title: Single-cell transcriptomic profiling uncovers cellular complexity and microenvironment in gastric tumorigenesis associated with Helicobacter pylori

status: Public on Dec 11 2023

city: Nanchang

first: Pan

last: Zheng

address: 17 of Yongwaizhengjie Street

institute: The Affiliated Hospital of Nanchang University

summary: Helicobacter pylori (H. pylori) infection is a key initiating factor in the Correa cascade of gastric carcinogenesis, but the comprehensive understanding of the pathogenic mechanisms underlying H. pylori-induced GC remains elusive. Here, we generated a single-cell atlas of gastric tumorigenesis comprising 18 specimens of gastritis, intestinal metaplasia and gastric cancer (GC) with or without H. pylori infection.  We identified 48 distinct cell subpopulations including novel rare subtypes, and revealed the influence of H. pylori infection on cellular heterogeneity across neoplastic lesions.

overall_design: A total of 18 patients pathologically diagnosed with gastric lesions at The First Affiliated Hospital of Nanchang University, including 6 of GS, 6 of IM, and 6 of GC, were enrolled in this study. The specimens of GS and IM were obtained during endoscopy, and the gastric carcinoma specimens were obtained from surgical samples without adjuvant therapy. The patients with gastric mucosal lesions were then divided into two groups according to H. pylori status. The sections with H&E staining were reviewed by senior pathologists. Status of H. pylori infection for these clinical specimens was determined with 13C-urea breath test (UBT), immunohistochemistry (IHC) and immunofluorescence (IF) staining. Additionally, formalin-fixed paraffin-embedded (FFPE) specimens including GS, IM and GC were collected from 120 patients for experimental validation. The clinical characteristics of patients were summarized in Table S1. The study protocol was approved by the Ethics Committee of the First Affiliated Hospital of Nanchang University under protocol number of (2023) CDYFYYLK (01-009). All tissue samples were obtained under informed consent.

first: Nianshuang

last: Li

first: Yin

last: Zhu

first: Xinbo

last: Xu


title: Effect of Usp17l overexpression on 2c gene in mouse embryonic stem cells

status: Public on Dec 18 2023

city: Tianjin

first: Linlin

last: Liu

address: Weijin Road 97

country: China

institute: Nankai university

type: Expression profiling by high throughput sequencing

summary:
In order to study the regulation of Usp17l on 2c gene, we overexpressed  Usp17le
We then performed gene expression profiling  with the data obtained from the RNA-seq 48h after Usp17le overexpression .

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Control  group  and  OE  group.

first: Panpan

last: shi

first: Xukun

last: Lu

first: Kairang

last: Jin

first: Guoxing

last: Yin

first: Dai

last: Heng

first: Jiao

last: Yang

first: Huiyu

first: Xiaoyan

last: Sheng

first: Xiaoying

last: Ye

first: Wei

last: Xie

first: Lin


title: Glial Reactivity and Cognitive Decline Follow Chronic Heterochromatin Loss in Neurons

status: Public on Jan 10 2024

city: Berlin

first: Andrew

last: Newman

address: Charitéplatz 1

department: Institute for Cell and Neurobiology

country: Germany

institute: Charité Universitätsmedizin Berlin

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: In aging cells and animal models of premature aging, heterochromatin loss coincides with transcriptional disruption including the activation of normally silenced endogenous retroviruses (ERVs). Here we show that loss of heterochromatin maintenance and de-repression of ERVs result in a chronic inflammatory environment characterized by neurodegeneration and cognitive decline in mice.  We identify distinct roles for HP1 proteins to ERV silencing where HP1γ is necessary and sufficient for H4K20me3 deposition and HP1β deficiency causes aberrant DNA methylation. Combined loss of HP1β and HP1γ results in loss of DNA methylation at ERVK elements. Progressive ERV de-repression in HP1β/γ DKO mice is followed by stimulation of the integrated stress response, an increase of Complement 3+ reactive astrocytes and phagocytic microglia.  This chronic inflammatory state coincides with age-dependent reductions in dendrite complexity and cognition.  Our results demonstrate the importance of preventing loss of epigenetic maintenance that is necessary for protection of postmitotic neuronal genomes.

overall_design: RNAseq in mouse young and aged hippocampus, RRBS and ChIPseq in mouse ESCs, RRBS in Hippocampal lysates

middle: G

first: Jafar

last: Sharif

first: Paraskevi

last: Bessa

first: Sami

last: Zaqout

first: Jeremy

last: Brown

first: Daniel

last: Richter

first: Rike

last: Dannenberg

first: Manabu

last: Nakayama

first: Susanne

last: Mueller

first: Theres

last: Schaub

first: Shairam

last: Manickaraj

first: Philipp

last: Boehm-Sturm

first: Osamu

last: Ohara

first: Haruhiko

last: Koseki

first: Prim

middle: B

last: Singh

first: Victor

last: Tarabykin


title: Single cell RNA-seq of single cell suspension from the HCC region of mice fed CD-HFD for 15 mice and treated with FABP5 inhibitor or control

status: Public on Feb 17 2024

city: New Haven

first: Jonathan

last: Sun

state: CT

address: 10 Amistad St

country: USA

institute: Yale University

summary: We perform scRNA-seq in the livers of C57BL/6 mice fed a CD-HFD for 15 months. Starting from the 13M, mice were treated with FABP5 inhibitor to ameliorate HCC.

overall_design: The HCC region of the liver was resected and digested in collagenase for 1 hour. After which an Annexin V enrichment kit was used to select for live cells for sequencing.

first: Carlos

last: Fernandez-Hernando


title: The effect of MYG1 knockout on gene expression in LoVo cells

status: Public on Dec 01 2023

city: Guangzhou

first: Jianxiong

last: Chen

state: Guangdong

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

institute: Southern Medical University

summary: Metabolic remodeling is a strategy for tumor to survival under stress and identifying the key genes driving the metabolic remodeling of colorectal cancer (CRC) and understanding its mechanisms may provide new targets for tumor intervention. Melanocyte proliferating gene 1 (MYG1) is a 3'-5' RNA exonuclease and plays key role in mitochondrial functions. Here, we uncover that MYG1 expression is upregulated in CRC progression and highly expressed MYG1 promotes glycolysis and CRC progression independent of its exonuclease activity through nuclear-mitochondrial collaboration.

overall_design: The control and MYG1 KO LoVo cells were performed RNA-seq

first: Jun

last: Zhou

first: Haoxuan

last: Zheng

first: Shiyu

last: Duan


title: Cross-species comparison reveals therapeutic vulnerabilities halting glioblastoma progression

city: Heidelberg

first: Leo

middle: Carl

last: Förster

state: Deutschland

address: Im Neuenheimer Feld 581

institute: DKFZ

summary: The growth of a tumor is tightly linked to the distribution of its cells along a continuum of activation states. Here, we systematically decode the activation state architecture (ASA) in a glioblastoma (GBM) patient cohort through comparison to adult murine neural stem cells. Modelling of these data forecasts how tumor cells organize to sustain growth and identifies the rate of activation as the main predictor of growth. Accordingly, patients with a higher quiescence fraction exhibit improved outcomes. Further, DNA methylation arrays enable ASA-related patient stratification. Comparison of healthy and malignant gene expression dynamics reveals dysregulation of the Wnt-antagonist SFRP1 at the quiescence to activation transition. SFRP1 overexpression renders GBM quiescent and increases the overall survival of tumor-bearing mice. Surprisingly, it does so through reprogramming the tumor’s stem-like methylome into an astrocyte-like one. Our findings offer a framework for patient stratification with prognostic value, biomarker identification, and therapeutic avenues to halt GBM progression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
performed Smart-seq2, Smart-seq3, 10X, and WGBS of tumor cells in xenograft or allograft models to investigate tumor lineages and compare to their healthy counterpart
NOTE FROM SUBMITTER: this submission contains only processed data (ie. non-PII) for sequencing experiments we carried out on human material subject to a DPA. Raw data is submitted to EGA.

first: Oguzhan

last: Kaya

middle: C

last: Foerster

first: Ana

last: Martin-Villalba


title: Disruption of Prostaglandin F2α Receptor Signaling Attenuates Fibrotic Remodeling and Alters Fibroblast Population Dynamics in A Preclinical Murine Model of Idiopathic Pulmonary Fibrosis

status: Public on Dec 04 2023

city: Philadelphia

first: Michael

middle: Francis

last: Beers

state: PA

address: 3450 Hamilton Walk

department: Pulmonary

institute: University of Pennsylvania

summary: Idiopathic Pulmonary Fibrosis (IPF) is a chronic, progressive, and diffuse parenchymal lung disease characterized by repetitive alveolar cell injury, myofibroblast proliferation, and excessive extracellular matrix deposition resulting in progressive loss of lung function.  Despite approved treatment options, unmet need persists for effective IPF therapeutics. The bioactive eicosanoid, prostaglandin F2a, and its cognate receptor FPr (Ptfgr) are implicated as a TGFb1 independent signaling hub for IPF. To further assess this signaling in IPF, we leveraged our published murine PF model (IER-SftpcI73T) expressing an inducible disease associated missense mutation in the SFTPC gene (I73T). Tamoxifen induction of IER-SftpcI73T mice resulted in an early multiphasic alveolitis and transition to spontaneous fibrotic remodeling by 28 days.  IER-SftpcI73T mice were crossed to a Ptgfr null (FPr-/-) line and resulted in attenuated weight loss and reductions in fibrotic endpoints. Through single cell RNA sequencing, pseudotime analysis, and in-vitro assays we demonstrated expression of Ptgfr predominantly within adventitial fibroblasts whichwere reprogrammed to an “inflammatory/transitional” cell state population in a PGF2a / FPr dependent manner..   Collectively, the findings provide added evidence a role for PGF2a signaling in IPF, mechanistically identify a susceptible fibroblast subpopulation, and establish a benchmark effect size for disruption of this pathway in mitigating fibrotic lung disease.

overall_design: To capture representative proportions of all major parenchymal and immune cell populations, we profiled IER-SftpcI73T/ Ptgfr+/+ and IER-SftpcI73T/ Ptgfr-/- animals with oral TAM and harvested the lungs at 14 and 28 days (n=2 per genotype per time point). Controls (n= 4) consisted of one mouse each of uninduced IER-SftpcI73T/ Ptgfr+/+, IER-SftpcI73T/ Ptgfr-/-, SftpcWT/ Ptgfr+/+, and SftpcWT/ Ptgfr-/- genotypes. Single cell suspension prepared by physical and enzymatic dissociation followed by MACS sorting by LS columns with CD45+ cell removal using CD45 micobeads followed by followed by “spike-back” of immune cells (~20% of final suspensions) with biological replicates for each timepoint loaded onto individual GemCodes

first: Luis

middle: R

last: Rodriguez

first: Soon

middle: Y

last: Tang

first: Willy

last: Roque Barboza

first: Aditi

last: Murthy

first: Yaniv

last: Tomer

first: Tian-Quan

last: Cai

first: Swati

last: Iyer

first: Katrina

last: Chavez

first: Ujjalkumar

middle: S

last: Das

first: Soumita

last: Ghosh

first: Thalia

last: Dimopoulos

first: Apoorva

last: Babu

first: Caitlin

last: Connelly

first: Garret

last: FitzGerald

middle: F


title: CAF variants control the tumor-immune microenvironment and predict skin cancer malignancy

status: Public on Feb 12 2024

city: Vienna

first: Beate

middle: Maria

last: Lichtenberger

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary: Cancer-associated fibroblasts (CAFs) play a key role in cancer progression and treatment outcome. Here, we elucidate the yet unresolved intra-tumoral CAF variety in three skin cancer types at molecular and spatial single-cell resolution in a large cohort. We show that two out of three CAF subtypes contribute to tumor immune surveillance with distinct mechanisms. Matrix CAFs (mCAFs) ensheath tumor nests and synthesize extracellular-matrix to prevent T cell invasion. Immunomodulatory CAFs (iCAFs), which express proinflammatory and immunomodulatory factors, are only detected in high abundance in aggressive tumors. Strikingly, iCAFs but not tumor cells are (apart from immune cells) the exclusive cell type producing chemokines and, thus, play a key role in immune cell recruitment and activation. Mechanistically, we show that cancer cells transform adjacent healthy fibroblasts into cytokine-expressing iCAFs, which subsequently recruit immune cells and modulate the immune response. In conclusion, targeting CAF variants holds promise for improved efficacy of immunotherapy.

overall_design:
Single cell RNA sequencing (Smart-seq2) of human skin tumors and healthy skin.

***************************************************************
According to the regulations of the Medial University of Vienna, raw data files are uploaded to the European Genome Archive and have restricted access.
***************************************************************

middle: M

first: Agnes

last: Forsthuber

first: Bertram

last: Aschenbrenner


title: A quantitative model of MET1-catalyzed establishment and epigenetic inheritance of DNA methylation

status: Public on Nov 13 2023

city: Klosterneuburg

first: Daniel

last: Zilberman

address: Am Campus 1

institute: Institute of Science and Technology Austria

summary: Methylation of CG dinucleotides (mCG), which regulates genome function in eukaryotes, is epigenetically propagated by Dnmt1/MET1 methyltransferases via a semiconservative mechanism. How these enzymes accomplish stable epigenetic inheritance despite imperfect fidelity remains mysterious. Here we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is delimited by active DNA demethylation and counterbalanced by histone variant H2A.Z, natural variation in which accounts for high genic methylation in accessions from northern Sweden. Based on these observations, we develop a mathematical model that precisely recapitulates mCG inheritance dynamics and successfully predicts steady-state intragenic mCG patterns and their population-scale variation given only CG site spacing as input. Our results demonstrate how methylation patterns are created in plant genes, reconcile imperfect mCG maintenance with long-term stability, and establish a quantitative model for the epigenetic inheritance of mCG.

overall_design: Bisulfite sequencing was carried out on leaf genomic DNA from a multi-generational Col-0 Arabidopsis thaliana lineage in different mutant genotypes

first: Elizabeth

last: Hollwey


first: Leo

last: Förster

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

overall_design: Refer to individual Series


title: Transcription factor ZNF263 enhances EGFR-targeted therapeutic response and reduces residual disease in lung adenocarcinoma [ChIP-seq]

status: Public on Jan 23 2024

city: Shanghai

first: Jiaqi

last: Liang

state: Shanghai

address: 180 Fenglin Road

institute: Zhongshan Hospital Fudan University

summary: EGF receptor (EGFR) tyrosine kinase inhibitors (TKIs) have achieved clinical successes in lung adenocarcinoma (LUAD). However, tumors often show profound but transient initial response and gain resistance. Here, we identified transcription factor ZNF263 as being significantly decreased in osimertinib-resistant or drug-tolerant persister LUAD cells and clinical residual tumor specimens. Exogenous expression of ZNF263 improved the initial response of cells and delayed the formation of persister cells with osimertinib. We elaborated that ZNF263 bound and recruited DNMT1 to the EGFR gene promoter, suppressing EGFR transcription with DNA hypermethylation. ZNF263 could also interact with nuclear EGFR (nEGFR), impairing the nEGFR-STAT5 interaction to enhance AURKA expression. Overexpressing ZNF263 also made tumor cells with wild-type EGFR expression or refractory EGFR mutations more susceptible to EGFR inhibition. More importantly, lentivirus or AAV-mediated plasmid delivery of ZNF263 synergistically suppressed tumor growth and regrowth with osimertinib in xenograft animal models. These findings suggest that enhancing ZNF263 may achieve complete response in LUAD with EGFR-targeted therapies.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ZNF263 in PC-9OR cells.

first: Guoshu

last: Bi

first: Qihai

last: Sui

first: Guangyin

last: Zhao


title: Localized T3 production modifies the transcriptome and promotes the hepatocyte-like lineage in iPSC-derived hepatic organoidslineage in iPSC-derived hepatic organoids

status: Public on Jan 24 2024

city: Galveston

first: Tatiana

middle: L

last: Fonseca

state: TX

department: Internal Medicine

institute: The University of Texas Medical Branch

summary: Thyroid hormone (TH) levels are low during development, and the deiodinases control TH signaling through tissue-specific activation or inactivation of TH. Here we studied human iPSC-derived hepatic organoids and identified a robust induction in DIO2 expression (the deiodinase that activates T4 to T3) that occurs in hepatoblasts. The surge in D2-T3 persists until the hepatoblasts differentiate into hepatocytes- or cholangiocytes-like cells, neither of which express DIO2. Preventing the induction of the D2-T3 signaling modified the expression of key transcription factors, decreased the number of hepatocyte-like cells by ~60%, and increased the number of cholangiocyte-like cells by ~55% without affecting the growth or the size of the mature liver organoid. Physiological levels of T3 could not fully restore the transition from hepatoblasts to mature cells. This indicates that the timed surge in D2-T3 signaling critically determines the fate of developing human hepatoblasts and the transcriptome of the maturing hepatocytes, with physiological and clinical implications for how the liver handles energy substrates.

overall_design: iPSC-derived HOs (hepatic organoids) were cultured in three conditions: without thyroid hormones (V-HOs), with free T4 at ~15 pM (T4-HOs) or free T3 at ~10 pM (T3-HOs) and dissociated into single cell at day 45.

first: Jorge

last: Hidalgo-Álvarez

first: Federico

last: Salas-Lucia

first: Diana

last: Vera Cruz

first: Antonio

last: Bianco


title: T cell landscape definition by multi-omics identifies Galectin-9 as novel immunotherapy target in chronic lymphocytic leukemia

status: Public on Nov 23 2023

first: Kwong Leong

last: Wong

state: Germany (DEU)

address: Im Neuenheimer Feld 280

department: Molecular genetics

summary: Failure of immunotherapy after applying checkpoint inhibitors or CAR-T cells is linked to T cell exhaustion. Here, we explored the T cell landscape in chronic lymphocytic leukemia (CLL) by single-cell omics analyses of blood, bone marrow and lymph node samples of patients and spleen samples of a CLL mouse model. By single-cell RNA-sequencing, mass cytometry (CyTOF), and multiplex image analysis of tissue microarrays, we defined the spectrum of phenotypes and transcriptional programs of T cells and and their differentiation state trajectories. We identified disease-specific accumulation of distinct regulatory T cell subsets and T cells harboring an exhausted phenotype exclusively in the CLL lymph node tissue. Integration of TCR data revealed a clonal expansion of CD8+ precursor exhausted T cells, suggesting their reactivity for CLL cells. Interactome analyses identified the TIM3 ligand Galectin-9 as novel immunoregulatory molecule in CLL. Blocking of Galectin-9 in CLL-bearing mice slowed down disease development and reduced the number of TIM3 expressing T cells. Galectin-9 expression correlated with shorter survival of CLL patients. Thus, Galectin-9 contributes to immune escape in CLL and represents a novel target for immunotherapy.

overall_design: Isolated T cells and leukemic CLL cells were isolated from spleens of leukemia TCL1-bearing mice.

first: John

first: Laura

last: Llaó Cid


title: Transcription factor ZNF263 enhances EGFR-targeted therapeutic response and reduces residual disease in lung adenocarcinoma [RNAseq]

overall_design: To investigate the ZNF263 effect in NSCLC cell lines, ZNF263 or control vector was overexpressed in three types of cell lines, and sequenced with duplicates each.


title: Genome-wide neonatal epigenetic changes associated with maternal exposure to the COVID-19 pandemic

status: Public on Nov 08 2023

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

type: Methylation profiling by genome tiling array

summary:
Background: During gestation, stressors to the fetus, including viral exposure or maternal psychological distress, can fundamentally alter the neonatal epigenome, and may be associated with long-term impaired developmental outcomes. The impact of in utero exposure to the COVID-19 pandemic on the newborn epigenome has yet to be described.
Methods: This study aimed to determine whether there are unique epigenetic signatures in newborns who experienced otherwise healthy pregnancies that occurred during the COVID-19 pandemic (Project RESCUE). The pre-pandemic control and pandemic cohorts (Project RESCUE) included in this study are part of a prospective observational and longitudinal cohort study that evaluates the impact of elevated prenatal maternal stress during the COVID-19 pandemic on early childhood neurodevelopment.
Using buccal swabs collected at birth, differential DNA methylation analysis was performed using the Infinium MethylationEPIC arrays and linear regression analysis. Pathway analysis and gene ontology enrichment were performed on resultant gene lists.
Results: Widespread differential methylation was found between neonates exposed in utero to the pandemic and pre-pandemic neonates. In contrast, there were no apparent epigenetic differences associated with maternal COVID-19 infection during pregnancy. Differential methylation was observed among genomic sites that underpin important neurological pathways that have been previously reported in the literature to be differentially methylated because of prenatal stress, such as NR3C1.
Conclusions: The present study reveals that the onset and continuation of the COVID-19 pandemic has fundamentally altered the epigenomes of newborns born during this time, even in otherwise healthy pregnancies, which should be considered in current and future epigenetic studies and may act as a critical biomarker of stress.

overall_design: DNA was extracted from buccal swab samples from pre-pandemic (CTL) and pandemic-exposed newborns (RES). Illumina Infinium EPIC BeadChip protocol was completed following manufacturer's specifications and DNA quality was determiend using Qubit Fluorometer. 300ng of DNA was bisulfite converted using Zymo DNA Methylation Lightning kit.

first: Kristen

last: Kocher

first: Surajit

last: Bhattacharya

first: Nickie

last: Niforatos-Andescavage

first: Miguel

last: Almalvez

first: Diedtra

last: Henderson

first: Eric

last: Vilain

first: Catherine

last: Limperopoulos

first: Emmanuele

last: Delot


title: The nucleolar protein NOL12 is required for processing of large ribosomal subunit rRNA precursors in Arabidopsis

status: Public on Nov 07 2023

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

summary:
NOL12 5'-3' exoribonucleases, conserved among eukaryotes, play important roles in pre-rRNA processing, ribosome assembly and export. The most well-described yeast counterpart, Rrp17, is required for maturation of 5.8 and 25S rRNAs, whereas human hNOL12 is crucial for the separation of the large (LSU) and small (SSU) ribosome subunit rRNA precursors.
In this study we demonstrate that plant AtNOL12 is also involved in rRNA biogenesis, specifically in the processing of the LSU rRNA precursor, 27S pre-rRNA. Importantly, the absence of AtNOL12 alters the expression of many ribosomal protein and ribosome biogenesis genes. These changes could potentially exacerbate rRNA biogenesis defects, or, conversely, they might stem from the disturbed ribosome assembly caused by delayed pre-rRNA processing. Moreover, exposure of the nol12 mutant to stress factors, including heat and pathogen Pseudomonas syringae, enhances the observed molecular phenotypes, linking pre-rRNA processing to stress response pathways. The aberrant rRNA processing, dependent on AtNOL12, could impact ribosome function, as suggested by improved mutant resistance to ribosome-targeting antibiotics.
Despite extensive studies, the pre-rRNA processing pathway in plants remains insufficiently characterized. Our investigation reveals the involvement of AtNOL12 in the maturation of rRNA precursors, correlating this process to stress response in Arabidopsis. These findings contribute to a more comprehensive understanding of plant ribosome biogenesis.

Founded by National Science Centre Grant, Poland (UMO-2018/29/B/NZ3/01980, UMO-2014/13/B/NZ3/00405, MINIATURA 2017/01/X/NZ1/00332, UMO-2021/41/B/NZ3/02605).

overall_design: RNA-seq data for nol12 mutant and Col-0 wild type seedlings.

first: Monika

last: Zakrzewska-Placzek

first: Joanna

last: Kufel


title: Toxicological Mechanisms and Potencies of Organophosphate Esters in KGN Human Ovarian Granulosa Cells as Revealed by High-throughput Transcriptomics

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

summary: Despite the growing number of studies reporting potential risks associated with exposure to organophosphate esters (OPEs), their molecular mechanisms of action remain poorly defined. We used the high-throughput TempO-Seq platform to investigate the effects of frequently detected OPEs on the expression of ~3000 environmentally responsive genes in KGN human ovarian granulosa cells. Cells were exposed for 48 h to one of five OPEs (0.1 to 50 μM): tris(methylphenyl) phosphate (TMPP), isopropylated triphenyl phosphate (IPPP), tert-butylphenyl diphenyl phosphate (BPDP), triphenyl phosphate (TPHP), or tris(2-butoxyethyl) phosphate (TBOEP). The sequencing data indicate that four OPEs induced transcriptional changes, whereas TBOEP had no effect within the concentration range tested. Multiple pathway databases were used to predict alterations in biological processes based on differentially expressed genes. At lower concentrations, inhibition of the cholesterol biosynthetic pathway was the predominant effect of OPEs; this was likely a consequence of intracellular cholesterol accumulation. At higher concentrations, BPDP and TPHP had distinct effects, primarily affecting pathways involved in cell cycle progression and other stress responses. Benchmark concentration (BMC) modelling revealed that BPDP had the lowest transcriptomic point of departure. However, in vitro to in vivo extrapolation modeling indicated that TMPP was bioactive at lower concentrations than the other OPEs. We conclude that these new approach methodologies provide information on the mechanism(s) underlying the effects of data-poor compounds and assist in the derivation of protective points of departure for use in chemical read-across and decision-making.

overall_design: We used a high-throughput transcriptomic approach, TempO-Seq, to examine the expression of 3386 probes covering 2730 genes in the human S1500+ gene set in KGN cells following OPE exposures for 48 hrs.

first: Xiaotong

last: Wang

first: Andrea

last: Rowan-Carroll

middle: J

first: Andrew

last: Williams

first: Carole

last: Yauk

first: Barbara

last: Hales

first: Bernard

last: Robaire


title: Transcriptomic analysis of dynamic dysregulation in brainstem autonomic nuclei during the development of hypertension

status: Public on Jan 30 2024

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

address: 1 University of New Mexico

institute: University of New Mexico

summary: Neurogenic hypertension stems from an imbalance in autonomic function that shifts the central cardiovascular control circuits towards a state of dysfunction. Using the female spontaneously hypertensive rat (SHR) and the normotensive Wistar Kyoto (WKY) rat model, we compared the transcriptomic changes in three autonomic nuclei in the brainstem, the nucleus of the solitary tract (NTS), caudal ventrolateral medulla (CVLM), and rostral ventrolateral medulla (RVLM) in a time series at 8, 10, 12, 16, and 24 weeks of age, spanning the pre-hypertensive stage through extended chronic hypertension.

overall_design: Transcriptomic timecourse for the hypertensive SHR and normotensive WKY rats in 3 brainstem regions. Samples were collected from the nucleus of the solitary tract (NTS), rostral ventrolateral medulla (RVLM), and caudal ventrolateral medulla (CVLM) at 8, 10, 12, 16, and 24 weeks of age. N=3-6 for each sample group.

first: Alison

last: Moss

first: Lakshmi

last: Kuttippurathu

first: Ankita

last: Srivastava

first: James

last: Schwaber


title: Decreased adipocyte-specific Olfactomedin 2 in obesity is a critical driver of defective fat cell cycle and adipose tissue accretion

status: Public on Dec 31 2023

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: Olfactomedin 2 (OLFM2) is a central player in development that also appears to be a critical mediator for energy handling. Here we report that in adipose tissue, expression of OLFM2 is opposite to obesity, being increased upon weight loss. Concurrently, we show steadily increased OLFM2 during adipogenesis, with expression levels reaching its zenith in terminally differentiated adipocytes. Notably, we demonstrate that the loss of this specific olfactomedin domain-containing protein in fat cell progenitors dampens adipogenesis, while the adipogenic conversion is bolstered in engineered 3T3-L1 cells with increased OLFM2. Our seminal findings also bound dwindled expressions of adipocyte-specific OLFM2 to the inflammatory state in the context of obesity, mainly characterized by the influence of macrophage-derived cytokines. Then, we show that the loss of OLFM2 in human adipocytes displays the transient downregulation of genes related to cell cycle, also coupled to deranged energy storage. Next, we transitioned our results to mice models in which whole-body knockout and transcriptionally regulated adipose-specific Olfm2 compel a cluster of molecular changes tightly related to impaired cell cycle (in both) and fat mass accretion (in the later). Current findings unveil the previously unknown expression of OLFM2 in adipocytes and the control of cellular mechanisms related to the obese phenotype exercised by this scaffold protein in adipose tissues.

overall_design: 20 samples were analyzed (gOLFM2=10, scPKP2=10)

first: Francisco

last: Ortega


title: Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer (RNA-Seq)

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: Treatment of prostate cancer relies predominantly on the inhibition of androgen receptor (AR) signaling. Despite the initial effectiveness of the AR-targeted therapies, the cancer often develops resistance to the AR blockade. One mechanism of the resistance is glucocorticoid receptor (GR)-mediated replacement of AR. Nevertheless, the mechanistic ways and means how the GR-mediated antiandrogen resistance occurs has remained elusive. Here, we have discovered several crucial features of GR action in prostate cancer cells through genome-wide techniques. We detected that the replacement of AR by GR in antiandrogen-exposed prostate cancer cells occurs almost exclusively at pre-accessible chromatin sites displaying FOXA1 occupancy. Counterintuitively to the classical pioneer factor model, silencing of FOXA1 potentiated the chromatin binding and transcriptional activity of GR. This was attributed to FOXA1-mediated repression of the NR3C1 (gene encoding GR) expression via the corepressor TLE3. In comparison to FOXA1, inhibition of coregulator activity efficiently restricted GR-mediated gene regulation and cell proliferation. Overall, we identified chromatin pre-accessibility and FOXA1-mediated repression as important regulators of GR action in prostate cancer, pointing out new avenues to oppose steroid receptor-mediated drug resistance.

overall_design: Gene expression profiling by RNA-seq from VCaP and 22Rv1 cells grown in the presence or absence of ENZ. Gene expression profiling before and after AR-V7 depletion by RNA-seq from 22Rv1 prostate cancer cells grown in the presence or absence of ENZ. All sequencing was done with Illumina NextSeq 500 or Illumina NextSeq 2000.

first: Laura

last: Helminen


title: Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer


title: Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer (ATAC-Seq)

overall_design: Examination of chromatin accessibility by ATAC-seq from VCaP and 22Rv1 prostate cancer cells grown in the presence or absence of ENZ. All sequencing was done with Illumina NextSeq 500.


title: Ndufs4-knockout mouse with mitochondria complex I inhibitor treatment

city: Rochester

first: Liewei

state: MN

address: 200 2st Str SW

department: Neurology

institute: Mayo Clinic

summary: Glucose hypometabolism is one of the major characteristics of Alzheimer's disease (AD). The energy deficiency in AD brain has been at least partially attributed to accelerated mitochondrial dysfunction than normal aging. In earlier publications, we have shown that small molecule mitochondrial complex I inhibitor CP2 facilitated mitochondrial regeneration and rescued mitochondrial deficiency in familial AD mice model APP-PS1. Here in this study, we investigated whether a typical mitochondrial deficiency mouse model could recapitulate molecular expression signatures of AD brain and whether CP2 was able to rescue the AD brain phenotype. Ndufs4 is one of the regulatory subunits of mitochondria complex I. Knockout of Ndufs4 resulted in complex I assembly failure and approximately half mitochondrial function loss. Ndufs4-knockout mice are viable but are short in lifespan (up to about 90 days). This model has been previously used to study Leigh syndrome, a heritable mitochondrial deficiency disease. In this dataset, we performed RNAseq on brains of CP2 treated Ndufs4-knockout mice and examined the expression changes upon CP2 treatment.

overall_design: Ndufs4-knockout and WT mice of 37-45 days old were gavage fed with CP2 or vehicle for 3 consecutive days. At the end of third day of gavage feeding, mice were sacrificed and hippocampus and cortex brain tissue was quickly collected for RNA isolation.

first: Eugenia

last: Trushina

first: Huanyao

last: Gao


title: CUT&TAG analysis of H3K27ac in granulosa cells from control and POI patients

status: Public on Dec 25 2023

city: Jinan

first: Nianyu

last: Li

state: ShanDong

address: 44 wenhua xi road

institute: Shandong University

summary: To reveal the role of NCOA7 in cellular senescence, we performed the CUT&TAG assay using the H3K27ac antibody to map acetylation in granulosa cells from control and POI patients. We conducted the DNA sequencing of libraries from CUT&TAG assay using the H3K27ac antibody in human primary granulosa cells.

overall_design: CUT&TAG-seq for acetylation using the H3K27ac antibody in granulosa cells of control and POI patients.

first: Xue

last: Jiao


title: Persistence of homeostatic sleep drive is encoded by plasticity of a thalamic reuniens circuit

status: Public on Oct 21 2023

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

summary: Purpose: snRNA-Seq was performed to characterize molecular differences that occur with sleep deprivation in the nucleus reuniens of the thalamus

overall_design: The nucleus reuniens of the thalamus (RE) were collected from 7-8 wk old male FosTRAP;tdTomato mice using a previously published protocol(Kim et al. 2021).  In brief, the RE was dissected using a micropunch from a single mouse and placed into Hibernate-A media with a 2% B-27 and GlutaMAX supplement (0.5 mM final concentration). Collected tissues were then processed using a modified 10x Genomics protocol. Lysis buffer containing (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet-P40, 0.01% Digitonin, 1 U/ml Rnase inhibitor, 1% BSA) was added into a tube containing the RE. The samples were incubated on ice for 15 min with gentle pestle grinding with 5 strokes every 3 minutes.  Following this, a wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.2 U/ml RNase inhibitor, 1% BSA) was added, and nuclei were filtered through a 50 μm filter. Debris was removed using OptiPrep density gradient media, and nuclei morphology was accessed under a light microscope.  Nuclei were then immediately processed for snRNA-Seq. The nuclei from the RE were loaded into the 10x Genomics Chromium Single Cell System (10x Genomics) and libraries were generated using v3.1 chemistry following the manufacturer’s instructions.  Three biological replicates for each control and SD were conducted. Libraries were then sequenced on an Illumina NovaSeq6000.  snRNA-Seq data were first processed through Cell Ranger (v.5.0.0, 10x Genomics) with default parameters with ‘include-introns’, aligned to the custom mm10 genome with tdtomato-WPRE (Ai14) sequence. Matrix files generated from these processes were used for subsequent analysis.

first: SangSoo

last: Lee

first: Qiang

last: Liu

first: DongWon

first: Isabelle

last: Palmer

first: Kristen

last: Park

first: Heike

last: Muenzberg-Gruening

first: Seth

last: Blackshaw

first: Mark

middle: N

last: Wu


title: Gene expression profile at single cell level of nucleus pulposus cells (NPCs) from the nucleus pulposus (NP) tissue in the mild degenerative intervertebral discs (MDD) and server degenerative intervertebral discs(SDD).

status: Public on Oct 30 2023

first: Jianru

last: Wang

address: No. 58, Zhongshan road II, Guangzhou 510080, People’s Republic of China

institute: Sun Yat-sen University First Affiliated Hospital

summary: It has been shown that the divergence of NPCs plays an important role in the progression of intervertebral disc degeneration (IVDD). We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of NPCs in the IVDD.

overall_design: NP tissue of the different degenerative grade of  IVDs  were isolated in patient IVDs  and analyzed using scRNAseq.


title: Drosophila model for studying cystic fibrosis pathophysiology of the gastrointestinal system

status: Public on Oct 26 2023

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Cystic fibrosis (CF) is a recessive disease caused by mutations in theCF transmembrane conductance regulator(CFTR) gene. The most common symptoms include progressive lung disease and chronic digestive conditions. CF is the first human genetic disease to benefit from having five different species of animal models. Despite the phenotypic differences among the animal models and human CF, these models have provided invaluable insight into understanding disease mechanisms at the organ-system level. Here, we identify a member of the ABCC4 family, CG5789, that has the structural and functional properties expected for encoding theDrosophilaequivalent of human CFTR, and thus refer to it asDrosophila CFTR(Dmel\CFTR). We show that knockdown ofDmel\CFTRin the adult intestine disrupts osmotic homeostasis and displays CF-like phenotypes that lead to intestinal stem cell hyperplasia. We also show that expression of wild-type humanCFTR, but not mutant variants of CFTR that prevent plasma membrane expression, rescues the mutant phenotypes ofDmel\CFTR.Furthermore, we performed RNA sequencing (RNA-Seq)-based transcriptomic analysis usingDmel\CFTRfly intestine and identified a mucin gene,Muc68D, which is required for proper intestinal barrier protection. Altogether, our findings suggest thatDrosophilacan be a powerful model organism for studying CF pathophysiology.

overall_design: We performed RNA sequencing (RNA-Seq)-based transcriptomic analysis usingDmel\CFTRfly intestine, a transgenic RNAi line targeting CG5789 from NIG (National Institute of Genetics Stock)

first: Kevin

first: Weihang

last: Chen

first: Norbert

last: Perrimon


title: Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer (ChIP-Seq)

first: Ville

last: Paakinaho

overall_design: Examination of AR, GR, and FOXA1 chromatin binding by ChIP-seq from VCaP and 22Rv1 prostate cancer cells grown in the presence or absence of ENZ. Examination of H3K27ac chromatin occurrence by ChIP-seq from 22Rv1 prostate cancer cells grown in the presence or absence of ENZ. Examination of GR and TLE3 chromatin binding before and after FOXA1 depletion by ChIP-seq from VCaP prostate cancer cells grown in the presence or absence of ENZ.  Examination of GR chromatin binding before and after AR-V7 depletion by ChIP-seq from 22Rv1 prostate cancer cells grown in the presence or absence of ENZ. All sequencing was done with Illumina NextSeq 500 or Illumine NextSeq 2000.

first: Laura

last: Helminen


title: Epigenetic Switch Reshapes Epithelial Stem/Progenitor Cells Signatures and Contributes to Inflammatory Programming in Hidradenitis Suppurativa [CUT&RUN]

status: Public on Oct 18 2023

city: birmingham

first: lin

last: jin

state: alabama

address: 1824 6th ave s

institute: university of alabama at birmingham

summary:
1) By using dual-omics profiling for both chromatin accessibility and gene expression as well as CUT&RUN sequencing for chromatin modification states, we identified that numerous disease-associated inflammatory enhancers were epigenetically activated and co-exist with the transcriptional states of their target genes in basal progenitor cells.
2) By using  CUT&RUN sequencing , we identified numerous S100A8 binding DNA sequences in HS epidermal cells.

overall_design:
1) The Institutional Review Board of the University of Alabama at Birmingham approved the protocol (IRB-300005214) for obtaining surgically discarded skin tissues from heathy and HS (Hurley II/III stage) subjects. Surgical excisions from 4 patients with HS (axillary or groin lesions) and 2 healthy controls (discarded tissue from breast or abdominoplasty reduction surgery) were collected.
2) The Institutional Review Board of the University of Alabama at Birmingham approved the protocol (IRB-300005214) for obtaining surgically discarded skin tissues from heathy and HS (Hurley II/III stage) subjects. Surgical excisions from 3 patients with HS (axillary or groin lesions) and 2 healthy controls (discarded tissue from breast or abdominoplasty reduction surgery) were collected.

first: Lin

last: Jin

first: Mohammad

last: Athar


title: Molecular programs of regional specification and neural stem cell fate progression in developing macaque telencephalon

status: Public on Oct 13 2023

city: New haven

first: Nenad

last: Sestan

address: 333 Cedar street

institute: Yale University

summary: During early telencephalic development, intricate processes of regional patterning and neural stem cell (NSC) fate specification take place. However, our understanding of these processes in primates, including both conserved and species-specific features, remains limited. Here, we profiled 761,529 single-cell transcriptomes from multiple regions of the prenatal macaque telencephalon. We deciphered the molecular programs of the early organizing centers and their cross-talk with NSCs, revealing primatebiased galanin-like peptide (GALP) signaling in the antero-ventral telencephalon. Regional transcriptomic variations were observed along the fronto-temporal axis during early stages of neocortical NSC progression and in neurons and astrocytes. Additionally, we found that genes associated with neuropsychiatric disorders and brain cancer risk might play critical roles in the early telencephalic organizers and during NSC progression.

overall_design: Employing timed-pregnant rhesus macaques, we dissected multiple prospective regions of the prenatal telencephalon, from embryonic day (E)37, prior to neurogenesis, up to mid-gliogenesis at E110 (12). Anterior (A)/frontal (FR), dorso-lateral (DL)/putative motor-somatosensory (MS), putative temporal, posterior (P)/occipital (OC) areas, and ganglionic eminence (GE) were recognized at the earliest stages (E37-E78). Then, at the latest stages (E93-E110), we collected the cortical wall of up to 13 regions of the neocortex, including multiple sub-areas from the prefrontal (dorsolateral: DFC; orbital: OFC; medial: MFC; ventrolateral: VFC), primary motor (M1C), parietal (primary somatosensory: S1C; inferior parietal: IPC; posterior cingulate: PCC), insula (Ins), temporal (inferior: ITC; superior: STC; primary auditory: A1C), occipital (primary visual: V1), and three regions from GE (medial: MGE; lateral: LGE; caudal: CGE) (24). Eighty-two samples categorized were processed for scRNA-seq. After stringent quality control, a total of 761,529 high-quality individual cells were obtained.

first: Nicola

last: Micali

first: Shaojie

last: Ma

first: Mingfeng

last: Li

first: Suel-Kee

last: Kim

first: Xoel

last: Mato-Blanco

first: Suvimal

last: Sindhu

first: Jon

middle: I

last: Arellano

first: Tianliuyun

last: Gao

first: Alvaro

last: Duque

first: Gabriel

last: Santpere

first: Pasko

last: Rakic


title: Altered hepatic lipid droplet morphology and lipid metabolism in fasted Plin2 null mice

city: OSLO

first: Knut

middle: Tomas

last: Dalen

state: OSLO

address: Sognsvannsveien 9

department: Department of Nutriton

country: Norway

institute: University of Oslo

summary: Perilipin 2 (Plin2) binds to the surface of hepatic lipid droplets (LDs) with expression levels that correlate with triacylglyceride (TAG) content. We investigated if Plin2 is important for hepatic LD storage in fasted or high-fat diet-induced obese Plin2+/+ and Plin2-/- mice. Plin2-/- mice had comparable body weights, metabolic phenotype, glucose tolerance, and circulating TAG and total cholesterol levels compared to Plin2+/+ mice, regardless of the dietary regime. Both fasted and high-fat fed Plin2-/- mice stored reduced levels of hepatic TAG compared to Plin2+/+ mice. Fasted Plin2-/- mice stored fewer, but larger hepatic lipid droplets compared to Plin2+/+ mice. Detailed hepatic lipid analysis showed substantial reductions in accumulated TAG species in fasted Plin2-/- mice compared to Plin2+/+ mice, whereas cholesteryl esters and phosphatidylcholines were increased. RNA sequencing revealed minor differences in hepatic gene expression between fed Plin2+/+ and Plin2-/- mice, in contrast to marked differences in gene expression between fasted Plin2+/+ and Plin2-/- mice. Our findings demonstrate that Plin2 is required to regulate hepatic lipid droplet size and storage of neutral lipid species in the fasted state, while its role in obesity-induced steatosis is less clear.

overall_design: Female 15-week old Plin2+/+ and Plin2-/- mice on C57BL/6N background fed chow or fasted for 24h.

first: Atanaska

last: Doncheva

middle: T


title: Activation of Coagulation and Proinflammatory Pathways in Thrombosis with Thrombocytopenia Syndrome and Following COVID-19 Vaccination

first: Dan

last: Barouch

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

summary: Thrombosis with thrombocytopenia syndrome (TTS) is an extremely rare but potentially serious adverse event following immunization with the adenovirus vector-based COVID-19 vaccines Ad26.COV2.S (Janssen / Johnson & Johnson) or ChAdOx1 (AstraZeneca). However, no cases of TTS have been reported in over 1.5 million individuals who received a second immunization with Ad26.COV2.S in the United States, suggesting that anti-vector immunity may reduce TTS risk.  Here we show robust stimulation of platelet activation and coagulation pathways and innate immune pathways in patients with TTS but only transient activation of these pathways following vaccination.  We evaluated proteomic profiles in 2 patients with TTS and transcriptomic and proteomic profiles in 20 people following an initial dose and a booster dose of Ad26.COV2.S and in 14 people who received the mRNA vaccines BNT162b2 or mRNA-1273. Initial Ad26.COV2.S vaccination induced transient activation of platelet activation and coagulation pathways and innate proinflammatory pathways that resolved by day 7.  TTS patients showed enhanced and sustained upregulation of these pathways, whereas a second immunization with Ad26.COV2.S or a reduced initial dose of Ad26.COV2.S resulted in lower activation of these pathways.  These data provide insight into TTS pathogenesis and suggest a potential strategy for reducing TTS risk by lowering the dose of Ad26.COV2.S.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: 30 outbred Indian-origin adult male (10) and female (20) rhesus macaques (Macaca mulatta) were randomly allocated to groups21. Animals were 5-8 kg. All animals were housed at Bioqual, Inc. (Rockville, MD). Animals received a single immunization of 1x1011, 5x1010, 1.125x1010, or 2x109 viral particles (vp) Ad26.COV2.S (Janssen; n = 5/group) or sham (n = 10) by the intramuscular route without adjuvant at week 0. Animal studies were conducted in compliance with all relevant local, state, and federal regulations and were approved by the Bioqual Institutional Animal Care and Use Committee (IACUC). Blood, PBMC, and serum samples were collected at baseline (D1) and on days 1 (D2), 7 (D8), and 14 (D14) following vaccination.

first: Malika

last: Aid

middle: H


title: Unraveling the Mechanisms of Sensitivity to Anti-FGF Therapies in Imatinib-Resistant Gastrointestinal Stromal Tumors (GIST) Lacking Secondary KIT Mutations

status: Public on Nov 09 2023

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

type: Non-coding RNA profiling by high throughput sequencing

summary: Acquired resistance of gastrointestinal stromal tumors (GISTs) to imatinib mesylate (IM) is one of the most critical challenges in GIST therapy. Here we show that a long-term culture of GIST T-1 cells with IM induces clonal heterogeneity resulting in the appearance of cancer cells exhibiting activation of the FGFR-signaling pathway which was associated with KIT loss. The first one was due to the overexpression of FGFR1/2 and increased production of FGF-2 ligand. These events maintained GIST resistance to IM and rendered these GIST cells highly sensitive to all types of pan-FGFR-inhibitors used in the current study. Knockout of FGFR2 in this GIST subclone significantly attenuated pro-apoptotic and anti-proliferative activities of infigratinib (BGJ 398) both in vitro and in vivo, thereby suggesting the activation of FGFR-signaling pathway via FGFR2-mediated axis as the predominant molecular mechanism in these GIST cells. Collectively, the extended inhibition of KIT-signaling in GISTs induces clonal heterogeneity of cancer cells and might change the tumor’s sensitivity to FGFR-inhibitors due to selection of cancer cells with an FGFR-overactivated pathway. For siCLDN1-transfected and PDS-0330-treated GIST T-1 cell line transcriptomes see GSE296175.

overall_design: The transcriptomes of naive (imatinib mesylate sensitive) GIST-T1 cells and their IM-resistant counterparts GIST-R1 and GIST-R2 cells. GIST T-1 was established from a metastatic pleural tumor from a stomach and contains heterozygous 57-base pair deletion (V570-Y578) in KIT exon 11. IM-resistant GIST-R1 subline was established in our laboratory after a continuous induction from 0.4 nM to 1000 nM IM in a stepwise increasing concentration manner. GIST-R2 subclone was derived from GIST-R1 cells continuously treated with IM for up to 12 months.

first: Sergei

last: Boichuk

first: Pavel

last: Dunaev

first: Vera

last: Skripova

first: Aigul

last: Galembikova

first: Firyuza

last: Bikinieva

first: Elena

last: Shagimardanova

first: Guzel

last: Gazizova

last: Valeeva

first: Ekaterina

last: Mikheeva

first: Maria

last: Vasilyeva

last: Kopnin

first: Vladimir

last: Strelnikov

first: Ramziya

last: Kiyamova


title: BMP4 and BMP6 stimulation of adult mouse muscle stem cells activates the Notch signaling pathway [array]

status: Public on Oct 01 2023

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

summary: Muscle stem cell (MuSC) activation, proliferation, self-renewal, and differentiation are tightly regulated processes that enable muscle development and regeneration without exhaustion of the stem cell pool. BMP signaling keeps MuSCs in a proliferative state and prevents their differentiation. We investigated the effect of bone morphogenetic protein 4 and 6 (BMP4 and BMP6) on transcriptional regulation and intracellular signaling of adult murine MuSCs using RNA-sequencing, RNA expression arrays, pathway-specific qPCR arrays, and Cleavage Under Targets and Tagmentation (CUT&Tag), which identifies the binding sites of transcription factors and the presence of specific histone marks with high spatial resolution. Freshly isolated MuSCs were grown for 42 to 72 hours, kept serum deprived for 6 hours, and then stimulated with BMP4/6. BMP4/6 addition resulted in a rapid increase in Inhibitor of DNA binding 1 (Id1)-expression, a typical BMP target gene, which peaked after one hour. As expected, stimulation with BMP4/6 resulted in a significant increase in transcription of BMP target genes such as Smad7, Nog, Id1, Klf10, and Lif, but also a strong increase in transcription of Notch pathway genes such as Hes1, Lfng, and Hey1. We showed that the important BMP pathway effectors SMAD4 and pSMAD1/5/9 bind to the promoters of these Notch targets. Our results suggest that the rapid expression of genes encoding Notch signaling components is due to direct regulation by BMP signaling.

overall_design: Muscle stem cells were isolated from muscle of female 6-8-week-old mice, cultured on Matrigel® for expansion over 2 days. In order to limit the effect of BMPs in the culture medium (e.g. from serum supplements), cells were cultured prior to the BMP stimulation for 6 h in serum-free medium containing BMP soluble receptor (recombinant mouse BMPR-IA/ALK3-Fc Chimera, R&D Systems, 437-MR) in a concentration of 200 ng/ml. Cells were then stimulated with a pulse of 1 h with 100 ng/ml BMP4 or BMP6 or only with vehicle used for reconstitution of BMP in the case of controls. Cells were harvested thereafter and total RNA was extracted. Microarray analysis was performed on three biological replicates of cultured adult mouse muscle stem cells stimulated with BMP4 or verhicle after serum starvation

first: Birthe

middle: K

last: Lange

first: Ioanna

last: Polydorou

first: Helge

last: Amthor


title: Epigenetic Switch Reshapes Epithelial Stem/Progenitor Cells Signatures and Contributes to Inflammatory Programming in Hidradenitis Suppurativa

status: Public on Oct 17 2023

first: lin

last: jin

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

overall_design: Refer to individual Series


title: Mpox infection protects against re-challenge in rhesus macaques

status: Public on Sep 29 2023

first: Dan

last: Barouch

summary: The mpox outbreak of 2022–2023 involved rapid global spread in men who have sex with men. We infected 18 rhesus macaques with mpox by the intravenous, intradermal, and intrarectal routes and observed robust antibody and T cell responses following all three routes of infection. Numerous skin lesions and high plasma viral loads were observed following intravenous and intradermal infection. Skin lesions peaked on day 10 and resolved by day 28 following infection. On day 28, we re-challenged all convalescent and 3 naive animals with mpox. All convalescent animals were protected against re-challenge. Transcriptomic studies showed upregulation of innate and inflammatory responses and downregulation of collagen formation and extracellular matrix organization following challenge, as well as rapid activation of T cell and plasma cell responses following re-challenge. These data suggest key mechanistic insights into mpox pathogenesis and immunity. This macaque model should prove useful for evaluating mpox vaccines and therapeutics.

overall_design: We infected 18 rhesus macaques with mpox by the intravenous, intradermal, and intrarectal routes and observed robust antibody and T cell responses following all three routes of infection. Numerous skin lesions and high plasma viral loads were observed following intravenous and intradermal infection, whereas few skin lesions and low plasma viral loads were observed following intrarectal infection. Skin lesions generally peaked on day 10 and resolved by day 28 following infection. On day 28, we re-challenged all convalescent animals and 3 naïve control animals with mpox by the intravenous route.

first: Malika

last: Aid

first: Michaela

last: Sciacca

first: Katherine

last: McMahan

first: David

last: Hope

first: Jinyan

last: Liu

first: Catherine

last: Jacob-Dolan

first: Olivia

last: Powers

first: Julia

last: Barrett

first: Cindy

last: Wu

first: Audrey

last: Mutoni

first: Tetyana

last: Murdza


title: Identification and analysis of differently expressed genes in liver macrophages from WT and FABP7 KO mice with MC38 metastatic.

status: Public on Sep 30 2023

city: Guangzhou

first: shaowan

last: xu

address: Jingxi

institute: southern medical university

summary: Studies have shown that FABP7 is involved in the occurrence and development of various tumors and can serve as a prognostic marker for tumors.  But, the function and molecular mechanism of FABP7 in the tumor microenvironment have not been reported.

overall_design: Liver macrophages isolated from WT (n=1) or FABP7 KO (n=1) mice with MC38 metastatic

first: Li

last: Liang

first: Shaowan

last: Xu

first: Xin

last: Peng

first: Zhenfang

last: Wang


title: Sex specific role of KDM5B demethylase in Alcohol-associated Liver Disease development and resolution

status: Public on Oct 07 2023

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

institute: University of Kansas Medical Center

summary: Alcohol-associated liver disease (ALD) is a major cause of alcohol related mortality. Recently we identified hepatic demethylases KDM5B and KDM5C as important sex-specific epigenetic regulators of alcohol response in the liver. In this study we aimed to study the molecular mechanisms of KDM5-dependent ALD development and resolution. We found that alcohol induces pathological changes in cell-cell communication in the liver that are in part mediated by epigenetic changes in hepatocytes mediated by histone demethylase KDM5B.  Using cell type specific knockout mice, we found that KDM5B histone demethylase was a key regulator of alcohol-induced epigenetic changes in hepatocytes. Moreover, it regulated hepatocytes-non-parenchymal cell crosstalk that promoted inflammation and fibrosis development in ALD. This mechanism was specific to females. In males KDM5B deficiency was not sufficient to prevent fibrosis development. In contrast KDM5B demethylase loss promoted fibrosis resolution in both males and females. This mechanism involved changes in hepatocyte-macrophage crosstalk and LXRα activation, which we identified to be critical for the fibrosis resolution process. CONCLUSION: In summary, KDM5B demethylase is a regulator of cell-cell crosstalk involved in disease progression in females and in disease resolution in both sexes.

overall_design: Whole liver mRNA analysis in alcohol fed (WDA - western diet with alcohol in the drinking water) Kdm5b floxed mice treated with different AAV-Cre vectors

first: Michal

middle: P

last: Schonfeld


title: BMP4 and BMP6 stimulation of adult mouse muscle stem cells activates the Notch signaling pathway [RNA-seq I]

first: Markus

last: Schuelke

overall_design: Muscle stem cells were isolated from muscle of female 6-8-week-old mice, cultured on Matrigel® for expansion over 2 days. In order to limit the effect of BMPs in the culture medium (e.g. from serum supplements), cells were cultured prior to the BMP4 or BMP6 stimulation for 6 h in serum-free medium containing BMP soluble receptor (recombinant mouse BMPR-IA/ALK3-Fc Chimera, R&D Systems, 437-MR) in a concentration of 200 ng/ml. Cells were then stimulated with a pulse of 1 h with 100 ng/ml BMP4 or BMP6 or only with vehicle used for reconstitution of BMP in the case of controls. Cells were harvested thereafter and total RNA was extracted.

first: Birthe

last: Lange

first: Ioanna

last: Polydorou

first: Helge

last: Amthor


title: METTL3 modulates colonic epithelium integrity via maintaining the self-renewal and differentiation of Lgr5+ stem cell

status: Public on Oct 31 2023

city: Shanghai

first: Chenbo

last: Ding

state: None Selected

address: 280 Chongqing South Rd

institute: Shanghai Jiao Tong University School of Medicine

summary: We show that METTL3 expression is decreased in the colon mucosa in ulcerative colitis (UC) patients, and its expression is strongly associated with the differentiation and maturation of goblet cells during inflammation.Depletion of METTL3 significantly inhibits the self-renewal and differentiation of Lgr5+ stem cells, especially the differentiation and maturation of goblet cells, results in intestinal dysplasia and spontaneous inflammation.

overall_design: To further explore the potential molecular mechanism of Mettl3 regulating the self-renewal and differentiation of A cell stemness, we performed bulk RNA-seq using organoids.


title: Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus [small RNA-Seq]

status: Public on Sep 26 2023

city: Cambridge

first: Susanne

last: Bornelöv

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

country: United Kingdom

institute: University of Cambridge

summary: The PIWI-interacting RNA (piRNA) pathway plays a crucial role in preventing endogenous genomic parasites, transposable elements (TEs), from damaging the genetic material of animal gonadal cells.  Specific regions in the genome, called piRNA clusters, define each species’ piRNA repertoire and therefore its capacity to recognize and silence transposons.  In the somatic cells of the Drosophila melanogaster ovary, the flamenco (flam) unistrand cluster is the main source of piRNAs and primarily regulates Gypsy family TEs that are able to form virus-like particles and infect neighbouring germ cells.  Disruption of the flam locus or failure to process flam precursor transcripts into piRNAs results in sterility, yet it remains unknown whether this silencing mechanism is employed widely across Drosophilidae.  Here, using both synteny-based analyses and de novo TE annotation, we identify candidate loci sharing both their organisation and TE targeting repertoire with flam in widely divergent Drosophila species groups. Small RNA-sequencing validated these loci as bona-fide unistrand piRNA clusters and revealed their predominant expression in somatic cells of the ovary, likely to counter TE mobilisation in this tissue.  This study provides compelling evidence of co-evolution between virus-like Gypsy family transposons and a host defence mechanism in form of soma-expressed, unistrand piRNA clusters.

sample_organism:
Drosophila ananassae
Drosophila bifasciata
Drosophila erecta
Drosophila melanogaster
Drosophila mojavensis
Drosophila persimilis
Drosophila pseudoobscura
Drosophila simulans
Drosophila subobscura
Drosophila virilis
Drosophila yakuba
Drosophila azteca
Drosophila suzukii
Drosophila takahashii
Drosophila ficusphila
Drosophila biarmipes

overall_design: Small RNA-seq from dissected ovaries (total or enriched for somatic follicle cells) from 15 Drosophila species, 1-3 replicates per species and library type.

first: Jasper

last: van Lopik

first: Azad

last: Alizada

first: Maria-Anna

last: Trapotsi

first: Gregory

last: Hannon

first: Benjamin

last: Czech Nicholson


title: Prostate tissue explant, epithelial cell, stromal cell, and extracellular vesicle microRNA characterization by NGS

status: Public on Sep 22 2023

city: Chicago

first: Morgan

last: Zenner

state: IL

address: 909 South Wolcott Ave

department: Pathology

institute: University of Illinois at Chicago College of Medicine

summary: Intracellular and extracellular vesicle-contained microRNAs were profiled by next-generation sequencing from prostate cancer patient cells, tissues and serum.

overall_design: N= 4 patient samples for tissue explants/EVs, epithelial cells/EVs, and stromal cell/Evs. N = 20 patient serum EV samples.

first: Larisa

last: Nonn

first: Trevor

last: Leonardo


title: Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox [Screen]

status: Public on Sep 13 2023

city: New York

first: Megan

middle: D

last: Schertzer

state: New York

address: 101 Avenue of the Americas, 4th Floor, Knowles lab

institute: New York Genome Center

summary: Alternative splicing is an essential mechanism for diversifying proteins, with different mature RNA isoforms producing different proteins with potentially distinct functions. Two major challenges in characterizing the cellular function of isoforms are the lack of both experimental methods to specifically and efficiently modulate isoform expression and computational tools for complex experimental design. To address these gaps, we developed and methodically tested a strategy which pairs the RNA-targeting CRISPR/Cas13d system with guide RNAs (gRNAs) that overlap exon-exon junctions in the mature RNA. We perform a high-throughput essentiality screen, numerous qPCR assays, and PacBio long read sequencing to affirm that our strategy works to specifically target the unique junctions of isoforms to robustly knockdown their RNA. In parallel, we provide computational tools for experimental design and screen analysis. Considering all possible splice junctions in current GENCODE annotations and our predictions of gRNA efficacy, we estimate that this strategy can target 94% of all human isoforms, including 29,238 protein-coding and 9,638 lncRNA isoforms that are specifically targetable with a gRNA spanning a unique splice junction.

overall_design: Essentiality screen in an A375 monoclonal Cas13d-expressing cell line

first: Laura

last: Pereira

first: Stella

last: Park

first: David

middle: A

last: Knowles


title: ChIA-PET from HCT116 (ENCSR263OBH)

status: Public on Sep 07 2023

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
CTCF ChIA-PET in HCT116, CDK7 tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox [LR-RNA-Seq]

overall_design: PacBio long read RNA-sequencing of RBFOX2 isoform-specific knockdown


title: Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus

sample_organism:
Drosophila ananassae
Drosophila erecta
Drosophila melanogaster
Drosophila mojavensis
Drosophila persimilis
Drosophila pseudoobscura
Drosophila simulans
Drosophila subobscura
Drosophila virilis
Drosophila yakuba
Drosophila azteca
Drosophila suzukii
Drosophila takahashii
Drosophila ficusphila
Drosophila biarmipes


title: ChIA-PET from embryonic stem cell (ENCSR214BLK)

summary:
CTCF ChIA-PET in 129S1CastF1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox [RNA-seq]

overall_design: RNA-sequencing to identify expressed isoforms/junctions in relevant cell types


title: ChIA-PET from T-cell (ENCSR743YTL)

summary:
RNAPII ChIA-PET in CD3_Resting_donor4

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR180DXE)

summary:
RNAPII ChIA-PET in HCT116, SMARCA5 tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from embryonic stem cell (ENCSR179IQN)

summary:
CTCF ChIA-PET in C57BL6J

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from WTC11 (ENCSR972JTN)

summary:
RNAPII ChIA-PET in WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR741AGK)

summary:
CTCF ChIA-PET in HCT116, BRD4 tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from embryonic stem cell (ENCSR995XUW)

summary:
RNAPII ChIA-PET in C57BL6J

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from Calu3 (ENCSR723YJG)

summary:
CTCF ChIA-PET in Calu-3

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR956HZZ)

summary:
CTCF ChIA-PET in HCT116, MED14 tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from Caco-2 (ENCSR185PEE)

summary:
CTCF ChIA-PET in Caco-2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from WTC11 (ENCSR176OZL)

summary:
RNAPII ChIA-PET in WTC11_clone6

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from T-cell (ENCSR722NQM)

summary:
RNAPII ChIA-PET in CD3_Resting_donor11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from Caco-2 (ENCSR713NCY)

summary:
RNAPII ChIA-PET in Caco-2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from IMR-90 (ENCSR966RPQ)

summary:
RNAPII ChIA-PET in IMR90

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from activated T-cell (ENCSR538SBO)

summary:
RNAPII ChIA-PET in CD3_Activated_donor1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR711IEI)

summary:
RNAPII ChIA-PET in HCT116, BRD4 tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Real-time quantitative PCR analysis of pre-treatment serum microRNAs from patients with prostate cancer

summary: The overall goal of the study was to determine if serum or serum EV microRNAs added prognostic value to current clinical nomograms for prostate cancer. Serum was collected from 203 patients with biopsy-proven prostate cancer. EVs were isolated from the 132 serum samples. RNA was isolated from these serum and serum EV samples, and 61 microRNAs were quantified per sample on a custom qPCR plate. The microRNA data was normalized using NormFinder. The normalized microRNA data was then compared to adverse pathology and prostate biopsy Gleason grade group.

overall_design: Serum was collected in BD gold top (serum-separator) vacutainers from each patient and separated by centrifugation. Extracellular vesicles (EVs) were isolated from 500 µL using ExoQuick (System Biosciences). RNA was isolated from 200 µL serum per sample or the EV pellet using miRNeasy Serum/Plasma kit (Qiagen). RNA was quantified by Nanodrop and Qubit microRNA Assay. 5 µL of RNA was input for each cDNA reaction using the miRCURY LNA RT Kit (Qiagen). 61 microRNAs were quantified per sample on a custom PCR plate using the miRCURY LNA miR SYBR Green PCR Kit/Handbook (Qiagen). The samples were run on the Applied Biosystem ViiA7 instrument for 40 cycles.


title: ChIA-PET from embryonic stem cell (ENCSR466YGP)

summary:
CTCF ChIA-PET in B6CASTF1J

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR910WPE)

summary:
CTCF ChIA-PET in HCT116, RAD21 tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox

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


title: ChIA-PET from HCT116 (ENCSR674UYO)

summary:
CTCF ChIA-PET in HCT116, SUPT16H tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from activated T-cell (ENCSR165FXG)

summary:
RNAPII ChIA-PET in CD3_Activated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from Panc1 (ENCSR447IUA)

summary:
RNAPII ChIA-PET in Panc1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR160MHZ)

summary:
CTCF ChIA-PET in HCT116, SMARCA5 tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from activated T-cell (ENCSR891IMI)

summary:
RNAPII ChIA-PET in CD3_Activated_donor3

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR440JFJ)

summary:
CTCF ChIA-PET in HCT116, MED14 tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR918GSZ)

summary:
RNAPII ChIA-PET in HCT116, BRD4 tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from OCI-LY7 (ENCSR882BUM)

summary:
RNAPII ChIA-PET in OCI-LY7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR641SOU)

summary:
RNAPII ChIA-PET in HCT116, SUPT16H tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from Panc1 (ENCSR145PYF)

summary:
CTCF ChIA-PET in Panc1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from activated T-cell (ENCSR411UEL)

summary:
CTCF ChIA-PET in CD3_Activated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from PC-9 (ENCSR863QCN)

summary:
CTCF ChIA-PET in PC-9

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from A673 (ENCSR623KNI)

summary:
RNAPII ChIA-PET in A673

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR407ATL)

summary:
CTCF ChIA-PET in HCT116, POLR2A tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR106EOT)

summary:
CTCF ChIA-PET in HCT116, CTCF tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from OCI-LY7 (ENCSR401JWQ)

summary:
CTCF ChIA-PET in OCI-LY7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from PC-3 (ENCSR854YJR)

summary:
CTCF ChIA-PET in PC-3

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from T-cell (ENCSR592BWZ)

summary:
CTCF ChIA-PET in CD3_Resting_donor11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR394XYY)

summary:
CTCF ChIA-PET in HCT116, BRD4 tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from PC-3 (ENCSR567RHZ)

summary:
RNAPII ChIA-PET in PC-3

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from H1 (ENCSR095SXC)

summary:
CTCF ChIA-PET in H1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR830FZR)

summary:
RNAPII ChIA-PET in HCT116, SUPT16H tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from Patski (ENCSR564BAB)

summary:
RNAPII ChIA-PET in Patski

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR388DDH)

summary:
RNAPII ChIA-PET in HCT116, CDK7 tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from mammary epithelial cell (ENCSR819BBB)

summary:
CTCF ChIA-PET in HMEC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from H1 (ENCSR782EKZ)

summary:
RNAPII ChIA-PET in H1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR353XNY)

summary:
RNAPII ChIA-PET in HCT116, RAD21 tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from embryonic stem cell (ENCSR067GFU)

summary:
RNAPII ChIA-PET in B6CASTF1J

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from embryonic stem cell (ENCSR780SBE)

summary:
CTCF ChIA-PET in 129S1SvImJ

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR553HMH)

summary:
RNAPII ChIA-PET in HCT116, MED14 tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR557OAJ)

summary:
CTCF ChIA-PET in HCT116, SMARCA5 tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR356GHP)

summary:
CTCF ChIA-PET in HCT116, CTCF tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR326KGW)

summary:
CTCF ChIA-PET in HCT116, SUPT16H tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from A673 (ENCSR549TMF)

summary:
CTCF ChIA-PET in A673

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from WTC11 (ENCSR779QAB)

summary:
CTCF ChIA-PET in WTC11_clone28

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from WTC11 (ENCSR353ASS)

summary:
CTCF ChIA-PET in WTC11_clone6

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR779BUF)

summary:
RNAPII ChIA-PET in HCT116, CDK7 tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR066MHC)

summary:
RNAPII ChIA-PET in HCT116, MED14 tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from spleen (ENCSR314BGZ)

summary:
CTCF ChIA-PET in C57BL6J spleen tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR332LKV)

summary:
RNAPII ChIA-PET in HCT116, CTCF tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from T-cell (ENCSR545NUL)

summary:
CTCF ChIA-PET in CD3_Resting_donor4

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from embryonic stem cell (ENCSR309NAP)

summary:
RNAPII ChIA-PET in 129S1CastF1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from embryonic stem cell (ENCSR543IIL)

summary:
RNAPII ChIA-PET in 129S1SvImJ

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR281XBJ)

summary:
CTCF ChIA-PET in HCT116, RAD21 tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from Patski (ENCSR045WUV)

summary:
CTCF ChIA-PET in Patski

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR771PKY)

summary:
RNAPII ChIA-PET in HCT116, RAD21 tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from WTC11 (ENCSR543HLV)

summary:
RNAPII ChIA-PET in WTC11_clone28

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from PC-9 (ENCSR274ZVY)

summary:
RNAPII ChIA-PET in PC-9

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR758BJW)

summary:
CTCF ChIA-PET in HCT116, CDK7 tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from activated T-cell (ENCSR038GON)

summary:
CTCF ChIA-PET in CD3_Activated_donor1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from AG04450 (ENCSR037FPN)

summary:
CTCF ChIA-PET in AG04450

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from WTC11 (ENCSR016VPZ)

summary:
CTCF ChIA-PET in WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR010NWN)

summary:
RNAPII ChIA-PET in HCT116, SMARCA5 tag and IAA untreated, control

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Finerenone added to RAS/SGLT2 blockade for non-diabetic chronic kidney disease. Results of a preclinical double-blinded randomized controlled trial.

status: Public on Sep 01 2023

city: München

first: ZHIHUI

last: ZHU

address: Geiselgasteigstr. 62, 2.0G

institute: LMU Klinikum

summary: The goal of this study was to compare Next Generation mRNA (RNA-seq) data obtained from whole kidney tissue from WT and untreated, Ramipril treated, and Ramipril/Empagliflozin treated, and Ramipril/Empagliflozin/Finerenone treated Col4a3-/- mice in the 129/SvJ background.

overall_design: Comparison in WT vs Col4a3-/- Vehicle, Col4a3-/- Vehicle vs Ramipril/Empagliflozin/Finerenone, Col4a3-/- Ramipril vs Ramipril/Empagliflozin/Finerenone, and Col4a3-/-  Ramipril/Empagliflozin vs Ramipril/Empagliflozin/Finerenone kidneys of RNA expression of significantly altered canonical pathways.

first: Zhihui

last: Zhu

first: Chenyu

last: Li

first: Hans-Joachim

last: Anders


title: Peripheral Blood Biomarkers in ART-Suppressed, SIV-Infected Rhesus Macaques Predict Viral Rebound Following ART Discontinuation

status: Public on Aug 30 2023

first: Dan

last: Barouch

summary: The development of biomarkers that can predict viral rebound following discontinuation of antiretroviral therapy (ART) in HIV-1-infected humans would be an important advance in HIV-1 cure research.  In a prior study, we initiated ART in 20 rhesus macaques on days 0, 1, 2, and 3 following SIVmac251 infection prior to plasma viremia1.  Following 6 months of suppressive ART, we discontinued ART and observed viral rebound in 9 of 20 animals.  Here we show that transcriptomic and proteomic signatures of inflammation and immune activation in peripheral blood during ART suppression predicted viral rebound following ART discontinuation.  Higher levels of proinflammatory and cellular immune activation pathways, including TNF, IL-1, IL-6, monocyte, and T cell activation signaling pathways, correlated with viral rebound following ART discontinuation.  Immune modulatory IL-10 and TGF-b signaling also correlated with viral rebound.  We then validated these candidate biomarkers of viral rebound in a second cohort of SIV-infected, ART-suppressed macaques.  Taken together, these data suggest that persistent upregulation of inflammatory and immune activation pathways despite suppressive ART may represent a peripheral blood biomarker signature of the rebound-competent viral reservoir.  The development of interventions that target the viral reservoir and modulate this signature may open new avenues in HIV-1 cure research.

overall_design: We evaluated transcriptomic and proteomic features in peripheral blood and lymph nodes prior to ART discontinuation to identify potential biomarkers that predicted rebound viremia following ART discontinuation. We performed transcriptomic profiling in this cohort of 20 macaques at week 24 of ART suppression and showed that signatures in macaques that subsequently exhibited viral rebound following ART discontinuation (9 macaques) were different than signatures in macaques that did not rebound (11 macaques).

first: Malika

last: Aid

first: Alessandro

last: Colarusso

first: Victoria

last: Walker-Sperling


title: Developmental programming of Kupffer cells by maternal obesity causes fatty liver disease in the offspring II

status: Public on Aug 22 2023

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

department: LIMES

institute: University of Bonn

summary: Kupffer cells (KCs) are tissue-resident macrophages which colonize the developing liver early during embryogenesis1. Throughout development and adulthood, KCs have distinct core functions that are essential for liver and organismal homeostasis, such as supporting fetal erythropoiesis as well as postnatal erythrocyte recycling and liver metabolism2. KCs acquire their tissue-specific transcriptional signature immediately after colonizing the liver, mature together with the tissue, and adapt to the tissue’s function1,3,4. However, whether perturbation of macrophage core functions during development may contribute to or cause disease at postnatal stages is poorly understood. Here, we utilize a maternal obesity model to disturb KC functions during gestation. We show that offspring born to obese mothers develop fatty liver disease that is accompanied by a local pro-inflammatory response, a phenotype that is augmented if the offspring is kept on control diet after birth. Further, transcriptional analyses reveal that KCs undergo developmental programming through the maternal high-fat diet, which lasts until adulthood. The offspring’s KC developmental programming is irreversible despite the switch to control diet and leads to increased lipid uptake in hepatocytes mediated via paracrine factors stemming from KCs. The transcriptional programming of KCs and the fatty liver disease phenotype are rescued by genetic depletion of hypoxia-inducible factor alpha (Hif1a) in macrophages during gestation. These results demonstrate that macrophages rely on an undisturbed development to fulfil their core functions and support organ homeostasis during adulthood, and establish developmental programming of KCs as a therapeutic strategy for metabolic disorders, such as fatty liver disease.

overall_design: Three-week-old female mice were initially fed with a control diet (CD) for two weeks and were thereafter divided into two groups: one continued on the CD while the other received a high-fat diet (HFD) for eight weeks. The homeostatic model for insulin resistance (HOMA-IR) was used to assess metabolic changes. Mice with higher HOMA-IR on the HFD were selected to create a maternal obesity model and mice fed with CD were used to generated maternal lean offspring. All females were mated with CD males. Offspring born to maternal obese were cross-fostered to generate both lactating groups and offspring born to maternal lean mothers were crossed-fostered by other maternal lean mothers. Male offspring were weaned into CD or HFD postweaning cages. Livers of offspring were harvested at 11-12 weeks of age and subsequently dissociated into single-cell suspension. Kupffer cells were then sorted using flurescence-activated cell sorting on an BD FACSAria lII cell sorter directly into 500μl QIAzol lysis buffer (Qiagen) and proceeded for sequencing using SMART-Seq2 protocol.

first: Nora

last: Balzer

first: Iva

last: Splichalova

first: Hao

last: Huang

first: Lea

last: Seep


title: Developmental programming of Kupffer cells by maternal obesity causes fatty liver disease in the offspring

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


title: intact Hi-C from lower lobe of left lung (ENCSR446NJD)

status: Public on Jul 24 2023

summary:
w73 lower lobe of left lung intact dnase hic

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: intact Hi-C from right lobe of liver (ENCSR874EIH)

summary:
w61 right lobe of liver

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Developmental programming of Kupffer cells by maternal obesity causes fatty liver disease in the offspring I

overall_design: Three-week-old female Hif1αflox/flox female mice were initially fed with a control diet (CD) for two weeks and were thereafter divided into two groups: one continued on the CD while the other received a high-fat diet (HFD) for eight weeks. The homeostatic model for insulin resistance (HOMA-IR) was used to assess metabolic changes. Mice with higher HOMA-IR on the HFD were selected to create a maternal obesity model and mice fed with CD were used to generated maternal lean offspring. All females were mated with Hif1αflox/flox;LyzMCre/+ CD males to generate Hif1αflox/flox;LyzMCre/+ (KO) or Hif1α flox/flox;LyzM+/+ (WT) offspring. All neonatal mice were cross-fostered by females with the same diet as their mothers. WT or KO male offspring were weaned into CD or HFD postweaning cages. KCs or hepatocytes from 11-12 weeks old male mice were sorted for bulk RNA-sequencing.