title: Genome-wide Mapping of Gata4 and Cul4b in MOVAS Cell Chromatin State.

city: Jinan

first: wenqian

last: yu

state: Shandong

address: No.105, jiefang road

department: Research Center of Translational Medicine

institute: Central Hospital Affiliated to Shandong First Medical University

summary:
To investigate the functional role of Gata4 in aortic smooth muscle cells, we employed ChIP-seq analysis to identify Gata4's genome-wide transcription targets. The ChIP experiment began with the use of anti-Gata4 antibodies in MOVAS cells. Subsequently, Gata4-related DNA was unbiasedly amplified, labeled, and sequenced. Using Illumina Novaseq 6000, we identified numerous Gata4-specific binding peaks. We observed a strong enrichment of Gata4 on the promoters of specific genes involved in classical pathways. This study has provided us with new insights into the role of Gata4 in chromatin state and gene transcription.
To investigate the functional role of Cul4b in aortic smooth muscle cells, we employed ChIP-seq analysis to identify Cul4b's genome-wide transcription targets. The ChIP experiment began with the use of anti-Cul4b antibodies in MOVAS cells. Subsequently, Cul4b-related DNA was unbiasedly amplified, labeled, and sequenced. Using Illumina Novaseq 6000, we identified numerous Cul4b-specific binding peaks. We observed a strong enrichment of Cul4b on the promoters of specific genes involved in classical pathways. This study has provided us with new insights into the role of Cul4b in chromatin state and gene transcription.

overall_design:
Examination of  Gata4 target genes in MOVAS cell line
Examination of  Cul4b target genes in MOVAS cell line

first: Wenqian

first: Shuai

last: Leng


title: AreB, the nitrogen and carbon regulator in Aspergillus nidulans

status: Public on Dec 31 2025

city: Warsaw

first: Agnieszka

last: Dzikowska

address: Pawinskiego 5A

department: Biology

country: Poland

institute: University of Warsaw

type: Expression profiling by high throughput sequencing

summary: Nitrogen and carbon repression general regulatory systems modulate the expression of target genes participating in utilization of alternative nitrogen/carbon sources, resulting in transcription only when preferred sources are limiting. In Aspergillus nidulans, the GATA transcription factor AreB was identified as nitrogen regulator whose activity depends on both nitrogen and carbon source (Conlon et al., 2001; Macios et al., 2012; Chudzicka - Ormanec et al., 2019). In this work, we performed a transcriptomic analysis of areB deletion and the wild type strains grown under different carbon/nitrogen conditions and showed that AreB          participates both in nitrogen and carbon regulation. Observed positive and negative effects of areB deletion are at least partially, indirect as the expression of some transcription factor coding genes is changed in areB deletion strain.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for areBΔ and the control areB+ (wild type) strains, grown under carbon repressing (1% glucose) or non-repressing (0.1% fructose); and under nitrogen repressing (10 mM ammonium tartrate) or non-repressing (5mM urea) conditions in three biological replicates.

first: Patrycja

last: Chudzicka-Ormaniec

first: Michal

last: Koper


title: Codon Pair-Specific Translation Defects Induce Ribosome-Associated Quality Control to Avoid Proteotoxic Stress [5P-seq]

city: Bern

first: Jie

last: Wu

state: Bern

address: Freiestrasse 3

country: Switzerland

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

summary: tRNA modifications tune translation rates and codon optimality, thereby optimizing co-translational protein folding, but how codon optimality defects trigger cellular phenotypes remains unclear. Here, we show that ribosomes stall at specific modification-dependent codon pairs, triggering ribosome collisions and inducing a coordinated and hierarchical response of cellular quality control pathways. Ribosome profiling reveals an unexpected functional diversity for wobble-uridine (U34) modifications during decoding. The same modification can have different effects at the A and P sites. Furthermore, modification-dependent stalling codon pairs induce ribosome collisions, triggering ribosome-associated quality control (RQC) to prevent protein aggregation by degrading aberrant nascent peptides and mRNAs. RQC inactivation stimulates the expression of molecular chaperones to remove protein aggregates. Our results show that loss of tRNA modifications primarily disrupts translation rates of suboptimal codon pairs and reveal the coordinated regulation and adaptability of cellular surveillance systems to ensure efficient and accurate protein synthesis and maintain protein homeostasis.

overall_design: mRNA degradation intermiates of strains lacking tRNA modifications and/or the ribosome-associated quality control pathway were sequenced using 5P-seq

first: Cristian

last: Eggers

first: Olga

last: Sin

first: Hector

last: Mancilla

first: Fabienne

last: Mollet

first: Hans

middle: R

last: Schöler

first: Hannes

last: Drexler

first: Tristan

last: Ranff

first: Christian

last: Fufezan

first: Claudine

last: Kraft

first: Jan

middle: M

last: Bruder

first: Sebastian

middle: A

last: Leidel


title: Codon Pair-Specific Translation Defects Induce Ribosome-Associated Quality Control to Avoid Proteotoxic Stress [mono_di_profiling]

overall_design: Ribosome profiling data of monosomes and collided ribosomes (disomes) from yeast strains lacking tRNA modifications and/or the ribosome-associated quality control pathway.


title: The effects of cell-cell orientation in modeling the hallmarks of lung cancer in vitro

city: La Jolla

first: Sandra

middle: L.

last: Leibel

state: CA

address: 9500 Gilman Dr

department: Pediatrics

country: USA

institute: University of California, San Diego

summary: To better understand and develop treatments for lung cancer, it is important to have reliable and physiologically relevant culture models. Traditional methods of growing lung cancer cells in two-dimensional monolayers have limitations in mimicking the complex architecture and microenvironment of lung tumors in vivo, limiting their value as reliably informative disease models. In this study, we introduce a new cell culture platform called "tumoroids," which involves growing HCC827 lung cancer cells in three-dimensional configurations for more accurately predicting how cell-cell orientation and signaling affects the cancer-driving properties of lung cancer. By comparing transcriptional profiles of HCC827 cells grown as tumoroids versus the same cells grown in two-dimensional monolayers, we investigate how cell-cell orientation and signaling impact the cancer-driving properties of lung cancer. We examine key features associated with cancer progression, such as epithelial mesenchymal transition, replicative ability, and induction of angiogenesis. Additionally, we assess the functional characteristics of the 3D tumoroid culture system by subjecting the cells to irradiation. Through comparing the gene expression profiles of the 3D tumoroid cultures with those of primary human lung adenocarcinoma, we find that the 3D tumoroid cultures closely resemble the characteristics of primary human lung cancer. This suggests that the 3D tumoroid culture platform can serve as a valuable in vitro model for studying lung cancer, offering greater clinical relevance compared to traditional 2D cultures. Overall, this study highlights the importance of using advanced culture models like 3D tumoroids to improve our understanding of lung cancer and facilitate the development of effective treatments.

overall_design: Gene expression comparison of  HCC827 cells in both 2D and 3D culture environments using RNA-seq.

first: Andres

middle: S

last: Espinosa

middle: L


title: Lung-innervating neurons expressing TMC3 control broncho-constriction and dilation with direct impact on lung tidal volume (scRNA-Seq)

city: South San Francisco

first: Kevin

last: Huang

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

summary: Sensory neurons of the vagal ganglia (VG) innervate lungs and play a critical role in maintaining airway homeostasis. However, specific VG neurons that innervate lungs, and mechanisms by which these neurons sense and respond to airway insults, are not well understood. Here, we identify a subpopulation of lung-innervating VG neurons defined by their expression of TMC3. Single cell transcriptomics illuminated several subpopulations of TMC3+ VGs afferents, revealing distinct Piezo2 and Trpv1-expressing subclusters. Furthermore, TMC3 deficiency in VG neurons leads to global and subcluster specific transcriptional changes involved in metabolic and ion channel function. Importantly, we show that broncho-constriction and dilation can be modulated through inhibition or activation of TMC3+ VG neurons with a direct impact on lung tidal volume. Together, our data show that TMC3 is a marker of specific lung-innervating neurons and may play a pivotal role in maintaining fundamental inspiratory and expiratory processes.

overall_design: Single nuclei sequencing of vagal ganglion from Tmc3 knockout and wildtype littermates via 10x Genomics

first: Jens

last: Kortmann

first: Josh

last: Kaminker

first: Shannon

last: Turley


title: Decoding the DNA sequence of MAP1S promoter region interacting with HBx

city: beijing

first: yanjun

last: wang

address: Xitoutiao,8#,Youanmenwai Street,Fengtai District, Beijing, 100069, China

country: China

institute: Beijing Institute of Hepatology, Beijing You An Hospital, Capital Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Our previous research found that the X protein encoded by the hepatitis B virus (HBx) induces high levels of MAP1S expression. To determine the binding motif and enrichment of HBx in the promoter region of MAP1S gene, we transfected HEK293T cells with pHBx. The chromatin complex was extracted, followed by immunoprecipitation with HBx antibodies, and DNA sequencing. A binding region 1180bp upstream of the MAP1S transcription initiation site (TSS) was found, demonstrating that HBx up-regulated the expression of MAP1S by interacting with the MAP1S gene promoter region.

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) was utilized to investigate the interaction of the HBx protein with the promoter region of the MAP1S gene.

first: Yuanyue

last: Guan

first: Jiaxi

last: Li

first: Yang

last: Zhang

first: Yanjun

last: Wang


title: A single-cell gene expression analysis in an in vitro co-culture model containing fibroblast cells directly mixed with NMU-manipulated lung adenocarcinoma cells

city: Miaoli County

first: Shihmiao

address: 35, Keyan Road, Zhunan Town

country: Taiwan

institute: National Health Research Institutes

summary: NMU gene expression was known to be over-represented in lung adenocarcinoma and negatively associated with overall survival or progression-free survival of patients. However, the mechanism(s) underlying the oncogenic roles of NMU are still not clear. Based on the transcriptome analysis of bulk-tissue of lung cancer datasets in the public domain, we found that NMU expression was significantly associated with those of some pro-fibrotic genes. Using subcutaneous mice xenograft model of human lung adenocarcinoma cells, we found significant increase of fibrotic phenotypes in xenograft derived from cell lines over-expressing NMU, including expression levels of marker proteins of myofibroblast, activation of fibroblast migration, and number of cells with morphology of fibroblast, while these changes can be reversed by knocking down the NMU expression of lung cancer cell lines. These suggest NMU from lung cancer cells may contribute to fibrosis of tumor microenvironment by recruiting and activating fibroblast and/or myofibroblast. Here we perform single-cell analysis of cell mixture containing co-cultured lung cancer cells and fibroblast cells.

overall_design:
scRNA profiles on hESC-derived lung cells and lung-macrophage co-cultured cells
Lung fibroblast cell line WI-38 was cultured in 10-cm dish for 24 hours. Each of lung cancer cell line H1975 or PC9 (and their stable transfectant cells with overexpressed or knock down NMU) was added to dish of fibroblast with ratio of 1:3 of numbers of lung cancer cell to that of fibroblast cell and co-cultured for 72 hours. Cells mixture was trypsinized and subject to single cell isolation and library construction using mRNA Targeted Library kit (BD Rhapsody System). After paired-end sequencing, fastq files were analyzed by Rhapsody Sequence Analysis Pipeline.

first: Shih-Miao

first: Shih Sheng

last: Jiang

first: Fang-Yu

last: Tsai

first: Wen-Tsen

last: Fang

first: Zih-Syuan

last: Cao

first: Fang-Yuu


title: Codon Pair-Specific Translation Defects Induce Ribosome-Associated Quality Control to Avoid Proteotoxic Stress [RNA-seq]

first: Jie

last: Wu

overall_design: Gene expression analysis of strains lacking tRNA modifications and/or the ribosome-associated quality control pathway

first: Cristian

last: Eggers

first: Olga

last: Sin

first: Hector

last: Mancilla

first: Fabienne

last: Mollet

first: Hans

last: Schöler

first: Hannes

last: Drexler

first: Tristan

last: Ranff

first: Christian

last: Fufezan

first: Claudine

last: Kraft

first: Jan

last: Bruder

first: Sebastian


title: Lysosomal control of type I interferon induction via Ragulator-Rag complex

city: Guangzhou

first: Chun-Yan

last: Lim

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou National Laboratory

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

overall_design: Refer to individual Series


title: Temporal gene activation by TFEB and acetylation mutants result in distinct subsets of newly synthesized lysosomal proteins

city: Hamburg

first: Jiabin

last: Huang

address: Martinistr. 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary:
The target gene activation of TFEB and acetylation mutants differ from the newly synthesized lysosomal enzymes
Lysosomes are central to the degradation and recycling of cellular components. They harbor around 70 hydrolytic enzymes and over 250 membrane proteins, and play a key role in cellular homeostasis. One of the main proteins that regulates lysosomal activity is the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase. Additionally, the microphthalmia-associated transcription factor (MiTF) family members, including TFEB, influence lysosomal and autophagy gene expression by binding to specific DNA sequences. Their functionality is modulated by phosphorylation events. In this study, we discovered acetylation of TFEB at specific lysine residues (K237, K256, and K274) which impacted its DNA binding and localization. Mutations mimicking this acetylation led to cytoplasmic retention of TFEB, independent of mTORC1. Furthermore, while TFEB mutation at these sites didn't hinder its nuclear import, it did alter its gene activation profile. Interestingly, despite these alterations in gene expression, the synthesis of lysosomal proteins within 24 hours remained inconsistent with the transcriptional activity. This suggests that TFEB acetylation acts as a dominant retention signal in the cytoplasm and introduces an additional regulatory layer to phosphorylation-dependent transcriptional activity. The study further indicates a nuanced role for TFEB in modulating lysosomal components in response to cellular conditions.

overall_design: TFEB expression was induced with 1 µg/ml doxycycline for 3 hours. Post-induction, cells were either harvested immediately (chase 0 h) or were left without doxycycline for various time periods to track (chase) the expression. HeLa cells induced to express TFEB wt for 3 hours followed by a 21-hour chase (wt 3+21h). HeLa cells induced for a continuous 24-hour period (wt 24h). HeLa cells induced to express K3R for 3 hours followed by a 21-hour chase (K3R 3+21h). HeLa cells induced to express K3R for a continuous 24-hour period (K3R 24h). Control cells not induced by doxycycline. All samples were taken in triplicates.

first: Anastasia

last: Laudicina

first: Malte

last: Klüssendorf

first: Georgia

last: Makrypidi-Fraune

first: Anne

last: Sanger

first: Nicole

last: Fischer

first: Dominic

last: Winter

first: Thomas

last: Braulke


title: An Optimized Hepatocyte-like Cells Differentiation Protocol Using Machine Learning Assisted Approach and Multi-omics Analysis [RNA-seq and ATAC-seq]

first: Jian

last: Tu

address: #58 Zhongshan second road

institute: The First Affliated Hospitap of Sun Yat-sen University

summary: The hepatocyte is a vital cell type responsible for numerous physiological processes in the body. We developed a machine learning-based AI algorithm to monitor morphological changes in hESCs during their differentiation into mature hepatocytes.Furthermore, we developed a modified strategy that safely and efficiently produces HLCs from hESCs.

overall_design: RNA-seq and ATAC-seq are used to profile hESC,HPC,HLCs during HLCs differentiation process.

first: Zijun

last: Huo

first: Dung-Fang

last: Lee

first: Ruiying

last: Zhao

first: Yao

last: Yu


title: Lysosomal control of type I interferon induction via Ragulator-Rag complex [ATAC-seq]

summary: The type I interferon (IFN) response is a pivotal transcription program in the host innate immunity against infectious viruses that induces a multitude of interferon-stimulated genes (ISGs) to antagonize every stage of viral replication. Aberrant IFN response often leads to enhanced viral susceptibility or autoimmune conditions. Accordingly, type I IFN induction is tightly regulated from viral recognition to signaling propagation and transcriptional activation to cytokine production. Lysosomes, which are essential organelles for cellular homeostasis and metabolic signaling, play an evolutionarily conserved role in viral clearance. Through their degradative capacity and recycling function, lysosomes facilitate the containment and destruction of viral particles or debris delivered via endocytic, autophagic, and phagocytic routes. Despite the central role of lysosomes in virus-host interactions, it remains unclear whether type I IFN induction requires direct lysosomal input. Here, we identified the lysosomal scaffold Ragulator as crucial for IFN-β transcriptional activation through an antiviral screen using a GFP-expressing Influenza A virus as a readout. Independent of their known roles in mTORC1 regulation, the Ragulator-dependent antiviral response requires downstream heterodimeric Rag GTPases that alter their nucleotide-loading states to establish the IFN-I gene signature. Depleting Ragulator or Rag GTPases causes exhaustion of a regulatory pool of interferon-regulator factors (IRFs), leading to abrogated Ifnb1 transcription, IFN-β secretion, and ISG response, thereby enhancing susceptibility to viral infections both in cells and in vivo. Thus, our findings reveal a new role for lysosomes in the nuclear transcription of antiviral innate immunity.

overall_design: Three biological replicates were analyzed for each of 2 conditions (two genotypes; 2 treatments per genotype)

first: Miao

last: Lei

first: Wenxiang

last: Hu

first: Zeming

last: Feng

first: Lulu

last: Wang


title: Extracellular vesicles derived from HuMSCs alleviate daunorubicin-induced cardiac microvascular injury via miR-186-5p/PARP9/STAT1 signal pathway

first: Shule

last: Zhang

address: 107 Wenhua Xilu

institute: Qilu Hospital of Shandong University

summary: It is essential to acknowledge the long-term cardiovascular toxicity associated with anthracycline drugs, which can be partially attributed to the harm inflicted on endothelial cells. Extracellular vesicles (EVs) derived from mesenchymal stem cells (MSCs) have the potential to repair cellular processes and promote tissue regeneration through the transfer of signaling molecules such as miRNAs. In the present study, we investigated the effects of MSC-EVs on daunorubicin (DNR)-damaged human cardiac microvascular endothelial cells (HCMEC). We found that MSC-EVs improved the migration, proliferation, and angiogenesis of HCMEC, while also alleviating cellular senescence. Through RNA sequencing analysis and RNA interference experiments, we identified that MSC-EVs downregulated the expression of PARP9, thereby inhibiting the STAT1/pSTAT1 signaling pathway. This downregulation effect is likely mediated by the transfer of miR-186-5p from MSC-EVs to HCMEC. Overexpression of miR-186-5p in DNR-damaged HCMEC also exhibited the aforementioned downregulation effect. In conclusion, our study reveals that MSC-EVs can restore the cellular function of DNR-damaged HCMEC and alleviate cellular senescence through the miR-185-5p-PARP9-STAT1/pSTAT1 pathway. This finding highlights the potential of MSC-EVs as a therapeutic strategy for mitigating the detrimental effects of anthracycline-induced cellular damage.

overall_design: RNA sequencing was performed on the following three groups of human cardiac microvascular endothelial cells, including: the Blank group, the DNR-damaged group, and the DNR-damaged + MSC-EVs group. Two replicates were performed for each group.

first: Dong

last: Li

first: Linghong

last: Liu

first: Huixian

last: Ma

first: Qing

last: Shi

first: Xiuli

last: Ju


title: Loss of MEF2A in myocardial cells exacerbates cardiomyocyte senescence following myocardial infarction by modulating the COX family

city: Jining

first: xueying

last: Chen

address: No.89 Guhuai Road

department: Department of Cardiology

institute: Affiliated Hospital of Jining Medical University

summary: Stress-induced cell senescence plays a crucial role in maintaining cardiac function after AMI, but the specific mechanism remains unclear. The objective of this study was to investigate the regulatory role of myocyte enhancer factor 2A (MEF2A) in cardiomyocyte senescence and its impact on cardiac function following AMI. Cardiomyocyte-specific MEF2A knockout mice (MEF2A-MyH6-CreErt2(f/f,+)) were generated, and their anterior descending branches were ligated to establish an AMI model. Ultrasound assessment of cardiac function 30 days post-AMI revealed that the specific knockout of MEF2A in cardiomyocytes worsened cardiac dysfunction and fibrosis, increased biomarkers of myocardial necrosis, and led to senescence in cardiomyocytes. Through high-throughput sequencing analysis of mRNA and protein in myocardial tissue from both MEF2A-MyH6-Creert2 (f/f,+) and wild-type mice, it was discovered that there was a decrease in expression levels for the enzymes of the cyclooxygenase (COX) family after MEF2A knockout. Additionally, KEGG analysis showed that differentially expressed genes were linked to cellular senescence processes . This suggests that MEF2A plays a regulatory role in cellular senescence through its interaction with the cox family. Meanwhile, COX inhibitors were found to weaken the beneficial effects of MEF2A overexpression on cardiomyocyte senescence in H9C2 cells. Our observations showed that knocking out MEF2A led to a decrease in H3K4me3 methylation levels and an increase in H3K4me3 antibody binding to specific cox family promoters when overexpressed. The use of MM102, a methylation inhibitor, nearly eliminated the positive effects of MEF2A overexpression on cell senescence, providing evidence that regulation of methylation is how MEF2A influences COX family expression changes. After screening, it was found that MEF2A can affect the methyltransferase activity partly by regulating the transcription level of SET1A subunit.

overall_design: Chromatin immunoprecipitation DNA-sequencing(Chip-seq) for histone H3K4me3 in H9C2 cells with  MEF2A overexpression and control.

first: Xueying

first: yugang

last: Yan

first: Baoyu

last: He

first: Bin

first: Lijun

last: Gan


title: Comparison of Renal Transcriptome Profiles in Patients with Active Lupus Nephritis Reveals Possible New Mechanisms of Disease Progression

city: Izumo

first: Kunihiro

last: Ichinose

address: 89-1 Enya-cho

department: Department of Rheumatology

country: Japan

institute: Shimane University Faculty of Medicine

summary: To identify factors that influence the progression of lupus nephritis (LN), we performed RNA sequencing on renal biopsy samples obtained from patients with active LN. The renal biopsy pathology followed the classification of the International Society of Nephrology and Renal Pathology Society (ISN/RPS) for 21 lupus nephritis patients: 2 in Class II, 3 in Class III, 10 in Class IV, 5 in Class V, and 1 patient with mixed type LN. The duration of disease from onset of systemic lupus erythematosus (SLE) to the onset of lupus nephritis was 26 months. Proteinuria was 2.5 (g/gCr or g/24hr), estimated Glomerular Filtration Rate (eGFR) was 72.9 (ml/min/1.73 m2), Index of activity was 5, and Index of chronicity was 3. Among different gene expression variations, the type I interferon (IFN) signature showed high expression in patients with shorter disease duration, preserved eGFR, and lower Index of chronicity. The type I IFN signature contributes to fibrosis in the tubulointerstitial space and worsens chronic lesions. Early control of the type I IFN signature may limit disease progression. Our results reveal a potential molecular mechanism for active LN and the link between functional and structural changes and differential gene expression observed in patients with early-stage LN.

overall_design: Twenty-one patients with lupus nephritis (LN) proven by renal biopsy who were admitted to Nagasaki University Hospital between January 2012 and May 2018 were enrolled in this study.RNA-seq was performed on 21 LN samples.

first: Hiroko

last: Hagiwara

first: Tomoya

last: Nishino

first: Atsushi

last: Kawakami


title: The role of the SOR-cluster transporter sor4 in light and darkness in Trichoderma reesei

city: Tulln

first: Miriam

last: Schalamun

address: Konrad Lorenz Strasse 24

country: Austria

institute: Austrian Institute of Technology

summary: We investigated the function of the transporter sor4 (TR_43701) on cellulose in light and darkness in Trichoderma reesei

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Trichoderma reesei wild-type QM6aΔku80 and deletion mutants QM6aΔku80Δsor4

first: Alberto

last: Monroy

first: Monika

last: Schmoll


title: Immune gene expression profiling to inform individualized treatment of early-stage basal-like breast cancer

city: Oslo

first: Andreas

middle: Hagen

last: Røssevold

email: andreashr@gmail.com, anharo@ous-hf.no

address: Ullernchausséen 70

country: Norway

institute: Oslo University Hospital

summary: A gene expression-based positive prognostic marker for early-stage basal-like breast cancer was proposed based on expression analysis of 753 immune-related genes in primary tumor samples from 45 patients with early-stage basal-like breast cancer on the NanoString platform.

overall_design: Genes were selected based on correlation with subsequent distant disease recurrence and disease-specific mortality to obtain a prognostic score.

middle: H

first: Xavier

last: Tekpli

first: Ole

middle: C

last: Lingjærde

first: Hege

last: Russnes

first: Johan

last: Vallon-Christersson

first: Elin

last: Borgen

first: Jon

last: Lømo

first: Øystein

last: Garred

first: Esmaeil

last: Dorraji

first: Vessela

last: Kristensen

first: Bjørn

last: Naume

last: Kyte


title: The role of protein phosphatases in cellulase regulation in Trichoderma reesei

summary: We investigated the functions of three different protein phosphatases, pp2a, pph5 and pph5-2 in Trichoderma reesei

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Trichoderma reesei wild-type QM6aΔmus53 and deletion mutants QM6aΔmus53Δpp2A and QM6aΔmus53Δpp5h and QM6aΔmus53Δpp5h-2

first: Aroa

last: Iglesias


title: Lung-innervating neurons expressing TMC3 control broncho-constriction and dilation with direct impact on lung tidal volume

first: Kevin

last: Huang


title: Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity [ATAC-Seq]

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

summary: Human type-II topoisomerases, TOP2A and TOP2B, remove DNA supercoiling associated with transcription, have been shown to affect several gene-expression programs, and have been correlatively linked to 3D genome architecture, although through a still poorly understood function. To study in depth the regulatory roles of TOP2 paralogs, we have used the well-characterized cellular response to estrogen as a model of acute transcriptional induction involving a rewiring of genome organization. We find that, as expected for a topoisomerase, TOP2A facilitates transcription. TOP2B, however, limits the expression of estrogen responsive genes under basal non-induced conditions, while, in response to estrogen treatment, its activity is locally downregulated to allow an accumulation of DNA supercoiling, and to favor the necessary regulatory chromatin contacts. Furthermore, this estrogen-mediated inhibition of TOP2B function requires estrogen receptor α (ERα), a non-catalytic function of TOP2A, and the action of the atypical SUMO-ligase ZATT. This mechanism of topological transcriptional-control may be shared by additional gene-expression circuits, in particular those involving a rewiring of genome organization, and highlights the relevance of DNA supercoiling and topoisomerases as central actors of genome dynamics.

overall_design: We examined chromatin structure upon TOP2B inhibition and E2 induction in MCF-7 cells using ATACseq assay.

first: José

last: Terrón-Bautista

first: Gonzalo

last: Millán-Zambrano

last: Cortés-Ledesma


title: Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity [ChIP-Seq]

overall_design: ChIP-seq for RNA POLII, TOP2A, TOP2B, ERA, RAD21 and ZATT (ZNF-451) in MCF-7 cell line upon E2 induction. RNA POLII experiments performed upon TOP2A, TOP2B and ZATT depletion by siRNA as well as merbarone and ICRF-187 treatment. RAD21 ChIPseq performed upon TOP2B  depletion by siRNA.


title: Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity


title: The HOG and pheromone pathway MAPKinase-kinases (MAPKK) TR80186 and TR21168  in Trichoderma reesei

first: Miriam

last: Schalamun

summary: We investigated the functions of the  MAPKKs 80186 in the HOG pathway and of 21168 in the pheromone pathwahy in Trichoderma reesei

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for Trichoderma reesei wild-types QM6aand deletion mutants QM6aΔ21168, QM6aΔ80186
QM6a_transcript_seq.fa from Li WC, Huang CH, Chen CL, Chuang YC, Tung SY, Wang TF. Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters. Biotechnol Biofuels. 2017;10():170. doi: 10.1186/s13068-017-0825-x

first: Monika

last: Schmoll


title: The HOG pathway MAPKKK TR_57513  in Trichoderma reesei

summary: We investigated the functions of the MAPKKK (TR_57513)  from the HOG pathway in Trichoderma reesei

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for Trichoderma reesei wild-type QM6aΔmus53 and deletion mutant QM6aΔku80Δtmk3, QM6aΔmus53Δ57513
QM6a_transcript_seq.fa from Li WC, Huang CH, Chen CL, Chuang YC, Tung SY, Wang TF. Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters. Biotechnol Biofuels. 2017;10():170. doi: 10.1186/s13068-017-0825-x


title: Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity [ICE-Seq]

overall_design: We measured topoisomerase (TOP2A, TOP2B and TOP1) activity by ICEseq experiment upon E2 treatment in MCF-7 cell line


title: The MAPKinase TMK3 in Trichoderma reesei

summary: We investigated the functions of the HOG pathway MAPKinase tmk3 = TR_45018  in Trichoderma reesei

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for Trichoderma reesei wild-types  QM6aΔku80 and deletion mutant QM6aΔku80Δtmk3
QM6a_transcript_seq.fa from Li WC, Huang CH, Chen CL, Chuang YC, Tung SY, Wang TF. Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters. Biotechnol Biofuels. 2017;10():170. doi: 10.1186/s13068-017-0825-x


title: Single-cell genomic profile of articular chondrocytes from rheumatoid arthritis and osteoarthritis patients

city: Shenzhen

first: Yan

last: WANG

address: 1068 Xueyuan Ave

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

summary: The role of cartilage tissue and chondrocytes in the pathogenesis of rheumatoid arthritis (RA) has been underexplored despite extensive research on synovial tissue. This study utilized single-cell RNA sequencing (scRNA-seq) to compare the genomic profiles of articular chondrocytes in RA and osteoarthritis (OA) patients.

overall_design: scRNA-seq was employed to profile RA chondrocytes.

last: Wang

first: Qian

last: Xie

first: Jianhui

last: Liang

first: Yanni

last: Shen


title: Piezoeletric cold atmospheric plasma sensitizes head and neck cancer  to chemotherapy and immune checkpoint blockade therapy

city: Beijing

first: xinyu

last: mang

address: Dongdan Three

institute: Peking Union Medical College,

summary:
To investigate the effects of Piezo-CAP on various types of HNC cells and elucidate the underlying mechanisms. Additionally, we examined the efficacy of combining Piezo-CAP with chemotherapy drugs (cisplatin) or immune checkpoint blockade (ICB) in head and neck tumor treatment.
RNA-sequence (RNA-seq), Western blot and quantitative real-time PCR (qRT-PCR) were utilized to investigate the mechanism of Piezo-CAP treatment HNC cells.

overall_design: RNA sequencing (RNA-seq) was performed to detect the mRNA expression profiles of Piezo-CAP treated Head and neck cancer (HNC) cells using the HiSeq3000 System (Illumina, USA).

first: Yanhong

first: Xinyu

last: Mang

first: Danni

last: Li

first: Zhao

first: Yiliang

last: Chen

first: Khawar

last: Ali Shahzad

first: Zhenyu

last: Cai

first: Fei

last: Tan


title: Lysosomal control of type I interferon induction via Ragulator-Rag complex [RNA-seq]

first: Chun-Yan

last: Lim

overall_design: Three biological replicates were analyzed for each of 6 conditions (two genotypes; 6 treatments per genotype)

first: Zeming

last: Feng

first: Lulu


title: Transcriptomic taxonomy analysis of ovarian cells during primordial assembly in goats

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: To understand how the development of primordial follicles is controlled by a complex network of interactions between oocytes and ovarian somatic cells in goat, we performed single cell RNA sequencing (scRNA-seq) from goat E85 and E125 fetal ovaries.

overall_design: we obtained goat ovary tissues from 2 embryonic stages (E85 and E125) with ethical approval and performed scRNA-seq in this study

first: Min

first: Hang

last: Yang


title: Whole genome sequencing i.e. DNA seq in WT S. cerevisiae WT post treatment with six different replication inhibitors

city: Syracuse

first: Wenyi

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

summary: Replication–transcription conflicts have long been identified as a source of genome instability, leading to DNA double-strand break (DSBs) formation at the site of encounter.  The encounter between replication and transcription is significantly increased when cells encounter stress, such as by treatment with agents that alter either of these processes.  Alterations in either of these processes increase the probability of their encounter, ultimately inducing DSBs.  Previous studies with hydroxyurea (HU)-treated synchronous cell cultures showed that HU-induced DSBs are a result of replication-transcription collisions.  Here, we sought to determine whether replication-transcription collision is a general phenomenon used by replication inhibitors to induce DSBs.  In our study, we used six different replication inhibitors, HU, methyl methane sulfonate (MMS), camptothecin (CPT), actinomycin D (AD), doxorubicin (DOX), and methotrexate (MTX), each of which acts differently.  The replication inhibitor-specific DSBs tend to be enriched at gene exons and are also well correlated with the origins of replication.  Gene expression around these DSBs tends to be upregulated, thus increasing the probability of encounter between the two. These results support our hypothesis that DSBs result from replication-transcription conflicts.  We also observed enrichment in the transcription-dependent histone mark deposition-H3K4me3 and H3K36me3 at one DSB locus.  Taken together, these results suggest that replication inhibitor treatment induces the expression of certain genes, depositing active histone marks, which upon encountering the incoming replication fork result in collision.  Overall, our study maps the genome-wide location of DSBs as well as the gene expression profile induced by different replication inhibitors and provides insight into the role of chromatin architecture in regulating genome integrity.

overall_design:
Asynchronously grown WT cells from the W303 background were treated with  six different replication (HU,MMS,CPT, AD,DOX,MTX) inhibitors at their IC50 concentration. DNA-seq  was done each of the replication inhibitor treatment as well as its vehicle control. Two independent experiments were performed for each with each having a technical replicate (4 total experiments per each replication inihibitor and vehivle control).
**Please note that DNA-seq data was used as a control to normalize Break-seq data for copy number variation. Hence, no processed files for this dataset.

first: Ishita

last: Joshi


title: MAPKinases

first: Miriam

last: Schalamun

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

overall_design: Refer to individual Series


title: Break-Seq to map DNA double stranded breaks in WT S. cerevisiae WT post treatment with six different replication inhibitors

overall_design: Asynchronously grown WT cells from the W303 background were treated with  six different replication (HU,MMS,CPT, AD,DOX,MTX) inhibitors at their IC50 concentration. DSBs were mapped in each of the replication inhibitor treatment as well as its vehicle control. Two independent experiments were performed for each with each having a technical replicate (4 total experiments per each replication inihibitor and vehicle control).


title: Replication Inhibitors induce DNA DSBs by causing replication-transcription collision.


title: Recombination suppression on fungal mating-type chromosomes without mating-type loci linkage and with loss of function of HD mating-type genes

city: Louisville

first: Michael

last: Perlin

state: KY

address: 214 W. Barbee Street Walk

institute: University of Louisville

summary: So as to compare fungal mating-type chromosomes across a range of Microbotryum species, comparative genomics analyses were conducted, and were informed by RNASeq data. In this instance, different stages of the lifecycle of M. violaceum infecting D. pavonius were compared via RNASeq.

overall_design: Haploid strains of Microbotryum violaceum Dianthus pavonius, grown on PDA; Mated haploid strains of compatible mating types were incubated on water agar plates; Buds from infected Dianthus pavonius were isoalted and pooled according to size. RNAs from these samples were isolated and used for RNASeq so as to inform comparative genomic analyses across a variety of Microbotryum species.

first: Roxanne

middle: K

last: Hayes


title: Single-cell transcriptomics reveals diverse and complex gene expression alterations in human fetal spinal cord

city: Xiamen

first: Jing

last: Wang

state: Fujian

address: 668 Jimei Road

department: School of Medicine and School of Biomedical Sciences

institute: Huaqiao University


title: Single-cell genomic profile of articular chondrocytes from CIA rats

first: Yan

last: WANG

summary: The inflammation of articular cartilage in RA is caused by pro-inflammatory factors secreted by the synovium. However, a recent study has shown that chondrocytes in RA patients can spontaneously secrete pro-inflammatory cytokines and MMPs, which undoubtedly provided new thinking for the treatment of RA diseases. We built a CIA model in rats, took the knee cartilage for single-cell sequencing, and sought to verify whether the contribution of chondrocytes to the inflammatory response in CIA rats was consistent with that of cartilage in RA patients. Our present work is the first to show the genome-wide gene expression of CIA rats cartilage and its assciation with chondrocytes in inflammation response by single-cell RNA sequencing. It was the first time to verify that cartilage destruction in RA disease was involved in the spontaneous inflammation of chondrocytes through CIA model animals. Moreover, the specific pro-inflammatory response cell subtypes have also been identified, which was marked as effector chondrocytes (EC) in the CIA rats cartilage. This not only proved that the cartilage of the CIA rat model can well simulate the inflammatory manifestations of RA patients in vitro, but also provided detailed and complete genomic data for the future study of RA cartilage in vitro.

overall_design: scRNA-seq was employed to profile sham and CIA rats.

first: Qian

last: Xie

first: Jianhui

last: Liang

first: Yanni


title: Lung-innervating neurons expressing TMC3 control broncho-constriction and dilation with direct impact on lung tidal volume (RNA-Seq)

first: Kevin

last: Huang

address: 1 DNA Way

institute: Genentech

summary: Sensory neurons of the vagal ganglia (VG) innervate lungs and play a critical role in maintaining airway homeostasis. However, specific VG neurons that innervate lungs, and mechanisms by which these neurons sense and respond to airway insults, are not well understood. Here, we identify a subpopulation of lung-innervating VG neurons defined by their expression of TMC3. Single cell transcriptomics illuminated several subpopulations of TMC3+ VGs afferents, revealing distinct Piezo2 and Trpv1-expressing subclusters. Furthermore, TMC3 deficiency in VG neurons leads to global and subcluster specific transcriptional changes involved in metabolic and ion channel function. Importantly, we show that broncho-constriction and dilation can be modulated through inhibition or activation of TMC3+ VG neurons with a direct impact on lung tidal volume. Together, our data show that TMC3 is a marker of specific lung-innervating neurons and may play a pivotal role in maintaining fundamental inspiratory and expiratory processes.

overall_design: Lumbar DRG, Thoracic DRG, and vagal ganglion bulk RNA-sequencing from both TMC3 wildtype and TMC3 knockout backgrounds

first: Jens

last: Kortmann

first: Josh

last: Kaminker

first: Shannon

last: Turley


title: RNA-Seq to map gene expression pattern in WT S. cerevisiae WT post treatment with six different replication inhibitors

overall_design: Asynchronously grown WT cells from the W303 background were treated with  six different replication (HU,MMS,CPT, AD,DOX,MTX) inhibitors at their IC50 concentration. DSBs were mapped in each of the replication inhibitor treatment as well as its vehicle control. Two independent experiments were performed for each with each having a technical replicate (4 total experiments per each replication inihibitor and vehivle control).


title: miR184 and miR499 in HSPC proliferation and differentiation

city: Pittsburgh

first: Partha

last: Dutta

state: PA

address: 200 Lothrop Street

department: Medicine

institute: University of Pittsburgh

summary: We observed that platelet-derived extracellular vesicles (pEV) are enriched in miR184 and miR499. These pEVs are taken up by hematopoietic stem and progentior cells (HSPC). We wanted to know the effects of miR184 and miR499 on HSPC proliferation and differentiation.

overall_design: We transfected mouse hematopoietic stem and progenitor cells with control miR, miR184, or miR499. Two days after the transfection, mRNA was extracted and RNAseq was performed.

first: Lee

last: Ohayon

first: Xinyi

last: Zhang


title: scATAC-seq of mouse 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) induced liver injury model

city: Cincinnati

first: Emily

last: Miraldi

state: OH

address: 3333 Burnet Avenue

department: Immunobiology

institute: Cincinnati children hospital

summary: Regulatory T cells (Tregs) were shown to protect from cholestatic liver injury. Here we investigate whether amphiregulin (AREG), a ligand for epithelial growth factor receptor (EGFR) which promotes epithelial repair, mediates innate Treg functions in cholangiopathies. Mice were fed with diet containing 0.1 % of the xenobiotic 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) for 14 days to induce sclerosing cholangitis, followed by a 28-day recovery period (without DDC). Liver mononuclear and epithelial cells were enriched and subjected to single-cell sequencing at four time points: baseline, at day 14 of DDC treatment, and following a 14- or 28-day recovery period from 14 days of DDC treatment.

overall_design: For our time course, 8-week wild type C57Bl/6 mice were fed with 5058 chow admixed with 0.1% DDC for 14 days and then allowed to recover for an additional 14-28 days (5058 chow without DDC).  Liver mononuclear and epithelial cells were enriched and subjected to single cell sequencing at four time points: baseline, at day 14 of DDC treatment, and following a 14- or 28-day recovery period from 14 days of DDC treatment.

first: Alexander

middle: G

last: Miethke

first: Joseph

last: Wayman

first: Ramesh

last: Kudira

first: Zi


title: Single-cell transcriptomics reveals diverse and complex gene expression alterations in human fetal spinal cord [Visium]

first: Jing

summary: We analyzed the transcriptomics of single cell of human fetal spinal cord at GW8-Gw12  using 10x Genomics.

overall_design: The Visium Spatial Tissue Optimization workflow includes placing tissue sections on 7 Capture Areas on a Visium Tissue Optimization slide. The sections are fixed, stained, and then permeabilized for different times. mRNA released during permeabilization binds to oligonucleotides on the Capture Areas. Fluorescent cDNA is synthesized on the slide and imaged. The permeabilization time that results in maximum fluorescence signal with the lowest signal diffusion is optimal. If the signal is the same at two time points, the longer permeabilization time is considered optimal.

first: Tao

last: Sun


title: scRNA-seq of mouse 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) induced liver injury model

summary: Regulatory T cells (Tregs) were shown to protect from cholestatic liver injury. Here we investigate whether amphiregulin (AREG), a ligand for epithelial growth factor receptor (EGFR) which promotes epithelial repair, mediates innate Treg functions in cholangiopathies. Mice were fed with diet containing 0.1 % of the xenobiotic 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) for 14 days to induce sclerosing cholangitis, followed by a 28-day recovery period (without DDC). Liver mononuclear and epithelial cells were enriched and subjected to single-cell sequencing at six time points: baseline, at days 7 or 14 of DDC treatment, and following a 7-, 14- or 28-day recovery period from 14 days of DDC treatment.

overall_design: For our time course, 8-week wild type C57Bl/6 mice were fed with 5058 chow admixed with 0.1% DDC for 14 days and then allowed to recover for an additional 7-28 days (5058 chow without DDC). Liver mononuclear and epithelial cells were enriched and subjected to single-cell sequencing at six time points: baseline, at days 7 or 14 of DDC treatment, and following a 7-, 14- or 28-day recovery period from 14 days of DDC treatment.

last: Yang


title: Transcriptome changes in lung after the intervention of Sang Ju Yin on ALI rats

city: Qiqihar

first: Song

last: Lin

address: Bukui

institute: Qiqihar Medical University

summary: The RNA-seq of lung tissues from Wistar rats was performed. Through the analysis of differentially expressed genes, we found the genes related to the therapeutic effects of SJY. Finally, representative differential genes were verified by RT-PCR.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ALI, SJY and control rats.

first: Ruinan

last: Ren

first: Fang

last: Wang

first: Zilong

last: He

first: Cuiyan

last: Han

first: Jinling

first: Wenbao

first: Jie

first: Huiyu

first: Huimin

last: Sui

first: Tianyang


title: Attenuation of DNMT1-mediated DNA methylation upregulates CYP11A1 expression in progesterone synthesis during syncytialization of placental trophoblasts

city: Xiangyang

first: Ya-nan

last: Zhu

address: No.136, Jingzhou Road, Xiangcheng District

institute: Xiangyang Central Hospital

summary: Progesterone synthesized in the placenta is essential for pregnancy maintenance after the luteo-placental shift. Cholesterol side chain cleavage cytochrome P450 (P450scc, also known as CYP11A1), is a key enzyme controlling progesterone synthesis，and its expression is greatly increased during placental trophoblast syncytialization. However, the molecular mechanism underlying CYP11A1 upregulation during syncytialization remains largely unresolved. Here, we investigated whether altered methylation in CYP11A1 gene promoter played a role and explored the transcription factor involved.

overall_design: Infinium MethylationEPIC (850K) human methylation Beadchip was used  to indetify the changes of genome-wide DNA methylation during placental trophoblasts syncytialization


title: HDAC7 is essential in early pre-germinal center formation and its deregulation is associated with DLBCL [Xenografts]

city: Badalona

first: Maribel

last: Parra

state: Barcelona

address: Ctra. de Can Ruti, Camí de les Escoles, s/n

department: Lymphocyte Development and Disease

institute: Josep Carreras Leukaemia Research Institute

summary: Histone deacetylase HDAC7 is required for early B cell development and governs the acquisition of B cell progenitors gene identity. In addition, HDAC7 has been identified as a novel biomarker and prognosis factor in infant pro-B-ALL. However, its role in mature B cell biology and associated malignancies is unknown. Here, by using a conditional mouse model for specific deletion in activated B cells, we demonstrate that HDAC7 is essential for the entry and initiation of the germinal center (GC) reaction. HDAC7 deficiency results in the blockade of B cell development at the pre-GC stage, leading to the generation of aberrant GC B cells, diminished class switch recombination and plasma cell formation. We demonstrate that, while it is generally underexpressed in diffuse large B cell lymphoma (DLBCL) tumors, the low expression of HDAC7 is associated with a poor prognosis of the patients. Importantly, exogenous expression of HDAC7 in DLBCL cell lines reduces the proliferative capacity of these latter, as well as DLBCL tumorigenecity in vivo. In summary, our data revealed first, the essential function of HDAC7 in the establishment of the GC, and second, the potential contribution of HDAC7 deregulation in DLBCL development.

overall_design: Cells were extracted from subcutaneosly injected MD901 cell line transfected with a two-step retroviral infection that allowed the ectopic expression of HDAC7 upon doxycicline induction. Doxicycline was added to the drinking water. Tumor was extrated and disgregated to obtain a single cell suspension. RNA was extracted using the Quiagen kit for RNA extraction. Samples were quantified and subjected to quality control using a Bioanalyzer apparatus (IRB, Barcelona). Samples were processed by Macrogene, Inc.

first: Ainara

last: Meler

first: Mar

last: Gusi-Vives

first: Oriol

last: de Barrios

first: Alba

last: Azagra

first: Olga

last: Collazo

first: Javier

last: Melchor

first: Alberto

last: del Monte

first: Balázs

last: Győrffy

first: Miriam

last: Verdu-Bou

first: José-Tomás

last: Navarro

first: José-Ignacio

last: Martín-Subero

first: Gaël

last: Roué

first: Almudena

last: Ramiro

first: Sergio

last: Roa


title: HDAC7 is essential in early pre-germinal center formation and its deregulation is associated with DLBCL

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Changes of miRNA expression profiling in GT1-7 cells after treated with dexamethasone(DEX)

city: Fujian

first: Rongmei

last: Lu

address: East Street No.134，Gulou District，Fuzhou

institute: Fujian Provincial Hospital

summary: Stress is defined as a systemic nonspecific adaptive response to the stimulations from internal and external environment or psychological factors through coordinating series of complex systems, like nervous system, immune system and respiratory system. While it is well known that stress have profound negative effects on reproductive function, the mechanism of reproductive dysfunction is still far from perfect. Kisspeptin, which are known for regulating GnRH synthesis and secretion, affect the initiation of puberty and reproduction, have been shown to express glucocorticoid receptors(GR),and both acute and chronic stress significantly inhibit Kisspeptin expression. So, this study speculated that Kisspeptin might participate in the process of reproductive regulation during stress. However, when constructed stress models of GT1-7 cells(Derived from mouse hypothalamic neurons, could not only transcribe endogenous GnRH mRNA and release GnRH when depolarization, but also express Kisspeptin, G protein-coupled receptors) with DEX and tried to analyze the specific mechanism of stress inhibited Kisspeptin expression, opposite results(Dex improved Kisspeptin expression of GT1-7 cells) were obtained. Based on the neuroimmune system hypothesis of stress, this study speculated that the direct reason of stress inhibited Kisspeptin expression might be stress-induced inflammatory response rather than stress-elevated GC. Even so, the transcription of Il-1β decreased in BV-2 cells(Derived from mouse Microglia) after treated with DEX. Due to the proximity of Kisspeptin neurons and Microgila in arcuate nucleus(ARC) of hypothalamus, it is speculated that there maight be interaction between them. So, this study co-cultured GT1-7 cells and BV-2 cells, and found transcription of Kiss1 decreased and Il-1β increased. Decreased Kisspeptin expression due to inflammation of BV-2 cells and inflammation of BV-2 cells must due to changes of certain substances or molecules in GT1-7 cells after treated with DEX. To further explore the possible mechanism, this study used the highly sensitive miRNAs array to screen miRNAs which not only changed significantly in GT1-7 cells after treated with DEX but also associated with inflammation. Finally, 10 miRNAs obtained and further confirmed mmu-miR-146a-5P could inhibited the LPS-induced BV-2 cells inflammation, M1 polarization and apoptosis.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, four samples (two were treated with absolute ethanol(etoh), anothers were treated with DEX),were used to acquire the miRNA expression profiling. After obtaining the raw data, firstly, miRNAs with fold change of expression more than 2 or less than 0.5 were screened. In total, there were 210 miRNAs that met the requirements. Then, logged on www.omicsbean.cn and input the eligible candidates of miRNAs to predicted their possible target genes. After that, KEGG pathway database was used to enrich the signaling pathway of the predicted target genes. Signaling pathways associated with inflammation and P value less than 0.05 were selected as the focus of this study. Next, by reviewing the literatures related on inflammation caused by activated microglia, Notch signaling pathway as the ultimate goal of this study.  Finally, based on Notch signaling pathway, screened the target genes and looked for matching miRNAs among the results provided by www.omicsbean.cn before. Finally, 10 miRNAs obtained and further confirmed mmu-miR-146a-5P could inhibited the LPS-induced BV-2 cells inflammation, M1 polarization and apoptosis.

first: Lisha

last: Li

first: Xiongfeng

last: Chen


title: HDAC7 is essential in early pre-germinal center formation and its deregulation is associated with DLBCL [GC]

first: Maribel

last: Parra

overall_design: Cells were extracted from spleens of Hdac7+/+ and Hdac7fl/ko mice. Cells were stained and sorted as germianl center B cells (B220+, FAS+, GL7+). Total RNA was extracted from HDAC7 deficient and control germinal center B cells in the Genomics facility of Institute for Research in Biomedicine (IRB) in Barcelona. Samples were quantified and subjected to quality control using a Bioanalyzer apparatus (IRB, Barcelona). Samples were processed at BGI Genomics Service, in China.

first: Ainara

last: Meler


title: NanotRNA-seq of Human WT and TRMT5 KO samples

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

institute: Center for Genomic Regulation

summary: tRNA samples from WT and TRMT5 KO OCI-AML2 cell lines and synthetic tRNA samples were sequenced using NanotRNA-seq.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: NanotRNA-seq of WT and TRMT5 KO OCI-AML2 cell lines and synthetic tRNA samples

first: Eva

first: Oguzhan

last: Begik

first: Cornelius

last: Pauli

first: Michaela

last: Frye


title: Identification of TEAD1-Regulated MicroRNAs

city: Chengdu City

first: Ruiping

last: Huai

state: Sichuan Province

address: Jiulidi Campus, Southwest Jiaotong University, No. 111, North 1st Section of Second Ring Road, Jinniu District

institute: Southwest Jiaotong university

type: Non-coding RNA profiling by high throughput sequencing

summary: The influence of TEADs on tumorigenesis, cancer immunity, drug resistance, metastasis and metabolism of various cancers have been well-studied. In recent years, microRNAs have been confirmed to regulate TEADs in several cancer types. However, it is still unclear how miRNAs orchestrate their regulation and function in TEAD1 network in hepatocellular carcinoma (HCC). Here, we investigated that TEAD1 is up-regulated in liver cancer and highly correlated with the effector YAP1, Smad2/3 of the Hippo, TGFβ pathway. Next, we used small RNA sequencing to characterize the differentially expressed miRNAs after the knockdown of TEAD1 in a time-dependent manner (0, 24, 36 and 48h) by using two siRNAs in HepG2. The most robustly TEAD1-induced 10 miRNAs with consistent trend over time were verified.

overall_design: Seven samples of HepG2 cells were subjected to small RNA-seq. The HepG2 cells were treated with siRNAs in a time-dependent manner (0, 24, 36 and 48h) to down-regulate the expression of TEAD1. The experimental group(siRNAs-treated HepG2：HepG2_24h_siRNA1, HepG2_36h_siRNA1, HepG2_48h_siRNA1, HepG2_24h_siRNA2, HepG2_36h_siRNA2, and HepG2_48h_siRNA2) and control group(untreated HepG2: HepG2_0h) were subjected to small RNA-seq to identify the TEAD1-regulated miRNAs.

first: L

last: Xiong

first: R

first: D

last: Yang


title: RNAi-mediated regulation of alg-3 and alg-4 coordinates the spermatogenesis developmental program in C. elegans [small RNA-seq]

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

summary: Developmental coordination of gene regulatory networks is necessary for maintaining fertility. Inappropriate activation or silencing of genes responsible for promoting the totipotent germ cell fate into oocytes and/or sperm can have detrimental effects on an organism’s reproductive potential. Spermatogenesis and oogenesis are temporally separated within the germline tissue during the L4 and adult developmental stages, respectively. Yet, it remains unclear how these developmental programs are robustly executed, particularly during stressful conditions. Here we show evolutionarily conserved RNA interference (RNAi) pathways act to restrict expression of spermatogenesis genes to the L4 developmental stage during heat stress. We performed differential expression analysis of mRNA-seq and small RNA-seq libraries from L4 and adult-stage wild-type and mut-16 mutants, which lack a critical RNAi pathway protein, grown at permissive (20ºC) and elevated temperature (25ºC). Our analyses revealed spermatogenesis-enriched gene expression is developmentally mis-regulated in a small RNA-dependent manner at elevated temperature. Many of the mis-regulated spermatogenesis genes are targets of the ALG-3/4 pathway, which is critical for thermotolerant male fertility. We found that the genomic loci of alg-3 and alg-4 are targeted by small RNAs, and that during heat stress, MUT-16-dependent small RNAs are required for L4 stage-specific expression of the Argonautes, ALG-3 and ALG-4. These findings indicate that RNAi pathways are essential for properly coordinating the developmental program of spermatogenesis during heat stress. We propose that appropriate expression of spermatogenesis genes is achieved through small RNA-mediated genetic switches that regulate the expression of ALG-3 and ALG-4 to control ALG-3/4 pathway function throughout development. Moreover, this work provides key insights into the different molecular mechanisms that RNAi pathways employ to maintain both maternal and paternal germ cells’ reproductive potential, and further highlights the complexities and importance of RNAi-mediated gene regulation in development.

overall_design: 8 mRNA-seq and 8 small RNA-seq libraries were generated and analyzed. Each genotype per condition were generated in duplicate.


title: A549-derived exosomes transform fibroblasts into cancer-associated fibroblasts (CUT&RUN)

city: Tianjin

first: Jian

last: Zhang

address: Huanhu West Road, Hexi District

institute: Tianjin Medical University Cancer Institute and Hospital

summary: With the in-depth study of exosomes, it has been discovered that tumor-derived exosomes could transform normal fibroblasts into cancer associated fibroblasts (CAFs) and further affect metastasis and drug resistance of CAFs. FOXN3 was the target of tumor-derived exosomes. The understanding of downstream genes regulated by FOXN3 is nessesary. An alternative ChIP-seq method, CUT&RUN was applied to explored the downstream genes directly regulated by FOXN3

overall_design: Chromatin immunoprecipitation DNA-sequencing (CUT&RUN) for FOXN3 in MRC5 cells.

first: Shuangli

last: Mi


title: ChIP-seq analysis of changes in H3K27me3 between WT and RORA-deficient primary mouse splenic regulatory T (Treg) cells activated in culture

city: Lille

first: Artemii

last: Nikitin

address: 1,  Rue du Professeur Calmette

country: France

institute: Inserm

summary: Treg cells were isolated from spleens of FOXP3-CRE or RORA-FLOX-FOXP3-CRE mice by FACS and activated in culture for 6 days, nuclei were isolated and frozen

overall_design: Treg cells nuclei were pooled from multiple experiments and split into 3 replicates per genotype.

first: David

last: Dombrowicz


title: ChIP-seq analysis of changes in H3K27ac between WT and RORA-deficient primary mouse splenic regulatory T (Treg) cells activated in culture


title: Selection, development and structural characterization of 2' FY-RNA aptamers for pyoverdine

city: Ames

first: Marit

last: Nilsen-Hamilton

state: Iowa

address: 2437 Pammel Dr

department: BBMB

institute: Iowa State University

summary: Pyoverdines are siderophores employed by a variety of pseudomonas species to capture essential iron by which their growth is supported in many environments in which they can be harmful or helpful to coinhabiting species or the organisms that they inhabit. Of the Pseudomonas fluorescens group, the pyoverdine of each pseudomonad species is constituted of a central chromophore and a unique peptide component that is produced by nonribosomal peptide synthetases. Pyoverdine Pf5 (PYO-Pf5) is the product of pseudomonas protegens, a species that supports plant growth, particularly in soils with limiting iron. To explore the dynamics of P. protegens activity in soil, we have selected 2’ FY modified RNA aptamers that selectively recognize PYO-Pf5 with high affinities. Two 2’FY-RNA aptamers, with different base sequences, were selected that specifically bind pyoverdine-Pf5 (PYO-Pf5) over pseudobactin (PSB), a related pyoverdine, and two other siderophores, enterobactin and ornibactin. The 2’FY-RNA aptamers were shown to be G-quadruplexes by computational prediction, N-methyl mesoporphyrin IX (NMM) binding and CD spectroscopy. They were compared with their counterparts (same base sequence) in RNA and DNA for function and structure. Whereas the 2’FY-RNA and RNA forms bound PYO-Pf5 and had circular dichroism (CD) spectra typical of a G-quadruplex, the DNA forms neither bound PYO-Pf5 nor showed diagnostic NMM binding or CD spectra for G-quadruplexes. The impact of 2’ moiety in aptamers on their structure and function have been explored and results revealed that the nature of the chemical group at the 2’ position influences binding activity and structure.The aptamers will be applied to a nanoporous aluminum oxide biosensor to detect PYO-Pf5. This sensor provides a future opportunity to track the locations around plant roots of P. protegens and to monitor PYO-Pf5 production and movement through the soil.

overall_design: SELEX was performed with PYO-Pf5 as target to select 2’FY-RNA aptamers. For the first round of selection libraries of 1015 2’ FY-RNA were used. The biotinylated capture oligos, which are complementary to the short constant region in the library sequence, were attached to streptavidin coated magnetic beads. The 2’ FY-RNA libraries were first hybridized with oligos complementary to the PCR primer regions and then immobilized on the beads by hybridization with the capture oligos. The length of the capture oligo varied with the SELEX round as did the hybridization temperature and the oligo: PYO-Pf5 ratio . The bound oligos were captured using a magnet and purified by ethanol precipitation in the presence of 2 µL linear polyacrylamide (LPA) . Purified 2’FY-RNA was reverse transcribed and amplified by low fidelity Taq polymerase. The ratio of 2’FY-RNA to PYO-Pf5 was reduced and the length of capture oligo increased in successive SELEX rounds to increase selection pressure .  Nine rounds of selection were performed, and two sequential rounds of counter selection were done after rounds 3 and 6. The targets for counter selection were enterobactin and ornibactin. All targets used in selection and counter-selection were the Fe3+-bound forms. PCR-amplified libraries were prepared for NGS using Nextera Illumina sequencing primers and the appropriate bar coding. Next generation sequencing was performed by  Novogene facility, Sacramento, California using HiSeq PE150 platform. The raw NGS data was demultiplexed and assigned to respective rounds by open-source software AptaSuite. Barcodes were used to assign DNA pools from different rounds of selection. A zero-nucleotide mismatch between the reference and matched barcodes, and two mismatches between the reference and matched primers were criteria for demultiplexing.  Further analysis was done with the sequences that met this standard. Clustering was done with 10 iterations of locality sensitive hashing, sampling 55% of the indices in the randomized regions and allowing no more than 10 nucleotide mismatches between the seed sequence of a cluster to each remaining member. Clusters were extracted for further analysis and aptamer screening.

first: Sharif

last: Anisuzzaman


title: NIT2 epigenetically restrains oxidative phosphorylation to overcome fluorouracil resistance in gastric cancer

city: Guangzhou

first: Ziyang

last: Wang

address: 58 Zhongshan Second Road

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

summary: Fluorouracil (5-FU) chemoresistance is an important reason for the postoperative recurrence and poor prognosis of gastric cancer, but there is still no effective way to overcome chemoresistance. Here, by using the CRISPR/Cas9 system, we identify nitrilase family member 2 (NIT2) reverses chemoresistance, regardless of its metabolic function. NIT2 depletion causes H3K14 acetylation (H3K14ac) increase and NF-κB signalling activation, in turn upregulating oxidative phosphorylation (OXPHOS) and promoting chemoresistance. Mechanistically, NIT2 prevents BRD1 from binding histones and releases ING4 to degrade the transcription factor RELA. Upon 5-FU stimulation, the E3 ligase CCNB1IP1 interacts with NIT2 to cause autophagic degradation of NIT2. In addition, NIT2 downregulation correlates with poor prognosis in gastric cancer patients, and this is probably related to the promotion of OXPHOS. Our finding highlights the nonenzymatic function of NIT2 in chemoresistance and show that the blockade of OXPHOS by metformin can enhance chemosensitivity to 5-FU upon loss of NIT2.

overall_design: Control and shNIT2 MKN45 cells were crosslinked with formaldehyde and quenched with 125 mM glycine. The fragmented chromatin fragments were pre-cleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti-H3K14ac antibodies. After reverse crosslinking, ChIP and input DNA fragments were end-repaired and A-tailed followed by adaptor ligation. The DNA libraries were amplified for 15 cycles and sequenced.

first: Yuqin

last: Di

first: Xiongjun

first: Weiling

last: He


title: RORA-deficient primary mouse splenic regulatory T (Treg) cells activated in culture

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

overall_design: Refer to individual Series


title: Chemical–induced generation of adult-like human hepatocytes from pluripotent stem cells

city: Beijing

first: Jie

last: Hao

state: 北京

address: Beijing

institute: Tsinghua University

summary: Hepatocytes differentiated from human pluripotent stem cells (hPSCs) may provide a truly unlimited cell source to model and treat liver diseases. However, immaturity of hPSC-derived hepatocytes significantly limited their applications. Here we devised a step-wise pharmacological approach to induce adult-like  hPSC-differentiated hepatocytes (a-Hep), which closely resemble primary human hepatocytes (PHHs) in terms of morphology, polarity, transcriptome, epigenome, and capacity to execute hepatic specific-functions. Importantly, a-Heps upon transplantation enabled unprecedented engraftment efficiency in liver parenchyma with comparably rapid dynamics as PHHs. Mechanically, inhibition of ERK pathway was indispensable for the generation of middle-stage hPSC-differentiated hepatocyte (mid-Hep), an essential step to obtain further mature a-Heps, by upregulating metabolic functions and repressing cell growth. In summary, our studies paved a promising avenue for clinical application of hPSC-derived hepatocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cell in different stages. Comparative gene expression profiling analysis of RNA-seq data for a-Hep at different days. Gene expression profiling analysis of RNA-seq data for f-Heps cultured with different chemical combinations.

first: Huan

last: Li

first: Tianhua

last: Ma

first: Sheng

last: Ding


title: AhR promotes Th17 cells differentiation in chronic hepatitis B via JAK1/STAT3/SOCS3 pathway

city: kunming

first: You

last: Jing

address: 295 Xichang Road

institute: The First Affiliated Hospital of Kunming Medical University

summary:
Objectives：The mechanism of Th17/Treg imbalance in chronic hepatitis B (CHB)remains unclear. The aim of the study is to explore the immunopathogenesis of Th17/Treg imbalance in CHB through RNA transcriptome sequencing.
Methods：This study included 15 instances in the healthy control (HC) and 15 cohortsin the chronic hepatitis B (CHB). Three patients from the CHB cohort and three participants from the HC subject were chosen at random. Their peripheral blood was used to separate CD4+ T cells, which were then subjected to RNA transcriptome sequencing. Finally, the RNA transcriptome sequencing results were validated by qRT-PCR and Western blotting.
Results：differential genes AhR, HLA-DQA1/DQB1were directly involved in Th17 cell differentiation; while gene IL-7 took part in theJAK-STAT pathway, ATP6V1D, SLC7A5, SGK1 participated in the mTOR pathway, PIK3R3 and SOS1 were engaged in signaling pathways of mTOR and the JAK-STAT. C-X-C motif chemokine 10, TRAF4, and CEBPB were involved in the IL-17 signaling pathway.
Conclusion：AhR may control Th17 cell development in CHB by activating the JAK1/STAT3/SOCS3 signaling pathway and regulated the Th17/Treg balance.

overall_design: differential genes between HC group and CHB group by RNA transcriptome sequencing

first: Ruyi

first: Huaier

last: Liu

last: Lin

first: Yinzhou

last: Zhao

first: Jiawei

last: Geng


title: ATAC-seq analysis of WT versus RORA-deficient primary mouse splenic regulatory T (Treg) cells activated in culture

first: Artemii


title: Small molecule-induced adult-like human hepatocytes from pluripotent stem cells (ATAC-Seq)

summary: Hepatocytes differentiated from human pluripotent stem cells (hPSCs) may provide a truly unlimited cell source to model and treat liver diseases. However, immaturity of hPSC-derived hepatocytes significantly limited their applications. Here we devised a step-wise pharmacological approach to induce adult-like hepatocytes (a-Heps) from hPSCs, which closely resemble primary human hepatocytes (PHHs) in terms of morphology, polarity, transcriptome, epigenome, and capacity to execute hepatic specific-functions. Importantly, a-Heps upon transplantation generated unprecedented engraftment in liver parenchyma with comparably high efficiency and rapid dynamics as PHHs. Mechanically, inhibition of ERK pathway was indispensable for the generation of middle-stage hepatocytes (mid-Heps), an essential step to obtain further mature a-Heps, by upregulating metabolic functions and repressing cell growth. In summary, our studies paved a promising avenue for the clinical applications of hPSC-derived hepatocytes.

overall_design: ATAC-seq profiles of cells in different stages were compared

first: Minglei

last: Shi


title: Effect of DHODH inhibitor on gene expression in 4T1 cells

first: Yujia

address: Dongdan

institute: Peking Union Medical College

summary:
To investigate the function of DHODH in 4T1 breast cancer cells, we treated 4T1 cells with DMSO or BRQ.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different samples in DMSO or BRQ treatment groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DMSO or BRQ treated 4T1 cells.


title: Effect of DHODH inhibitor on gene expression in Panc1 cells

summary:
To investigate the function of DHODH in the Panc1 cells, we treated Panc1 with DMSO or DHODH inhibitor BRQ.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different samples under two treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Panc1 cells treated with DMSO or BRQ).


title: Effect of DHODH on gene expression in 4T1 cells

summary:
To investigate the function of DHODH in 4T1 breast cancer cells, we knocked out DHODH in 4T1 cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different samples in WT or KO groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT or DHODH KO 4T1 cells.


title: Effect of DHODH inhibitor on gene expression in A549 cells

summary:
To investigate the function of DHODH in the A549 cells, we treated Panc1 with DMSO or DHODH inhibitor BRQ.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different samples under two treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A549 cells treated with DMSO or BRQ).


title: Transcriptomic landscape of human primary stromal cells (fibroblasts, endothelial cells and mesenchymal stem cells) upon therapy-induced senescence (genotoxic chemotherapy）

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary:
As a prominent hallmark of senescent cells, the senescence-associated secretory phenotype (SASP) accumulates over the course of chronological aging and in diverse age-related diseases, and is a crucial driver of chronic inflammation and aging-associated phenotypes. In humans, senescent cells accumulate in multiple tissues at different rates, from 2- to 20-fold when comparing young (<35 years) to old (>65 years) healthy donors. For decades of years, the identification, characterization and pharmacological elimination of senescent cells have gained attention in the research field of aging and age-related disorders. However, the non-specificity of current senescence markers and the existence of different senescence programs strongly limits these tasks. Despite recent advances in high-throughput technologies, there is still a lack of in-depth comparison of the senescence-associated expression profile among distinct cell lineages in the tissue microenvironment.
Here, we chose to profile the genome-wide expression of several primary normal human stromal cell lines including HBF1203, Huc068, HUVEC and IMR90 upon therapy-induced senescence (TIS), with the aim to determine molecular regulators of senescence phenotypes and define the potential contribution of senescent cells to human age-related pathologies. These data may provide a baseline to further explore how  senescent cells arising in the local microenvironment can promote tissue dysfunction and organ degeneration in the course of an individual aging.

overall_design:
High-throughput RNA-seq examination of genome-wide transcriptional alterations of primary normal human stromal cell lines in proliferating versus senescence phase generated by chemotherapeutic agents such as bleomycin.
HBF1203, Huc068, HUVEC and IMR90


title: Effect of IAPP insult and urolithin B treatment in beta-cell gene expression

city: Lisboa

first: Regina

last: Menezes

address: Campo Grande 376

country: Portugal

institute: Universidade Lusófona de Humanidades e Tecnologias

summary: To investigate the effects of IAPP insult and urolithin B treatment in the gene expression of a rodent cell line, we submitted the cells to different treatments: control, urolithin B, IAPP, annd urolithin B+IAPP

overall_design: Comparative gene expression profiling analysis of RNA-seq data for INS-1 832/3 cells receiving IAPP insult and/or urolithin B pretreatment

first: Ana

middle: F

last: Raimundo

first: Sofia

last: Ferreira

first: Vânia

last: Pobre

first: Mafalda

last: Lopes-da-Silva

first: José

last: Brito

first: Nuno

last: Saraiva

first: Cláudia

middle: N

last: Santos


title: Transcriptome sequencing reveals expression characteristics of osteosarcoma before and after neoadjuvant chemotherapy

city: Changsha

first: Lin

last: Qi

address: 139 Renmin Road

institute: The Second Xiangya Hospital, Central South University

summary: Osteosarcoma is the most common primary bone cancer in children, adolescents and young adults. It is a rare cancer type. To comprehensively reveal the transcriptomic characteristics of osteosarcoma  before and after neoadjuvant chemotherapy (NACT), we performed next-generation sequencing (NGS) on 5 osteosarcoma patients undergoing NACT.

overall_design: To comprehensively reveal the transcriptomic characteristics of osteosarcoma before and after NACT,  matched osteosarcoma samples before and after NACT from  five patients were sequenced using NGS.

first: Zhihong

last: Li

first: Chao

last: Tu

first: Wenchao

last: Zhang


title: Total RNA bulk sequencing of T helper cells [mRNA]

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

summary: Analysis of total RNA from naive, Th1/2/17 week 1 and Th1/Th2/Th17 week 4 mouse cells

overall_design: naive CD4+ CD62L+ T cells were isolated from murine spleens and either taken directly for total RNA isolation or activated under Th1, Th2 or Th17 polarizing conditions and cultures for 1 week or repeatedly stimulated for 4 weeks and then living cells were harvested for total RNA isolation

first: Gitta

last: Heinz

first: Cam

last: Loan Tran

first: Pawel

last: Durek

first: Afrah

last: Ghauri

first: Christopher

last: Kressler

first: Claudia

last: Haftmann

first: Patrick

last: Maschmeyer

first: Andrey

last: Kruglov

first: Zhuo

last: Fang

first: Vikram

last: Sunkara

first: Antje

last: Ostareck-Lederer

first: Dirk

last: Ostareck

first: Andreas

last: Radbruch

first: Mir-Farzin

last: Mashreghi


title: circIkzf1 and Ikzf1 overexpression in Th cells [scRNA-seq B]

summary: Cd4+ cells were isolated from mouse spleens, activated and retrovirally transduced to simultaneously express circIkzf1 and Ikzf1 or the respective controls to see how these two molecules would interfere with each other

overall_design:
Sequencing of RNA was performed from flow cytometry-sorted double-transduced living mouse Th cells (hCD4+ adn GFP+) expressing circIkzf1, Ikzf1 or controls, using the 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit.
scRNA-seq sets A and B are technical replicates.


title: circIkzf1 and Ikzf1 overexpression in Th cells [scRNA-seq A]


title: Total RNA bulk sequencing of T helper cells [circRNA]


title: Transcriptome analysis of osteosarcoma cell lines treated with FDA-approved drugs

first: Lin

last: Qi

summary: In order to understand the effect of FDA-approved drugs including doxorubicin (DOX) and HDACs inhibitors (PXD101 and PCI-24781) on osteosarcoma, 143B osteosarcoma cells were treated with the single agents or combinations of these drugs. Three biological replicates of each sample were processed for next-generation sequencing (NGS).

overall_design: 143B osteosarcoma cells were treated with 0.1μM DOX, 1.5μM PXD101, 1.5μM PCI-24781, the combination of 0.1μM DOX and 1.5μM PXD101, the combination of 0.1μM DOX and 1.5μM PCI-24781 and DMSO  for 24 hours and subjected to NGS.

first: Zhihong

last: Li

first: Chao

last: Tu


title: Circular RNA Ikzf1 is translated in a rolling circle fashion to balance Ikaros function in Th lymphocytes

first: Frederik

last: Heinrich


title: Single-cell transcriptomics reveals diverse and complex gene expression alterations in human fetal spinal cord [scRNAseq]

city: Xiamen

first: Jing

last: Wang

address: 668 Jimei Road

institute: Huaqiao University

summary: we analyzed the transcriptomics of single cell of human fetal spinal cord at GW8-Gw12  using 10x Genomics.

overall_design: The spinal cord tissue was first digested in 2 mg/ml collagenase IV and 10 U/μl DNase I in hibernate E medium and then in 1 mg/ml papain in hibernate E medium. Further pipetting was used to fully digest the tissue into single cells and analyzed using scRNAseq.

first: Tao

last: Sun


title: DHODH function

first: Yujia


title: An autonomous intrapulmonary inflammatory feedback response, mediated by surfactants, operates as an inherent viral defense mechanism: evidence from acute SARS-CoV-2 infection [Pseudovirus Infected Proximal Lung Organoid scRNA-seq]

city: La Jolla

first: Sandra

last: Leibel

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes an acute respiratory distress syndrome (ARDS) that resembles neonatal RDS – a condition attributable to the deficiency of the surface tension reducing factor surfactant. Using a novel multi-cell type, human-induced pluripotent stem cell (hiPSC)-derived lung organoid (LO) system, validated against primary lung cells, we found that surfactant proteins (SP) A, B, C and D are dynamically regulated by SARS-CoV-2 infection. In the absence of SP-B (including through the study of LOs from SP-B deficient patients), resistance to infection was impaired and inflammatory cytokine/chemokine production and interferon (IFN) responses were modulated in lung cells of non-hematopoietic origin and without a circulatory system, suggesting specialization of viral inflammatory responses by human lung cells. Such cells can be infected independent of ACE2 and TMPRSS2 expression via what we propose is a non-canonical endocytotic route. Single cell RNA sequencing revealed broad susceptibility of many lung cell types with differential expression of BSG, cathepsins, and ACE2 that all facilitate viral entry. SARS-CoV-2 triggers a rapid loss of lung cell viability via apoptosis that impairs viral dissemination evident in the presence of Bcl-xL antagonism. Treatment with exogenous surfactant, recombinant SP-B, or genomic correction of the SP-B deletion mutation restored resistance to SARS-CoV-2 infection and improved cell viability. These findings suggest an unrecognized specialized intrinsic intra-pulmonary inflammation-based feedback loop of developmental origin that autonomously, without the intercession of hematopoietic derivatives, attempts to restore lung homeostasis after infection by inhibiting viral dissemination, averting lung epithelial demise, and dampening inflammatory cascades -- an additional inherent host-pathogen defense system. Given that SP-B is central to this response, an antiviral role may now be ascribed to this structural component that heretofore had been regarded as necessary only for surface tension reduction.

overall_design: Single-cell transcriptomics comparison of pseudovirus-infected proximal lung organoids by scRNA-seq.

first: Ben

last: Croker

first: Evan

middle: Y

last: Snyder


title: MYCL-GFP and HEY1-GFP binding sites in primary airway mouse epithelial cells (mTECs) cultured at air-liquid interface for one day.

city: San Francisco

first: Jeremy

last: Reiter

address: 555 Mission Bay Boulevard South

institute: UCSF

summary: Tissue function depends on the relative proportions of multiple cell types. In the airway, basal stem cells differentiate into both multiciliated and secretory cells, which together protect the lungs from inhaled pathogens and particulates. To define how airway stem cells differentiate, we mapped differentiation trajectories using single-cell mRNA sequencing (scRNA-seq) and identified a transitional intermediate cell state in between basal stem cells and differentiated cells. These intermediate cells induce different gene expression programs that precede differentiation into either multiciliated or secretory cells. For example, we found that within the intermediate cell population, multiciliated cell precursors express Mycl, encoding a MYC-family transcription factor, and secretory cell precursors express Hey1, encoding a transcriptional repressor. We also found that Notch signaling acts on intermediate cells to repress Mycl and induce Hey1. We further show MYCL expression is sufficient to drive multiciliated cell fate, whereas HEY1 expression is sufficient to repress multiciliated cell fate. Using CUT&RUN, we made the surprising observation that MYCL and HEY1 bind to many of the same regulatory elements near genes encoding early regulators of multiciliated cell differentiation. We conclude that intermediate cells receiving Notch signals induce HEY1 to repress the multiciliated cell fate and become secretory cells, while intermediate cells not receiving Notch signals induce MYCL to promote the multiciliated cell fate.  These experiments reveal that during airway stem cell differentiation Notch signaling balances the production of two different cell types by regulating the functions of two opposing transcription factors, MYCL and HEY1.

overall_design: mTECs were transduced with MYCL-GFP or HEY1-GFP lentivirus, differentiated, and grown at air/liquid interface for one day. Cells were dissociated and analyzed by CUT&RUN with a GFP antibody to detect genomic binding sites of MYCL and HEY1.

first: Lauren

last: Byrnes

first: Rachel

last: Deleon

first: Semil

last: Choksi


title: Single-cell RNA-sequencing of Gmnc and Mcidas knockout primary mouse tracheal epithelial cells (mTECs)

overall_design: Guide RNAs targeting Gmnc, Mcidas or a control nontargeting guide were delivered to primary mouse tracheal epithelial cells (mTECs). mTECs were differentiated and analyzed by scRNA-seq.


title: Single-cell RNA-sequencing of cultured primary mouse tracheal epithelial cells (mTECs) at air/liquid interface for three days

overall_design: Mouse tracheal epithelial cells (mTECs) derived from Foxj1-CreERT Rosa-tdTomato mice at air/liquid interface for three days were isolated by Fluorescence-activated cell sorting (FACS) for tdTomato signal. tdTomato-enriched and unsorted fractions of mTECs were analyzed using scRNAseq.Two independent wild type mTEC populations at air/liquid interface for three days were also analyzed by scRNAseq.


title: An autonomous intrapulmonary inflammatory feedback response, mediated by surfactants, operates as an inherent viral defense mechanism: evidence from acute SARS-CoV-2 infection

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

overall_design: Refer to individual Series


title: Atg5  Deletion in Macrophages Protects Against Kidney Fibrosis in Mice

first: jiexing

last: tan

address: Experimental Animal Center, Nanfang Hospital, Southern Medical University No. 1838, North Guangzhou Avenue, Baiyun District, Guangzhou, Guangdong, China

summary: To identify the factors or genes associated with macrophages in a condition of ATG5 deficiency, we isolated F4/80+ cells from kidney single-cell suspensions of MΦ Atg5 -/- and WT mice(10 mouse per group) by immunomagnetic positive selection. we performed RNA-seq and heatmap analysis to identify the expression of chemokine receptor genes in MΦ Atg5-/- and WT mice.

overall_design: Total RNA was extracted from the kidney macrophages(10 mouse per group)  and was enriched using magnetic beads with oligo (dT). Total RNA quality was detected with Agilent 2100 bioanalyzer based on the RNA integrity. The constructed library was created using the Illumina TruSeq RNA Sample Preparation Kit v2(Illumina) with the standard protocol. and   sequenced using on the Illumina Novaseq 6000 platform. Reads were further filtered by fastp  (version 0.18.0). An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1.Genes with a false discovery rate < 0.05 and fold change > 2 were considered to be differentially expressed. We performed gene set enrichment analysis using software GSEAand MSigDB to identify whether a set of genes in specific GO terms\ pathways\ DO terms shows significant differences in two groups. Briefly, we input gene expression matrix and rank genes by SinaltoNoise normalization method. Enrichment scores and p value was calculated in default parameters.

first: Li

last: Gong

first: Jiexing

last: Tan

first: Yufeng

last: Zhu


title: An autonomous intrapulmonary inflammatory feedback response, mediated by surfactants, operates as an inherent viral defense mechanism: evidence from acute SARS-CoV-2 infection [Prox, Distal, and Whole Lung Organoid scRNA-seq]

overall_design: Single-cell transcriptomics comparison of normal proximal, distal, and whole and SARS-CoV-2 infected proximal organoids by scRNA-seq


title: An autonomous intrapulmonary inflammatory feedback response, mediated by surfactants, operates as an inherent viral defense mechanism: evidence from acute SARS-CoV-2 infection [Combined Proximal, Distal, and Whole Lung Organoid scRNA-seq]

overall_design: Single-cell transcriptomics comparison of control and SARS-CoV-2 infected of combined proximal, distal, and whole lung organoids by scRNA-seq.


title: An autonomous intrapulmonary inflammatory feedback response, mediated by surfactants, operates as an inherent viral defense mechanism: evidence from acute SARS-CoV-2 infection [bulk RNA-seq]

overall_design: Transcriptomics comparison of WT and SPB mutant proximal lung organoids by RNA-seq.


title: SEC16B is a novel regulator of glucose homeostasis

city: Shenzhen

first: li

last: anqi

address: No. 66, Gongchang Road, Guangming District

institute: School of Pharmaceutical Sciences (Shenzhen)

summary: Genome-wide association studies (GWAS) have so far identified a large number of genetic loci associated with metabolic diseases. SEC16B, an endoplasmic reticulum (ER) export factor, has emerged as a strong candidate associated with obesity in multiple GWAS yet its physiological function on metabolism has not been characterized. Here, by using global Sec16b knockout mice, we show that loss of Sec16b gene causes glucose intolerance without an effect on body weight. At the cellular level, Sec16b loss damages the morphology of the ER and mitochondria in pancreatic β cells. Mechanistically, Sec16b loss impairs insulin secretion via blocking intracellular Ca2+ influx via down-regulating cholinergic synapse signaling in β cells. Moreover, dSec16 loss disrupts glucose homeostasis in Drosophila melanogaster, highlighting a core and evolutionarily conserved role of dSec16 in glucose homeostasis. Taken together, our study has for the first time established SEC16B as a conserved key regulator of metabolic heath across phyla.

overall_design: Isolated pancreatic islets mRNA profiles of of 30 weeks old Sec16b+/+ and Sec16b-/- mice

first: Ruoxin

last: Zhang

first: Anqi

first: Xinyuan

last: Zhao

first: Bei

first: Zhican

last: Yang

first: Yanchuan

last: Shi

first: Greg

last: Neely

first: Qiaoping


title: The protective effects of exercise training on heart failure with preserved ejection fraction

city: Zhuzhou

first: Guo

last: Yuan

state: Hunan

address: No. 116, Changjiang South Road, Tianyuan District

institute: Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University

summary: Heart failure with preserved ejection fraction (HFpEF) is a serious health problem with limited treatment options. This study is designed to investigate the protective function of exercise training in regulating heart failure with preserved ejection fraction (HFpEF).

overall_design: High-fat diet combined with Nω-Nitro-L-arginine methyl ester hydrochloride (0.5g/L, Sigma- Aldrich, Germany) were used to establish a “two-hit” mouse model of HFpEF. After five weeks of HFpEF dietary regimen, cardiac diastolic function was measured. An incremental aerobic exercise was performed as a therapeutic protocol from the model successfully constructed last for 8 weeks. At the end of the study, heart tissue in each group was subjected to RNA sequencing to identify the differentially expressed genes and reveal the underlying mechanism.

first: Yuan

last: Guo

first: Zhu

last: Chen

first: Yuzi

last: He


title: Opposing transcription factors MYCL and HEY1 mediate the Notch-dependent airway stem cell fate decision

first: Jeremy

last: Reiter


title: RNAseq analysis of RBPMS, RBFOX2 and QKI knockdown in rat PAC1 pulmonary artery smooth muscle cells (SMCs)

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

summary: Investigation of the regulation of RNA binding proteins RBPMS, RBFOX and QKI via the global-scale analysis of alternative splicing changes in rat smooth muscle aorta. Bulk mRNA-Seq was carried out after panel knockdown of RBFOX2, RBPMS and QKI in PAC1 cells.

overall_design: RBPMS, RBFOX2 and QKI were parallel knockdown in PAC1 cells. RBPMS knockdown was treated with RBPMS-specific siRNA; RBFOX2 knockdown was treated with RBFOX2-specific siRNA; QKI knockdown was treated with QKI-specific siRNA. The nagative control was treated with control siRNA.

first: Yuling

last: Huang

first: Aishwarya

last: Jacob

first: Ilias

last: Moutsopoulos

first: Chris

last: Smith


title: Erk activity at naïve:prime transition biases lineage specification during gastrulation [scRNA-seq]

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

institute: The Francis Crick Institute

summary: FGF signaling is thought to be important for linegae specification during mouse develoipment. However, we have recently observed that FGF4 and FGF2 have opposing effects on Erk activity and ultimately on cell fate in both mouse embryonic stem cells and embryos. The aim of this study was to understand, at a single cell level, the impact in lineage specification of early exposure  to FGF2 or FGF4 in gastruloid formation, a new 3D in vitro model of mouse gastrulation.

overall_design: scRNA-Seq was performed on gastruloids primed with FGF2 or FGF4 for the first 48h (during naive to prime transition)

first: Borzo

last: Gharibi

first: Stephanie

last: Strohbuecker


title: Transcriptional regulation of ES cell by FGF signalling [RN18147]

summary: FGF4 paracrine signaling through FGF receptors is believed to induce Erk activity and promotes the exit from pluripotency. However,  we have recently observed that FGF4 and FGF2 have opposing effects on mES cell fate. The aim of this study was to understand the underlying transcriptional changes associated with these opposing actions.

overall_design: Mouse embryonic stem cells were grown in a naïve state of pluripotency using 2iLIF media and subsequently stimulated with FGF2 in N2B27 media for 0hrs, 15min, 1hrs,  24hrs and 48hrs.