies of patients with aggressive variant prostate cancer

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) (accession ID phs001813) for controlled access to the personally identifiable sequence data.
***************************************************************

middle: G

first: Anish

last: Thomas


title: QKI dysregulation induces extensive splicing changes in T-Cell Acute Lymphoblastic Leukemia (T-ALL)

city: Ghent

first: Bruno

last: Palhais

address: Corneel Heymanslaan 10

department: Department of Biomolecular Medicine

country: Belgium

institute: Ghent University

summary: Understanding the molecular mechanisms underlying T-cell acute lymphoblastic leukemia (T-ALL) is essential for developing more effective therapeutic strategies. Despite therapeutic advances, the role of RNA-binding proteins in the pathogenesis of T-ALL remains poorly understood. Here, we investigate the RNA-binding protein Quaking (QKI), identifying it as a key regulator of splicing with tumor-suppressive properties in T-ALL. Through the analysis of two independent pediatric T-ALL cohorts, we demonstrate that QKI expression is frequently reduced in T-ALL, particularly within the HOXA subtype, and this reduction correlates with poor overall and event-free survival. Using T-ALL cell lines, we show that QKI depletion induces widespread splicing alterations, with numerous events corroborated in patient samples. Transcriptome profiling indicates that QKI downregulation leads to broad changes in gene expression, notably affecting pathways related to cell cycle progression, cholesterol homeostasis, and epithelial?mesenchymal transition. Functional assays demonstrate that QKI overexpression in T-ALL cells significantly reduces cell proliferation, induces G0/G1 cell cycle arrest, and limits leukemia progression and dissemination, ultimately improving survival in xenograft models. Together, these findings provide compelling evidence that QKI functions as a regulator of RNA splicing with tumor-suppressive activity in T-ALL.

overall_design:
To investigate the role of QKI in T-ALL, we performed siRNA-mediated depletion of QKI in Jurkat cells and shRNA-mediated depletion of QKI in HPB-ALL cells, each in four biological replicates
We then performed differential gene expression and splicing analysis using the data obtained from RNA-Seq, comparing cells with reduced QKI expression to control cells.
In addition, to investigate the RNA splicing landscape according to QKI expression levels, we sequenced four replicates of six T-ALL cell lines and performed differential splicing analysis.

first: Nitesh

middle: D

last: Sharma

first: Igor

last: Fijalkowski

first: Tim

last: Pieters

first: Dieter

last: Deforce

first: Filip

middle: V

last: Nieuwerburgh

first: Ksenia

last: Matlawska-Wasowska

first: Pieter

last: Mestdagh

first: Panagiotis

last: Ntziachristos

last: Vlierberghe


title: CXCR4-LASP1-G9a-SNAIL Axis Drives NEPC Transdifferentiation via Induction of EMT and Downregulation of REST

status: Public on May 11 2025

city: Vancouver

first: Yen-Yi

last: Lin

state: British Columbia

address: 2660 Oak St

institute: University of British Columbia

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

overall_design: Refer to individual Series


title: [RelA ChIP-seq]: Characterization of transcriptional and chromatin accessibility landscape of human bronchial epithelial cells treated with synergistic immunostimulatory ligands.

status: Public on Jun 15 2025

city: Houston

first: Scott

middle: E

last: Evans

address: 6565 MD Anderson Blvd, Unit 1059

department: Pulmonary Medicine

institute: University of Texas MD Anderson Cancer Center

summary: Lower respiratory tract infections remain a leading cause of death worldwide. The increasing prevalence of antibiotic-resistant respiratory pathogens has been a key driver of efforts to develop host-directed therapies that protect patients against pneumonia. Our laboratory has previously reported discovery of an immunostimulatory therapeutic comprised of a synthetic diacetylated lipopeptide, Pam2CSK4 (Pam2), and a class C CpG oligodeoxynucleotide, ODN M362 (ODN). When delivered by inhalation, this dyad protects synergistically against pneumonias caused by Gram-positive and -negative bacteria, seasonal and pandemic viruses, and multiple fungi. Protection is achieved by manipulating the immune defense response from lung epithelial cells. Here, we dissect the lung epithelial transcriptional response to explain the observed synergistic signaling, using RNA-seq and dual transcription factor ChIP-seq. We find cooperation of RelA and cJun following Pam2+ODN treatment that synergistically confers broad inducible resistance against respiratory pathogens. Specifically, transcription factor binding site (TFBS) analysis revealed that cJun occupancy at promoter regions of Pam2+ODN-induced genes facilitated increased RelA occupancy during differential expression, demonstrating cJUN-assisted loading of RelA as a key mechanism of the synergistic signaling events. Increased or decreased RelA occupancy at promoter sites dictated gene up- or down-regulation, respectively, while increased or decreased cJun occupancy at promoter sites directed synergistic or antagonistic gene expression patterns. Together, RelA and cJun work at promoter regions to control directionality and magnitude of gene expression after Pam2+ODN stimulation, rapidly reprograming the lung epithelial transcriptome to combat respiratory infections.

overall_design: RelA peaks of HBEC3-KT cells were profiled after 4-hour treatment with PBS (Control), Pam2 (4 uM), ODN (1 uM) or Pam2+ODN (4+1 uM) using ChIP-seq. Input file of the dual TF ChIP-seq is stored under the [RelA ChIP-seq] GEO Series.

first: Jezreel

last: Pantaleón García


title: CXCR4-LASP1-G9a-SNAIL Axis Drives NEPC Transdifferentiation via Induction of EMT and Downregulation of REST [16D CRPC xenograft]

summary: Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer that can develop from prostate cancer following aggressive hormonal therapy. Unfortunately, there are few treatment options available and new therapeutic targets and more effective treatments are urgently needed to improve management of the disease. There is now little doubt that the majority of NEPC is derived from prostatic adenocarcinoma cells via “NE transdifferentiation” that is driven at least in part by AR-axis interference and lineage plasticity. We have developed a first-in-field patient-derived xenograft model of a prostatic adenocarcinoma (LTL331) that undergoes a complete transdifferentiation to NEPC (LTL331R) upon host castration. Using this unique, high-fidelity, patient-derived prostate cancer xenograft models and powerful genomic and transcriptomic analyses, we have obtained evidence that therapy induced development of NEPC may result from epigenetic alterations which drives lineage plasticity of dormancy-capable cancer cells and functional evaluation of key regulators.   These findings may lead to more suitable targets and better therapeutic strategies for prevention and treatment of NEPC.

overall_design: RNA-seq profiling of 16D CRPC xenograft

first: Christopher

last: Ong


title: [cJun ChIP-seq]: Characterization of transcriptional and chromatin accessibility landscape of human bronchial epithelial cells treated with synergistic immunostimulatory ligands.

overall_design: cJun peaks of HBEC3-KT cells were profiled after 4-hour treatment with PBS (Control), Pam2 (4 uM), ODN (1 uM) or Pam2+ODN (4+1 uM) using ChIP-seq. Input file of the dual TF ChIP-seq is stored under the [RelA ChIP-seq] GEO Series.


title: CXCR4-LASP1-G9a-SNAIL Axis Drives NEPC Transdifferentiation via Induction of EMT and Downregulation of REST [331R]

overall_design: ChIP-seq profiling of 331R

first: Yuzhuo

last: Wang


title: Identification of tumor-agnostic biomarkers for predicting prostate cancer progression and biochemical recurrence

status: Public on Oct 03 2024

city: Ribeirão Preto

first: William

last: Lautert Dutra

state: SP

address: Av. Bandeirantes, 3900

department: Genetics Department

country: Brazil

institute: Universidade de São Paulo

summary: The diverse clinical outcomes of prostate cancer have led to the development of gene signature assays predicting disease progression. Improved prostate cancer progression biomarkers are needed as current RNA biomarker tests have varying success for high-risk prostate cancer. Interest grows in universal gene signatures for invasive carcinoma progression. Early breast and prostate cancers share characteristics, including hormone dependence and BRCA1/2 mutations. Given the similarities in the pathobiology of breast and prostate cancer, we utilized the NanoString BC360 panel, comprising the validated PAM50 classifier and pathway-specific signatures associated with general tumor progression as well as breast cancer-specific classifiers. This retrospective cohort of primary prostate cancers (n=53) was stratified according to biochemical recurrence status and the CAPRA-S to identify genes related to high-risk disease

overall_design: we utilized the NanoString BC360 panel, comprising the validated PAM50 classifier and pathway-specific signatures associated with general tumor progression as well as breast cancer-specific classifiers. This retrospective cohort of primary prostate cancers (n=53) was stratified according to biochemical recurrence status and the CAPRA-S to identify genes related to high-risk disease.

last: Lautert-Dutra

first: Camila

last: Melo

first: Luiz

middle: P

last: Chaves

first: Fracisco

middle: C

last: Souza

first: Cheryl

last: Crozier

last: Sundby

first: Elizabeth

last: Woroszchuk

first: Fabiano

last: Saggioro

first: Felipe

middle: S

last: Avante

first: Rodolfo

last: dos Reis

first: Jeremy

middle: A

last: Squire

first: Jane

last: Bayani


title: Transcriptional Stress as a Cause of DNA Double-Stranded Breaks

status: Public on Dec 01 2024

first: Priyatansh

last: Gurha

state: Texas

address: 6770 Bertner Ave

department: School of Medicine

institute: UTHealth

summary:
ABSTRACT
Aims: Double-stranded breaks (DSBs) cause genomic instability, a hallmark of aging, and activate the DNA damage response (DDR) and the cytosolic DNA-sensing proteins (CDSP) pathways. The activated pathways induce cell cycle arrest, inflammation, senescence, cell death, fibrosis, and organ dysfunction. The purpose of the study was to identify and characterize genome-wide DSBs at the nucleotide resolution in adult cardiac myocytes.
Methods and Results: We identified the genome-wide DSBs in the genomes of ~ 6 million adult cardiac myocytes (1 million per sample) in the 3 wild-type and 3 myocyte-specific LMNA-deficient mice (Myh6-Cre:LmnaF/F) mice by END-Sequencing. We identified 6,774 differential DSBs between the wild-type and Myh6-Cre:LmnaF/F cardiac myocytes, which, except for 8, were exclusive to the Myh6-Cre:LmnaF/F genotype. The differential DSBs were enriched in the gene regions, transcription initiation sites, cardiac transcription factor motifs, and at the G quadruplex forming structures, suggesting the involvement of the transcriptional stress. Because LMNA regulates transcription, we performed a CUT&RUN assay with an anti-LMNA antibody (N=5) to test the role of transcriptional stress in an increased prevalence of DSBs. We identified an average of 818 genome-wide lamin-associated domains (LADs), which encompassed 30% of the mouse genome. LADs were associated with a 16-fold reduction in the transcript levels of protein-coding genes located at the LAD regions (N=3,975) as opposed to genes located at the non-LAD regions (N=~ 17,778). Consistent with increased transcription at the non-LAD regions DSBs were ~ 6-fold more prevalent in the non-LAD than LAD regions. Likewise, the loss of LAD was associated with a 2.3-fold higher prevalence of differential DSBs in the Myh6-Cre:LmnaF/F cardiac myocyte genomes, which were predominantly localized to the transcription start sites.
Conclusions: To our knowledge, this is the first identification of the DSBs, a hallmark of aging, at the nucleotide resolution in the cardiovascular system. The findings implicate transcriptional stress in the pathogenesis of DSB and the protective role of LMNA against DSBs likely through transcriptional suppression. Given the ubiquitous nature of transcriptional stress, DSBs are expected to be pervasive and pathogenic through activation of the DDR and CDSP pathways not only in cardiovascular diseases but also in other conditions, including aging.

overall_design: End-seq was performed from CM isolated from 3 WT and 3 Myh6-Cre:LmnaF/F mice.

first: Ali

last: Marian

first: Benjamin

last: Cathcart


title: SARS-CoV-2 produces a microRNA, CoV2-miR-O8, in patients with COVID-19 infection

status: Public on Dec 11 2023

city: Adelaide

first: Jonathan

last: Gleadle

state: SA

address: Renal Unit, FMC

country: Australia

institute: Flinders University

type: Non-coding RNA profiling by high throughput sequencing

summary: SARS-CoV-2 can generate viral microRNAs (v-miRNAs) that target host gene expression. This study used small RNAseq to identify the v-miRNAs present in COVID-19 patients' nasopharyngeal swabs. The study identified a specific conserved v-miRNA sequence (CoV2-miR-O8) unique to SARS-CoV-2 that is highly present in COVID-19 patients' samples, interacts with Argonaute, and has features consistent with Dicer and Drosha generation. CoV2-miR-O8 is predicted to target specific human genes and can be detected by RTPCR assays in patients.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: small RNA-seq analysis on RNA extracted from nasopharyngeal swabs obtained from patients with COVID-19 infection ascertained by a routine diagnostic RT PCR assay

first: Elise

last: Tucker

first: Soon Wei

last: Wong

first: Darling

last: Rojas-Canales


title: SATB1 Lowers The TCR Signaling Threshold For Thymocytes Positive Selection via Super-enhancer Reprogramming

status: Public on Dec 19 2025

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

country: China

institute: Southern Medical University

summary: The generation of mature CD4⁺ helper and CD8⁺ cytotoxic T cells from double-positive (DP) thymocytes is a central step in building an effective adaptive immune system. This process relies on positive selection, whereby αβTCR⁺ thymocytes are tested for recognition of self-peptide–MHC complexes presented by cortical thymic epithelial cells. Thymocytes with insufficient signaling die by neglect, while those receiving appropriately tuned signals survive and differentiate. Positive selection thus plays a dual role: establishing MHC restriction and directing lineage commitment into the CD4 or CD8 fate. After TCR rearrangement is completed, T cells can interact with APCs to transmit TCR signals and produce CD69 protein. SO, CD69+DP cells is undergoing positive selection. Here, we explored the mechanism of SATB1 regulating thymocyte positive selection. Firstly, We analysis the function of SATB1 in the transtion of CD69-DP to CD69+DP by CUT&Tag, ATAC and HiC assays. Then, Single-cell RNA sequencing assay of SATB1-deficient thymocytes showed that the cell identity of CD69+DP thymocytes was changed, and the genes differently expressed in CD69+DP cells. Smart-seq2 showed the similar tendency. CUT&Tag , ATAC-seq and HiC data show the mechanism for SATB1 in T cell positive selection or before this stage. ACC-seq confirms that SATB1 forms phase separation at these sites and regulates gene expression, These data helps us to understand the role of SATB1 in thymocyte positive selection.

overall_design: scRNA-seq analysis of Satb1+/+ and Satb1-/- CD69+DP thymocytes(2 replicates); Bulk Smart-seq2 analysis of Satb1+/+ and Satb1-/- for CD69-DP and CD69+DP thymocytes(4 replicates); SATB1, CTCF, RAD21, H3K4me3 and H3K27ac CUT&Tag analysis of Satb1+/+ and Satb1-/- for CD69-DP and CD69+DP thymocytes(3 replicates); ATAC-seq analysis of Satb1+/+ and Satb1-/- for CD69-DP and CD69+DP thymocytes(4 replicates);Hi-C analysis of Satb1+/+ and Satb1-/- CD69-DP and CD69+DP for thymocytes(4 replicates); ACC-seq analysis of Satb1+/+ and Satb1-/- for thymocytes(2 replicates).

first: Wei

last: Xue

first: Bingtao

last: Hao


title: CXCR4-LASP1-G9a-SNAIL Axis Drives NEPC Transdifferentiation via Induction of EMT and Downregulation of REST [331R-2D]

first: Yen-Yi

last: Lin

overall_design: RNA-seq profiling of 331R-2D

first: Yuzhuo

last: Wang


title: Runx1 transcriptional regulation of microglia critically modulates opioid analgesia and withdrawal in humans and rodents [ChIP-seq]

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

institute: University of Calgary

summary: Opioid pain-relief and adverse outcomes differ between individuals. We show that runt-related transcription factor 1 (Runx1) is a determinant of opioid responses in humans and rodents and modulates the microglial transcriptome. Electron microscopy and single-cell RNA-sequencing revealed that deletion of Runx1 from microglia produces distinct ultra-structural and transcriptomic signatures. Microglia Runx1-deficient mice have reduced morphine potency, despite having no prior opioid exposure and normal nociceptive thresholds. These mice required greater amounts of post-operative morphine and displayed robust morphine-induced hyperalgesia and exacerbated withdrawal. In humans, genome-wide linkage analyses (GWAS) revealed variations within the Runx1 gene is associated with inter-individual differences in perioperative opioid requirement and opioid withdrawal severity. Identification of Runx1 susceptibility genotypes has implications for individualizing opioid pain management and determining risk of opioid dependence.

overall_design: Spinal cord cells were isolated from male C57BL/6J mice at 8-10 weeks of age. For each immunoprecipitation, chromatin from 10 spinal cords was pooled, yielding a sample of approximately 10 µg, and incubated with 9 µg of antibody against Runx1 (rabbit polyclonal, ab23980, lot# 1017033-4, Abcam) overnight at 4 °C with rotation. ChIP-Seq library preparation and sequencing reactions were conducted by GENEWIZ, Inc/Azenta US, Inc. (South Plainfield, NJ, USA).

first: Heather

last: Leduc-Pessah

first: Sarthak

last: Sinha

first: Brendan

last: McAllister

first: Daisuke

last: Nishizawa

first: J√∫lia

last: Canet-Pons

first: Churmy

last: Fan

first: Marie-Kim

last: St-Pierre

first: Amyaouch

last: Bradaia

first: Manon

last: Defaye

first: Nynke

last: van den Hoogen

first: Nicole

last: Burma

last: Damblon

first: Einer

last: Muñoz-Pino

first: Luke

last: Healy

first: Valerio

last: Piscopo

first: Ken-ichi

last: Fukuda

first: Tatsuya

last: Ichinohe

first: Makoto

last: Nagashima

first: Masakazu

last: Hayashida

first: Emma

last: Johnson

first: Arpana

last: Agrawal

first: Louisa

last: Degenhardt

first: Nicholas

last: Martin

first: Elliot

last: Nelson

first: Christophe

last: Altier

first: Marie-Eve

last: Tremblay

first: Chad

last: Bousman

first: Stefano

last: Stifani

first: Yves

last: De Koninck

first: Kazutaka

last: Ikeda

last: Biernaske

first: Tuan

last: Trang


title: Runx1 transcriptional regulation of microglia critically modulates opioid analgesia and withdrawal in humans and rodents

first: Jeff

last: Biernaskie


title: Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease

status: Public on Jan 20 2026

city: Barcelona

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

country: Spain

institute: CNAG

summary: Assessing anti-tumor immune responses and immune microenvironment alterations in central nervous system (CNS) neoplasms like brain tumors and leptomeningeal disease (LMD) provides prognostic insights and predictive biomarkers. Cerebrospinal fluid (CSF) liquid biopsy (LB) is a promising minimally-invasive approach, but its ability to reflect these processes remains unclear. We used single-cell RNA and T cell receptor (TCR) sequencing of CSF cells and spatial transcriptomics of CNS lesions in LMD patients with CNS lymphoma (CNSL), glioblastoma (GB), and brain metastases (BrM), compared to neuroinflammatory CNS disorders to unveil the immune complexity during the disease course. We identified disease-specific CSF environments reflecting parenchymal tumor microenvironment features. CNSL showed robust T cell responses, while BrM and GB were dominated by myeloid cells. Unique mechanisms of disease progression and resistance linked to CSF cell dynamics highlight the potential of scRNAseq-based CSF LB for uncovering disease biology, predicting biomarkers, and developing personalized therapies for CNS neoplasms.

overall_design: Single-cell RNA and TCR sequencing of cerebrospinal fluid (CSF) cells from 17 patients, including serial samples to a total of 21 samples.

first: Svenja

last: Klinsing

first: Ginevra

last: Caratú

first: Joachim

last: Steinbach

first: Pia

last: Zeiner

first: Holger

last: Heyn

first: Juan


title: Impact of CTD truncation on co-transcriptional splicing.

status: Public on May 27 2024

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

summary: For overexpression of exogenous RPB1, 10 ug of purified HA-tagged RPB1 plasmids (wildtype or CTD-truncated, both α-amanitin resistant) were transfected into HeLa S3 cells per 10 cm dish using TurboFect transfection reagent (Thermo Fisher Scientific). Culture medium was changed to include 2 ug/ml of Doxycycline 12 hrs post-transfection for inducing exogenous gene expression and then treated with 2.5 ug/ml α-amanitin to block the function of endogenous RPB1. Cells were further cultured for 42 hrs before harvesting for subsequent analysis.

overall_design: We expressed a-amanitin resistant full-length and CTD truncated RBP1 and compared their impact on co-transcriptional splicing after inhibiting the endogenous Pol II in HeLa cells.

first: Changwei

last: Shao

first: Xiang-Dong

last: Fu


title: Rpb9 plays a critical role in global co-transcriptional splicing in mouse ESC (Fraction chrRNA-seq)

status: Public on May 27 2023

summary: To define the function of Rpb9 on co-transcriptional splicing, we used auxin-inducible Rpb9 degron system in mouse embryonic stem cells (mESCs) with auxin treatment for 3 hours to sufficiently deplete Rpb9. To measure co-transcriptional splicing, we fractionated mESCs cells (spiked in with Drosophila S2 cells for data normalization) into cytosolic (Cyt), nucleoplasm (NP), and chromatin/particle (Chr) fractions. We purified total RNA from Chr compartment, depleted ribosomal RNAs, and constructed two independent libraries for RNA-seq, which showed excellent reproducibility.

overall_design: Characterization of co-transcriptional splicing after degradating Rpb9 in mESC cells


title: Rpb9 plays a critical role in global co-transcriptional splicing (Fraction RNA-seq)

status: Public on Nov 15 2023

summary: In order to measure the impact of Rpb9 on co-transcriptional splicing, we treated HeLa cells with control siRNA or siRpb9, and for comparative analysis, we also depleted Rpb1 and confirmed by Western blotting the knockdown efficiency in all cases. To measure co-transcriptional splicing, we fractionated HeLa cells into cytosolic (Cyt), nucleoplasm (NP), and chromatin/particle (Chr) fractions. We purified total RNA from each compartment, spiked in with in vitro transcribed EGFP and FireFly luciferase RNA for data normalization, depleted ribosomal RNAs, and constructed two independent libraries for RNA-seq, which showed excellent reproducibility .

overall_design: Characterization of co-transcriptional splcing  after Rpb9 knock-down  in Hela cells


title: U2AF1 plays a critical role in global co-transcriptional splicing (Fraction chrRNA-seq)

summary: In order to measure the impact of U2AF1 on co-transcriptional splicing, we treated HeLa cells with control siRNA or U2AF1 siRNA. To measure co-transcriptional splicing, we fractionated HeLa cells into cytosolic (Cyt), nucleoplasm (NP), and chromatin/particle (Chr) fractions. We purified total RNA from Chr compartment, spiked in with in vitro transcribed EGFP and FireFly luciferase RNA for data normalization, depleted ribosomal RNAs, and constructed two independent libraries for RNA-seq.

overall_design: Characterization of co-transcriptional splcing  after U2AF1 knock-down in Hela cells


title: [Bulk RNA-seq]: Characterization of transcriptional and chromatin accessibility landscape of human bronchial epithelial cells treated with synergistic immunostimulatory ligands.

first: Scott

last: Evans

overall_design: Gene expression changes of HBEC3-KT cells were profiled after 4-hour treatment with PBS (Control), Pam2 (4 uM), ODN (1 uM) or Pam2+ODN (4+1 uM) using RNA-seq.

first: Jezreel

last: Pantaleón García


title: Identification of miR-151a as a universal endogenous control for exosome cargo normalization in human cancer

status: Public on May 26 2023

city: Madrid

first: Carlos

last: Rodríguez Antolín

address: Paseo castellana 261

department: Genetics

institute: Hospital Universitario La Paz

summary: The exosomal particles in the blood of cancer patients possess many times more tumor markers than free circulating. Among these elements, miRNAs have great biomedical relevance due to their stability and feasible detection. However, there is not available in the market any reliable endogenous control for the exosomal compartment, nor specific for the miRNA content, preventing the obtainment of standardization measures in cancer liquid-biopsy. In this study, we firstly identified three miRNAs out of a panel of nine potential normalizers that arised from an integrative analysis comparing the global miRNA exosomal profile by miRNA-seq of six lung and ovarian human cancer cell lines under different chemotherapy conditions. Their value as normalizers were also tested in 14 additional human cancer cell lines from different tumor types and after radiotherapy and an alternative chemotherapy treatment. Its translational validation comprised 124 prospective samples, 70 plasma from NSCLC patients, 12 from glioblastoma patients, 10 healthy donors and 16 paired samples from plasma and ascites fluid from ovarian cancer patients. The variability and normalizing properties were tested in comparison with the tissue-origin gold standard miR-16. Our results indicate that miR-151a is constantly represented in the exosomal content with minimal variability compared with miR16 independently of many conditions tested, providing for the first time a universal normalizer for the exosomal compartment that will impact the use of liquid biopsy.

overall_design: miRNA-seq from paired cisplatin-sensitive/resistant Cell line-derived exosomes was used to analyze small RNA expression profiling

first: Julia

last: Jiménez

first: Miranda

last: Burdiel

last: Rodríguez-Antolín

first: Olga

last: Pernía

first: Rocío

last: Rosas-Alonso

first: Ana

last: Sastre-Perona

first: Julian

last: Colmenarejo

first: Alvaro

last: Garcia-Guede

first: Carmen

last: Rodríguez-Jiménez

first: María

last: Diestro

first: Virginia

last: Martínez-Marín

first: Oliver

last: Higueras

first: Patricia

last: Cruz

first: Itsaso

last: Losantos-García

first: Javier

last: de Castro

first: Inmaculada

last: Ibáñez de Cáceres


title: Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [10x ATAC + GEX Multiome]

status: Public on Apr 02 2025

first: Alexis

last: Caulier

state: Massachusetts

address: 1 Blackfan street

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: We developed a strategy (Perturb-Multiome) to couple highly-efficient pooled CRISPR-mediated perturbation of master transcription factors in differentiating primary human hematopoietic cells with joint single-cell gene expression and chromatin accessibility profiling. This approach enabled the reconstruction of transcription factor-dependent gene regulatory networks throughout hematopoietic differentiation. Ultimately, we integrated GWAS datasets to explore the heritability of blood phenotypes explained by these identified transcription-factor regulatory networks.

overall_design:
Pooled CRISPR-mediated perturbation of transcription factors in primary human hematopoietic cells, harvested at day 7, day 9, day 11 and day 14 of in vitro erythroid differentiation with single cell RNA and ATAC readouts.

UPDATE: [June 05, 2025] The Sample titles were updated.

first: Jorge

last: Martin-Rufino

first: Vijay

last: Sankaran


title: Single-cell transcriptomics of spinal microglia from Cx3cr1-Cre-YFP x flxRunx1 mice

first: Jeff

last: Biernaskie

summary: Runx1 is a transcription factor known to be involved in microglial reactivity in the perinatal period, but its role in regulating microglia reactivity later in life is not well understood. Transgenic mice with a conditional inducible deletion of the transcription factor Runx1 in Cx3cr1 positive cells were generated to further investigate. Immunohistochemical labelling and electron microscopy, flow cytometry and quantitative PCR showed indications of altered microglial phenotype in knock-out mice. Single-cell seq was pursused to further delineate the microglial populations in wild-type and Runx1 knock-out mice.

overall_design:
scRNA-seq of Wild type (vehicle-treated and Runx1 Knock-out (tamoxifen-treated) spinal microglia.
To knock out the transcription factor Runx1 from microglia we crossed Cx3cr1-CreER-YFP mice with floxed Runx1 mice. Mice were treated with tamoxifen 1 mg or vehicle i.p. for 5 days to induce recombination. 4 weeks were allowed for repopulation of peripheral cx3cr1 expressing cells. FACS as used to isolate YFP-positive cells from the spinal cord of tamoixfen (knock-out) or vehichle (wild type) mice. All samples were processed according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent D1000 ScreenTape System. We recovered 4,500 and 2,600 cells for wild type and knock-out conditions, respectively. Next Generation Sequencing was done using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~75,000-100,000 reads/cell.

first: Heather

last: Leduc-Pessah

first: Sarthak

last: Sinha

first: Tuan

last: Trang


title: NKG2D-CAR memory T cells target pediatric T-cell acute lymphoblastic leukemia in vitro and in vivo but fail to eliminate leukemia initiating cells

status: Public on Mar 29 2023

first: Carlos

last: Rodríguez Antolín

summary: Refractory/relapsed pediatric acute leukemia are still clinically challenging and new therapeutic strategies are needed. Interactions between Natural Killer Group 2D (NKG2D) receptor, expressed in cytotoxic immune cells, and its ligands (NKG2DL), that are upregulated in leukemic blasts, are important for anti-leukemia immunosurveillance. Nevertheless, leukemia cells may develop immunoescape strategies as NKG2DL shedding and/or downregulation. In this report, we analyzed the anti-leukemia activity of NKG2D chimeric antigen receptor (CAR) redirected memory (CD45RA-) T cells in vitro and in a murine model of T-cell acute lymphoblastic leukemia (T-ALL). We also explored how soluble NKG2DL affected NKG2D-CAR T cells´ cytotoxicity and the impact of NKG2D-CAR T cells on Jurkat cells. In vitro, we found NKG2D-CAR T cells targeted leukemia cells and showed resistance to the immunosuppressive effects exerted by soluble NKG2DL. In vivo, NKG2D-CAR T cells controlled T cell leukemia burden and increased survival of the treated mice but failed to cure the animals. After CAR T cell treatment, Jurkat cells upregulated genes related to proliferation, survival and stemness, and in vivo, they exhibited functional properties of leukemia initiating cells. The data here presented suggest, that, in combination with other therapeutic approaches, NKG2D-CAR T cells could be a novel treatment for pediatric T-ALL.

overall_design: To explore how CAR T cells affected gene expression, Jurkat GFP-luc cells were co-cultured with NKG2D-CAR T cells for 16h, sorted and used to perform transcriptome analysis by RNAseq. Sorted Jurkat-GFP cells that remained after overnight exposition to NKG2D-CAR T cells were washed in PBS and pelleted in RLT lysis buffer supplemented with 1:1000 β-mercaptoethanol. RNA isolation and sequencing was carried out as our group previously reported (Fernández A et al. Cancers, 2021). Reads from RNA-seq were analyzed to quantify genes through the RSEM (Li B et al. Bioinformatics, 2011)  with hg19 as reference for annotation. The differential expression was carried out with edgeR (Robinson MD et al. Bioinformatics, 2009) and the statistical cut-off point was set as FDR < 0.05 and logFC >2. Genes were filtered based on a minimum expression of one Counts Per Million (CPM) in more than one sample. Normalization was performed by the TMM method (trimmed mean of M-values)(Robinson MD et al. Genome Biol, 2010). Functional enrichment of differentially expressed genes was carried out in PFAM (Mistry J. et al, Nucleic Acids Res, 2021), GOTERM_BP_DIRECT (Ashburner M et al. Nat. Genet, 2000) and KEGG REACTOME (Kanehisa M, et al. Protein Sci, 2022)

first: Marta

last: Ibáñez

first: Adrián

last: Fernández

first: Adela

last: Escudero

first: Gloria

last: Esteso

last: Campos-Silva

first: Miguel

last: Navarro-Aguadero

first: Alejandra

last: Leivas

first: Beatriz

middle: R

last: Caracuel

last: Rodríguez-Antolín

last: Ortiz

first: Alfonso

last: Navarro-Zapata

last: Mestre-Durán

last: Balaguer-Pérez

first: Cristina

last: Ferreras

first: Joaquín

last: Martínez

first: Mar

last: Valés-Gómez

first: Antonio

last: Pérez-Martínez

first: Lucía


title: PGC 1α Senses the CBC of Pre-mRNA to Dictate the Fate of Promoter-Proximally Paused RNAPII [RIP-seq native]

status: Public on Jan 19 2023

city: Rochester

first: Lynne

last: Maquat

state: New York

address: 601 Elmwood Ave # 712

institute: University of Rochester

summary: Although PGC 1α is well-established as a transcriptional coactivator for the metabolic adaptation of mammalian cells to diverse physiological stresses, its molecular dynamics at the start and during gene transcription are incompletely understood. Previously, we defined a CBP80-binding motif (CBM) within PGC 1α that binds CBP80 at the 5′-cap of nascent transcripts deriving from PGC 1α-responsive genes. Binding verifies proper 5′-cap assembly, after which gene transcription is somehow promoted. Here, using protein immunoprecipitations, size-exclusion chromatography, PRO-seq, RNA-seq, native RIP-seq, RIP-seq footprinting and CUT&RUN, we report that PGC 1α, serving as a DNA−RNA conduit between promoter-bound ERRα and nascent transcript-bound CBP80, overcomes promoter-proximal pausing of RNAPII by competing against the premature transcription termination complex Integrator and also by recruiting P-TEFb. Using mice homozygous for five amino-acid changes in PGC 1α that destroy CBM function, we demonstrate that efficient differentiation of primary myoblasts to myofibers and effective regeneration of skeletal muscle after injury requires PGC 1α binding to CBP80.

overall_design: Three biological replicates were generated to compare mRNA levels, using RIP-seq, in anti-FLAG IPs using lysates of PGC-1α KD C2C12 MBs (i.e. WT C2C12 MBs stably expressing a PGC-1α-mRNA targeting shRNA) transiently expressing FLAG alone, FLAG-PGC-1α(WT), or FLAG-PGC-1α(CBM5mut)

first: Xavier

last: Rambout

first: Hana

last: Cho

first: Hari

middle: K

last: Yalamanchili


title: PGC 1α Senses the CBC of Pre-mRNA to Dictate the Fate of Promoter-Proximally Paused RNAPII [RIP-seq footprint]

overall_design: Three biological replicates were generated to compare RNA footprints, using RIP-seq footprinting, in anti-FLAG IPs using lysates of PGC-1α KD C2C12 MBs (i.e. WT C2C12 MBs stably expressing a PGC-1α-mRNA targeting shRNA) transiently expressing FLAG alone, FLAG-PGC-1α(WT), or FLAG-PGC-1α(CBM5mut)


title: Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesi

status: Public on Feb 17 2023

city: Bonn

first: Amir Hossein

last: Kayvanjoo

address: Carl-Troll-Straße 31

country: Germany

institute: LIMES Institute

summary: We investigate the heterogeneity of macrophage populations in the murine fetal liver to define their specific roles during hematopoiesis. Using a single-cell omics approach and genetic fate-mapping models, we found that fetal liver macrophages cluster into distinct yolk sac-derived subpopulations and that long-term HSCs are interacting preferentially with one of the macrophage subpopulations.

overall_design: Refer to individual Series

first: Amir


title: Gene expression profile at bulk (24h, 48h & 72h) and single nucleus (24h) level of mouse right kidney post sham operation and unilateral nephrectomy.

status: Public on Jul 18 2024

first: Jonathan

last: Gleadle

summary: The mechanism driving the remarkable ability of the remaining kidney to enlarge and increase its function following removal of its contralateral pair remains elusive.  To explore the pathways driving compensatory renal hypertrophy, comprehensive RNA-seq transcriptional studies in the kidneys of mice undergoing hypertrophy 24, 48 and 72 hours following nephrectomy have been undertaken and compared with mice undergoing sham operations. The results reveal substantial time dependent enhancement of cholesterol biosynthesis pathways, increases in mitochondrial gene expression and cell cycle perturbations. Single nuclei RNA-Seq 24 hours post nephrectomy was used to further explore cholesterol biosynthesis signature and its driver SREBP2. In a cell specific manner, snRNA-seq demonstrated that SREBP2 activity increases in proximal tubules and medullary thick ascending limb and is responsible for cell size regulation following IGF-1 stimulation. These results suggest a previously undescribed role for SREBP2 in the mechanism underlying compensatory renal hypertrophy. This mechanism might be amenable to therapeutic manipulation to enhance kidney size and function.

overall_design: Mice were anaesthetised using 1.5-2.5% isoflurane/oxygen (1.5L/min), the left kidney was accessed with a mid-lateral skin incision and exposed. Adherent fat and the adrenal gland were bluntly dissected from the cranial pole. Renal blood supply was clamped and doubly ligated (Prolene 4-0). The clamp was removed, and the abdominal wall was closed by simple interrupted stitches (Prolene 4-0). Skin was closed with wound clips. Mice were given subcutaneous 0.5ml 0.9% sterile saline and Buprenorphine (0.05mg/kg) at time of surgery. Pain relief was given every 8-12h post-surgery as required for the first 24h. Sham operations were performed similarly without kidney removal. For bulk RNA-sequencing, RNA was extracted and quantified. Library preparation was performed using the Illumina TruSeq Stranded mRNA library preparation kit and sequenced using the NovaSeq system (Illumina) platform with 150bp paired end read length. For single nuclei RNA-sequencing, a small mid cross-section of the kidney was excised and processed for nuclei isolation using the EZ Nuclei Isolation Kit (Sigma-Aldrich) following the manufacturer's protocol. DAPI stained nuclei were isolated using FACS Aria Fusion (Becton Dickinson). The single nuclei suspension was then immediately loaded onto a Chromium Controller (10x Genomics) for single nuclei encapsulation, barcoding, and library preparation using the Chromium Single Cell 3' Reagent Kit v3 (10x Genomics) following the manufacturer's instructions. The prepared libraries were sequenced on an MGI FCL sequencer with 100bp paired end read length.

first: Darling

last: Rojas-Canales

first: Soon

middle: W

last: Wong

first: Elise

last: Tucker


title: Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [NG Capture-C]

status: Public on Jun 01 2022

city: Headington

first: Jim

last: Hughes

address: MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine

department: MRC WIMM

country: United Kingdom

institute: University of Oxford

summary: Mammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ~70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Of interest, the almost identical α1- and α2-globin genes interact differently with the enhancers, resulting in preferential expression of the proximal α1-globin gene which behaves as a partial boundary between the enhancers and the distal α2-globin gene. Together, these observations provide direct evidence that actively transcribed genes can behave as boundary elements.

overall_design: NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments; in this case promoters, enhancers and CTCF binding sites in the mouse alpha-globin sub-TAD were used as viewpoints. The method was applied to wild type mouse erythroid cells and to in vivo models in which CTCF sites HS+44/+48 (∆44-48), or θ1 and/or θ2 (∆θ1, ∆θ2, ∆θ1θ2) were deleted. Experiments performed on biological triplicates.

first: Caroline

last: Harrold

first: Matthew

last: Gosden

first: Jelena

last: Telenius

first: Douglas

last: Higgs


title: Single-Cell Transcriptomics of Human Substantia Nigra in Parkinson's Disease

status: Public on Mar 28 2022

city: New York

first: Bin

last: Zhang

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Parkinson’s disease (PD) is the most common neurodegenerative movement disorder with unknown etiology. Loss of neuromelanin-containing dopaminergic (DA) neurons in the substanstia nigra (SN) is the hallmark of PD neuropathology. Here we performed single-nucleus RNA sequencing (snRNA-seq) of nuclei from the postmortem SN of control and idiopathic PD patients across various disease stages. The resulting transcriptomic atlas revealed a landscape of cellular alterations associated with disease progression in PD.

overall_design: The SN from postmortem brains were requested from NIH Neurobiobank (www.neurobiobank.nih.gov) and fulfilled by Brain Endowment Bank at Miller School of Medicine, University of Miami. Specifically, frozen punches of substantia nigra were obtained and then pulverized in a liquid-nitrogen-chilled mortar and aliquoted. Approximately 50mg tissues were used for snRNA-seq. Single nucleus gene expression sequencing was performed on the samples using the Chromium platform (10x Genomics, Pleasanton, CA) with the Next GEM Single cell 3’GEX Reagent kit, and an input of ~10,000 nuclei from a debris-free suspension.

first: Qian

last: Wang

first: Minghui

first: Insup

last: Choi

first: David

last: Davis

first: Xiaoyan

last: Sun

first: Zhenyu

last: Yue


title: An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells

status: Public on Jun 14 2018

first: Carlos

last: Rodríguez Antolín

summary: Long noncoding RNAs are newly discovered regulators that play a critical role in cell biology, crucial to the correct functioning of the cell. Alterations in lncRNAs can lead to the development of diseases such as cancer. However, the role of lncRNAs in resistance to platinum chemotherapy is largely unknown. To screen for epigenetic changes involved in the development of resistance, we combined lncRNA and mRNA expression microarrays with whole genome bisulfite sequencing (WGBS) in four paired cisplatin-sensitive/resistant cells from non-small cell lung cancer and ovarian cancer. We found low levels of expression changes in lncRNAs (1.5%) and mRNAs (2%) when comparing resistant vs. sensitive cells. The correlation between lncRNA/mRNA arrays and WGBS identified two groups of lncRNAs, classified according to their relationship with the gene they have in silico complementarity or with their possible epigenetic regulation at the DNA methylation level. Validation of the results of expression and methylation levels allowed us to characterize lncRNAs in cisplatin-resistant phenotypes. In this study, we characterized lncRNAs that change in cisplatin-resistant cells due to epigenetic regulation at the DNA methylation level and the associated changes in expression levels. We have identified two groups of differentially expressed and methylated lncRNAs, indicating a new approach to the study of the mechanisms involved in the development of acquired resistance to cisplatin in cancer cells.

overall_design: A total of four cell lines were purchased from ATCC and ECACC (Sigma-Aldrich) and cultured as recommended. To analyze the changes in the transcriptome as a result of CDDP treatment, we established the CDDP-resistant variants of H23-R, H460-R, A2780-R and OVCAR3-R from the parental-sensitive variants H23, H460, A2780 and OVCAR3, after exposure to increasing doses of CDDP treatment in a time period of 6–18 months. Labelled cDNA from the 8 cell lines was hybridized by duplicate into the Human LncRNA Array v3.0 (8 x 60K, Arraystar).

first: Olga

last: Vera

last: Rodriguez-Antolin

first: Javier

last: de Castro

first: Florian

last: Karreth

first: Thomas

last: Sellers

first: Inmaculada

last: Ibañez de Caceres


title: Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [ChIP-seq]

first: Jim

last: Hughes

overall_design: CTCF ChIP-seq on chromatin isolated from primary erythroid Ter119+ cells obtained from the spleens of phenylhydrazine treated mice containing deletions for HS+44/+48 (∆44-48), or θ1 and/or θ2 (∆θ1, ∆θ2, ∆θ1θ2) CTCF binding sites. Experiments performed on biological triplicates.

first: Caroline

last: Harrold

first: Rosa

last: Stolper


title: Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells

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


title: Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [ATAC-seq]

overall_design: ATAC-seq on chromatin isolated from primary erythroid Ter119+ cells obtained from the spleens of phenylhydrazine treated mice containing deletions for HS+44/+48 (∆44-48), or θ1 and/or θ2 (∆θ1, ∆θ2, ∆θ1θ2) CTCF binding sites. Experiments performed on biological triplicates.

first: Matthew

last: Gosden

first: Jelena

last: Telenius

first: Douglas

last: Higgs


title: A Novel Role for the Tumor Suppressor Gene ITF2 in Tumorigenesis and Chemotherapy Response

status: Public on Apr 10 2020

type: Genome variation profiling by genome tiling array


title: A Novel Role for the Tumor Suppressor Gene ITF2 in Tumorigenesis and Chemotherapy Response [CGH]

summary: Despite often leading to platinum resistance, platinum-based chemotherapy continues to be the standard treatment for many epithelial tumors. In this study we analyzed and validated the cytogenetic alterations that arise after treatment in four lung and ovarian paired cisplatin-sensitive/resistant cell lines by 1-million microarray-based comparative genomic hybridization (array-CGH) and qRT-PCR methodologies. RNA-sequencing, functional transfection assays, and gene-pathway activity analysis were used to identify genes with a potential role in the development of this malignancy. The results were further explored in 55 lung and ovarian primary tumors and control samples, and in two extensive in silico databases. Long-term cell exposure to platinum induces the frequent deletion of ITF2 gene. Its expression re-sensitized tumor cells to platinum and recovered the levels of Wnt/β-catenin transcriptional activity. ITF2 expression was also frequently downregulated in epithelial tumors, predicting a worse overall survival. We also identified an inverse correlation between ITF2 and HOXD9 expression, revealing that Non-small cell lung cancer (NSCLC) patients with lower expression of HOXD9 had a better overall survival rate. We defined the implication of ITF2 as a molecular mechanism behind the development of cisplatin resistance probably through the activation of the Wnt-signaling pathway. This data highlights the possible role of ITF2 and HOXD9 as novel therapeutic targets for platinum resistant tumors.

overall_design: DNA from paired cisplatin-sensitive/resistant cell lines was used to analyze copy number variations by the Array-CGH SurePrint G3 Human CGH Microarray 1x1M (Agilent, USA).

last: Pernía

first: Ana

last: Sastre-Perona

last: Rodriguez-Antolín

first: Alvaro

last: García-Guede

first: María

last: Palomares-Bralo

first: Rocío

last: Rosas

first: Darío

last: Sanchez-Cabrero

first: Carmen

last: Rodriguez

first: Rubén

last: Martín-Arenas

first: Verónica

last: Pulido

first: Pilar

last: Santisteban

last: Ibáñez de Cáceres


title: miR-7 as novel predictive epigenetic biomarker for platinum-resistance in cancer

status: Public on Oct 05 2017

first: Carlos

last: Rodríguez Antolín

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


title: miR-7 as novel predictive epigenetic biomarker for platinum-resistance in cancer (miRNA)

summary: Background. One of the major limitations associated to the platinum use is the resistance that almost invariably will progress in lung and ovarian cancers. In the current study, we sought to identify epigenetically regulated miRNAs as novel biomarkers of platinum-resistance in those tumor types. Methods. We combined transcriptomic data from miRNA and mRNA under the influence of an epigenetic reactivation treatment, followed by qRT-PCR and epigenteic validations for an accurate candidate selection in 23 human cancer cell lines. Functional analysis were performed to study their biological and therapeutic implications, that were further tested in 257 primary samples obtained from lung and ovarian tumors. Results. We identified a group of 9 miRNAs belonging to the CM19 cluster and 7 potential miRNA-targets potentially involved in resistance development, in both tumor types. Deregulation of miR-7, -132, -335 and -148a may be a common event in the development of CDDP-resistance. miR-7 presented specific methylation in the resistant subtypes and its reexpression, decreased cell viability, suggesting a possible cell sensitization to cisplatin. Our translational approach indicated that miR-7 methylation is a frequent event that may play an important role in the early establishment of NSCLC tumorigenesis, and seems to play an additional platinum-predictive role in ovarian cancer.  Conclusions. miR-7 is a novel potential epigenetic biomarker tool for the selection of ovarian cancer patients with higher risk to earlier relapse and worst response to platinum-based chemotherapy. Funding. FIS (ISCIII): PI12/00386, PI13/01450, PI15/00186, and FEDER/FSE (Una manera de hacer Europa).

overall_design: Total RNA from Sensitive (S), Resistant (R) and Resistant under epigenetic reactivation treatment cells (RT) was extracted by the guanidine thiocyanate method using TRIZOL reagent (Invitrogen, CA) and purified with miRNeasy mini kit (Quiagen, CA), combined with DNAsa treatment. Labelled cDNA from the 12 cell lines was hybridized by duplicate into Agilent platforms for microRNA microarrays “Agilent miRNA microarray (8 x 15K)”

first: O

last: Vera

first: J

last: Jimenez

first: C

last: Rodriguez-Antolin

first: F

last: Sánchez Cabo

last: Soto

first: R

first: S

last: Lopez-Magallon

first: I

last: Esteban

first: A

last: Dopazo

last: Rojo

last: Belda

last: Alvarez

last: Benitez

last: Perona

last: De Castro

last: Ibanez de Cáceres


title: An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells [BiSulfite-seq]

type: Methylation profiling by high throughput sequencing

summary: Long noncoding RNAs are critical regulators of cell biology whose alteration can lead to the development of diseases such as cancer. The potential role of lncRNAs and their epigenetic regulation in response to platinum treatment is largely unknown. We analyzed four paired cisplatin-sensitive/resistant non-small cell lung cancer and ovarian cancer cell lines. The epigenetic landscape of overlapping and cis-acting lncRNAs was determined by combining human microarray data on 30,586 lncRNAs and 20,109 protein coding mRNAs with whole genome bisulfite sequencing. Selected candidate lncRNAs were further characterized by PCR, Gene-Ontology analysis and targeted bisulfite sequencing. Differential expression in response to therapy was observed more frequently in cis-acting compared to overlapping lncRNAs (78% vs 22%, fold change ≥1.5), while significantly altered methylation profiles were more commonly associated with overlapping lncRNAs (29% vs. 8%; p<0.001). Moreover, overlapping lncRNAs contain more CpG islands (CGIs) (25% vs. 17%) and the majority of CGI-containing overlapping lncRNAs share these CGIs with their associated coding genes (84%). The differences in expression between sensitive and resistant cell lines were replicated in 87% of the selected candidates (p<0.05), while our bioinformatics approach identifying differential methylation was confirmed in all of the selected lncRNAs (100%). Five lncRNAs under epigenetic regulation appear to be involved in cisplatin resistance (AC091814.2, AC141928.1, RP11-65J3.1-002, BX641110 and AF198444). These novel findings provide new insights into epigenetic mechanisms and acquired resistance to cisplatin that highlight specific lncRNAs, some with unknown function that may signal strategies in epigenetic therapies.

overall_design: A total of four cell lines were purchased from ATCC and ECACC (Sigma-Aldrich) and cultured as recommended. To analyze the changes in the transcriptome as a result of CDDP treatment, we established the CDDP-resistant variants of H23-R, H460-R, A2780-R and OVCAR3-R from the parental-sensitive variants H23, H460, A2780 and OVCAR3, after exposure to increasing doses of CDDP treatment in a time period of 6–18 months.

first: Olga

first: Javier

last: de Castro

first: Florian

last: Karreth

first: Thomas

last: Sellers

first: Inmaculada

last: Ibañez de Caceres


title: Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [RNA-seq]

first: Jim

last: Hughes

overall_design: RNA-seq of globin-depleted polyA-isolated RNA libraries isolated from primary erythroid Ter119+ cells obtained from the spleens of phenylhydrazine treated mice. Wild-type C57BL/6 mice were compared with mice containing deletions for θ1 and/or θ2 (∆θ1, ∆θ2, ∆θ1θ2) CTCF binding sites. Experiments performed on biological triplicates.

first: Caroline

last: Harrold

first: Douglas

last: Higgs


title: PGC 1α Senses the CBC of Pre-mRNA to Dictate the Fate of Promoter-Proximally Paused RNAPII [PRO-seq]

first: Lynne

last: Maquat

overall_design: Two biological replicates were generated to compare at single-nucleotide resolution, using PRO-seq, the gene localization of transcribing RNAPII in control (CTL) C2C12 myoblasts (MBs) (i.e. WT C2C12 MBs stably expressing a control GFP-mRNA-targeting shRNA) transiently expressing FLAG alone, and in PGC-1α KD C2C12 MBs (i.e. WT C2C12 MBs stably expressing a PGC-1α-mRNA targeting shRNA) transiently expressing FLAG alone, FLAG-PGC-1α(WT), or FLAG-PGC-1α(CBM5mut)

first: Xavier

last: Rambout

first: Hana

last: Cho

first: Geoffrey

last: Nelson

first: Karen

last: Adelman


title: Reanalyis of gene expression profiles from metastatic prostate cancer samples

status: Public on Jan 31 2026

first: Adam

last: Sowalsky

address: 37 Convent Drive Building 37 Room 1062B

institute: National Cancer Institute

summary: Metastatic prostate cancer is invariably lethal. In this study, we performed a harmonized re-analysis of whole-transcriptomic sequencing data from 105 samples to identify major pathways and cellular processes associated with prostate cancer subtype.

relation:
Reanalysis of: GSM5975848
Reanalysis of: GSM5975849
Reanalysis of: GSM5975850
Reanalysis of: GSM5975851
Reanalysis of: GSM5975852
Reanalysis of: GSM5975853
Reanalysis of: GSM5975854
Reanalysis of: GSM5975855
Reanalysis of: GSM5975858
Reanalysis of: GSM5975859
Reanalysis of: GSM5975860
Reanalysis of: GSM5975861
Reanalysis of: GSM5975862
Reanalysis of: GSM5975863
Reanalysis of: GSM5975864
Reanalysis of: GSM5975865
Reanalysis of: GSM5975866
Reanalysis of: GSM5975867
Reanalysis of: GSM5975868
Reanalysis of: GSM5975869
Reanalysis of: GSM5975870
Reanalysis of: GSM5975871
Reanalysis of: GSM5975872
Reanalysis of: GSM5975873
Reanalysis of: GSM5975874
Reanalysis of: GSM5975875
Reanalysis of: GSM5975876
Reanalysis of: GSM5975877
Reanalysis of: GSM5975878
Reanalysis of: GSM5975879
Reanalysis of: GSM5975880
Reanalysis of: GSM5975883
Reanalysis of: GSM5975884
Reanalysis of: GSM5975886
Reanalysis of: GSM5975887
Reanalysis of: GSM5975888
Reanalysis of: GSM5975889
Reanalysis of: GSM5975890
Reanalysis of: GSM5975891
Reanalysis of: GSM5975892
Reanalysis of: GSM5975893
Reanalysis of: GSM5975894
Reanalysis of: GSM5975897
Reanalysis of: GSM5975898
Reanalysis of: GSM5975901
Reanalysis of: GSM5975902
Reanalysis of: GSM5975798
Reanalysis of: GSM5975797
Reanalysis of: GSM5975799
Reanalysis of: GSM5975800
Reanalysis of: GSM5975801
Reanalysis of: GSM5975802
Reanalysis of: GSM5975803
Reanalysis of: GSM5975804
Reanalysis of: GSM5975805
Reanalysis of: GSM5975806
Reanalysis of: GSM5975807
Reanalysis of: GSM5975808
Reanalysis of: GSM5975810
Reanalysis of: GSM5975811
Reanalysis of: GSM5975812
Reanalysis of: GSM5975813
Reanalysis of: GSM5975814
Reanalysis of: GSM5975815
Reanalysis of: GSM5975816
Reanalysis of: GSM5975817
Reanalysis of: GSM5975818
Reanalysis of: GSM5975819
Reanalysis of: GSM5975820
Reanalysis of: GSM5975821
Reanalysis of: GSM5975822
Reanalysis of: GSM5975826
Reanalysis of: GSM5975824
Reanalysis of: GSM5975827
Reanalysis of: GSM5975828
Reanalysis of: GSM5975829
Reanalysis of: GSM5975830
Reanalysis of: GSM5975831
Reanalysis of: GSM5975832
Reanalysis of: GSM5975833
Reanalysis of: GSM5975834
Reanalysis of: GSM5975835
Reanalysis of: GSM5975836
Reanalysis of: GSM5975837
Reanalysis of: GSM5975838
Reanalysis of: GSM5975839
Reanalysis of: GSM5975840
Reanalysis of: GSM5975841
Reanalysis of: GSM5975842
Reanalysis of: GSM5975843
Reanalysis of: GSM5975844
Reanalysis of: GSM5975845
Reanalysis of: GSM5975846
Reanalysis of: GSM5975847

overall_design:
Harmonized re-analysis of RNA-seq data from 105 metastastic prostate cancer transcriptomes.

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The table below lists GEO accessions reused/reanalyzed for this study.
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title: miR-7 as novel predictive epigenetic biomarker for platinum-resistance in cancer (gene expression)

first: Carlos

last: Rodríguez Antolín

overall_design: Total RNA from Sensitive (S), Resistant (R) and Resistant under epigenetic reactivation treatment cells (RT) was extracted, by the guanidine thiocyanate method using TRIZOL reagent (Invitrogen, CA) and purified with miRNeasy mini kit (Quiagen, CA), combined with DNAsa treatment. Labelled cDNA from the 12 cell lines was hybridized by duplicate into Agilent platformsfor mRNA microarrays “Agilent Whole Human Genome Microarray (4x44K)”.

first: O

last: Vera

first: J

last: Jimenez

last: Pernía

first: C

last: Rodriguez-Antolin

first: F

last: Sánchez Cabo

last: Soto

first: R

last: Rosas

last: Rodriguez

first: S

last: Lopez-Magallon

last: Esteban

last: Dopazo

last: Rojo

last: Belda

last: Alvarez

last: Benitez


title: PGC 1α Senses the CBC of Pre-mRNA to Dictate the Fate of Promoter-Proximally Paused RNAPII

last: Maquat

last: Rambout


title: A Novel Role for the Tumor Suppressor Gene ITF2 in Tumorigenesis and Chemotherapy Response [RNA-seq]

last: Rodríguez Antolín

overall_design: RNA-seq from NSCLC patients were analyzed.

first: Olga

first: Ana

last: Sastre-Perona

last: Rodriguez-Antolín

first: Alvaro

last: García-Guede

first: María

last: Palomares-Bralo

first: Rocío

first: Darío

last: Sanchez-Cabrero

first: Carmen

first: Rubén

last: Martín-Arenas

first: Verónica

last: Pulido

first: Javier

last: de Castro

first: Pilar

last: Santisteban

last: Vera

first: Inmaculada

last: Ibáñez de Cáceres


title: Hippocampal estrogen levels, receptor types and epigenetics contribute to sex-specific memory-vulnerabilities to concurrent acute stresses [Cut & Run]

status: Public on Jan 27 2026

city: Philadelphia

first: Shuo

last: Zhang

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: It is increasingly recognized that acute traumatic events (e.g., mass shootings, natural disasters) can provoke enduring episodic memory deficits and generalization of trauma cues, and these are more common in women. We investigated mechanisms and sex differences of memory vulnerability to multiple acute concurrent stresses (MACS) in mice, focusing on the sex hormone 17β-estradiol and its receptors in hippocampus. Surprisingly, high physiological hippocampal estradiol levels, observed in proestrus females and males, were required for MACS-induced episodic memory disruption and sensitization and generalization of stress cues. High estradiol levels  were associated with permissive chromatin states in stress-vulnerable mice, while chromatin permissiveness and hippocampal estradiol were low in stress-resilient estrus females. Estrogen receptor (ER)β activation in resilient estrus females increased chromatin permissiveness and  enduring vulnerability to MACS, while ERα mediated milder stress-induced memory disruptions in males. Thus, hippocampal estradiol levels and sex modify chromatin states to enable long-lasting memory vulnerabilities to MACS.

overall_design: Cut&Run-seq profiling of H3K27me3 and H3K4me3 in the hippocampus of naive males, females in estrus or females in proestrus. Cut&Run-seq profiling of H3K27me3 and H3K4me3 of females in estrus with MACS, control vehicle or MACS and an ERβ agonist, Diarylpropionitrile (DPN).

first: Rachael

last: Hokenson

first: Kiara

last: Rodríguez-Acevedo

first: Yuncai

last: Chen

first: Annabel

last: Short

first: Sarah

last: Samrari

first: Brinda

last: Devireddy

first: Brittany

last: Jensen

first: Julia

last: Winter

first: Christine

last: Gall

first: Kiran

last: Soma

first: Elizabeth

last: Heller

first: Tallie

middle: Z

last: Baram


title: CAGE-seq Profiling of Transcription Start Site Usage in mock-infected and human cytomegalovirus (HCMV) infected human embryonic lung fibroblasts (HELF) cells at 12h and 72h post-infection (human)

status: Public on Oct 01 2025

city: Shenyang

first: Yang

last: Li

address: No. 36. Sanhao street, Heping District

institute: Shengjing Hospital of China Medical University

summary: CAGE-seq (Cap Analysis of Gene Expression coupled with deep sequencing) was used to map transcription start site (TSS) usage in human embryonic lung fibroblast (HELF) cells in response to infection with the human cytomegalovirus (HCMV) HAN strain. HELF cells were mock-infected or infected at a multiplicity of infection (MOI) of 3 and harvested at 12 hours post-infection (12 hpi) or 72 hours post-infection (72 hpi). This study provides genome-wide profiles of active promoters and capped 5' transcript ends to investigate dynamic changes in TSS usage during HCMV infection.

overall_design:
Human embryonic lung fibroblasts (HELF) were subjected to three conditions: mock infection, HCMV infection for 12 hours, and HCMV infection for 72 hours. Cells were infected with HCMV HAN strain (MOI=3) where applicable. Total RNA was isolated from each condition and used to generate CAGE libraries capturing the 5' ends of capped transcripts. Sequencing was performed on the Illumina HiSeq X Ten platform (150 bp paired-end reads). The primary experimental variables are infection status (mock vs. HCMV) and time post-infection (12 h vs. 72 h), with mock-infected HELF cells serving as the control.
Raw data uploaded to SRA under Bioprojects: PRJNA1299111; PRJNA1291936; PRJNA1441831

first: Yanping

last: Ma

first: Qiang

last: Ruan

first: Zhongwei

last: Zhao


title: RNA-seq analysis of Parkin (Prkn) expression in wild-type and TKO mouse hearts under normal chow and high-fat diet [RNA-Seq]

status: Public on Jan 30 2026

city: Bronx

first: Jeffrey

last: Pessin

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: High-fat diet (HFD) is known to promote metabolic stress and cardiac dysfunction. To examine genotype-dependent cardiac transcriptional responses, we performed RNA sequencing of hearts from wild-type (WT) and TKO mice fed either normal chow (NC) or a high-fat diet. RNA-seq analysis revealed significantly increased Parkin (Prkn) mRNA expression in TKO hearts compared with WT hearts under HFD conditions.

overall_design: Wild-type (WT) and TKO mice were maintained on either normal chow (NC) or high-fat diet (HFD). Hearts were collected at a defined time point, and total RNA was isolated for bulk RNA sequencing.

first: Yan

last: Tang

first: Li

last: Liu

first: Daorong

last: Feng


title: The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization [scRNA-seq]

city: Novosibirsk

first: Timofey

last: Lagunov

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences

summary: Lampbrush chromosomes are giant meiotic bivalents in growing oocyte nuclei that have served as a classic model system for studying chromatin organization and RNA synthesis for over a century. Despite their importance, the molecular mechanisms underlying lampbrush chromosomes formation and their distinctive chromomere-loop architecture have remained poorly understood. Here, we provide the first comprehensive genomic, cytological, and biophysical analysis of lampbrush chromosome organization by integrating single-cell Hi-C, RNA-seq, NOMe-seq, FISH mapping, and chromatin simulations. Single-nucleus Hi-C analysis revealed CTCF-independent contact domains with stable boundaries defined by transcription units in a convergent orientation. Сontact domains identified through Hi-C analysis correspond to insulated chromomeres in lampbrush chromosomes. Small transcriptionally inactive contact domains surrounded by transcription units in the diverged orientation form ‘chromatin knots’, which are often detached from the chromosome axis. Transcription loops frequently manifest as a 'cross' pattern with reduced contacts within chromatin domains. Integrative analysis of the whole-genome data uncovers the mechanisms underlying lampbrush chromosome structure, revealing how hypertranscription modulates chromatin stiffness and repositions SMC complexes to establish the distinctive chromomere-loop organisation. Biophysical modeling through polymer simulation reproduces key features of lampbrush chromosomes, including transcription loop formation, chromomere compaction, and insulation patterns. These findings offer a unifying framework for understanding the remarkable chromatin architecture of lampbrush chromosomes and their transcription-dependent organization.

overall_design: Strand specific scRNA-seq profiling of the WT lumpbrush chromosome stage chicken oocyte nucleus or ooplasm in two biological replicates.

first: Maria

last: Gridina

first: Artem

last: Nurislamov

first: Tatiana

last: Kulikova

first: Antonina

last: Maslova

first: Viktor

last: Konstantinov

first: Andrey

last: Popov

first: Alla

last: Krasikova

first: Veniamin

last: Fishman


title: The disruption of CtBP regulates DUX-dependent and -independent genetic program for the 2-cell-like state in murine embryonic stem cells [RNA-seq and RRBS]

status: Public on May 27 2024

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

country: Japan

institute: Kwansei Gakuin University

summary: After fertilization, maternally deposited mRNA is cleared, and de novo mRNA is transcribed from the zygotic genome through zygotic genome activation (ZGA), which is called maternal-to-zygotic transition (MZT) occurring in the mouse at 2-cell (2C) stage. 2C-like cells (2CLCs) marked by MERVL expression and transcriptionally similar to 2C embryos spontaneously emerge from mouse embryonic stem cells (mESCs). Although the emergence of 2CLCs completely depends on DUX function, a recent knockout study clearly showed that DUX is dispensable for mouse embryos, suggesting that DUX-independent molecular pathways are not recapitulated in 2CLCs. We present here that the disruption of C-terminal binding protein 1/2 (Ctbp1/2) activates DUX-dependent and -independent molecular pathway associated with the development of early mouse embryos mediated by the upregulation of Preferentially expressed antigen of melanoma family-like 7 (PRAMEL7). Furthermore, the abnormality of the gene expression profile caused by Dux KO is partially rescued by the overexpression of PRAMEL7 in mESCs. Our study provides new insights into the DUX-independent molecular pathway for developing early mouse embryos.

overall_design:
BMSCs were isolated from 3‑week‑old C57 mice. Osteogenic differentiation was induced in vitro at passage 1 (P1) on day 3 (D3)  The medium was changed every two days. The concentration of C69 was 0.5 μM.
RRBS experiements of WT and PRAMEL7-overexpressing embryonic stem cells.