title: Single RNAseq for hiPS-CMs induced to proliferate with 4 cell cycle factors

city: Louisville

first: Tamer

middle: M

last: Mohamed

state: KY

address: 580 S. Preston St., Baxter II Bldg., Room 122

department: Cardiology

institute: University of Louisville

summary: We conducted temporal single cell RNAseq on 60-day-old mature hiPS-CMs infected with either LacZ (control) or CDK1, CDK4, CCNB, CCND (4F) adenovirus for 24, 48 or 72 h.

first: Riham

last: Abouleisa


title: Translation initiation landscape of tomato-infecting virus

status: Public on May 04 2022

city: Taipei

first: Ming-Jung

last: Liu

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia sinica

type: Expression profiling by high throughput sequencing

summary: We report the global profile of ribosome profilig to reveal the in vivo translation initiation sites of tomato-infecting virus.

overall_design: We examined the initiating ribosome positonions to identify translaiton initiation sites and mRNA abundance of  the tomato yellow leaf curl thailand virus (TYLCTHV) in the TYLCTHV-infected tomato leaf.

first: Ya-Ru

last: Li


title: Multiplexed single cell mRNA sequencing of monolayer- and organoid-system differentiated cells derived from human iPSC with and without NKX2-5 genetic manipulations

city: Pittsburgh

first: Dennis

last: Kostka

state: PA

department: Developmental Biology

country: USA

institute: University of Pittsburgh

summary: Three wild type cell lines (WTC:ACTN2-eGFP, WTC:Myl2-eGFP, SCVI114) and three genetically modified cell lines (PM28, PM52, Del33) were differentiated using two monolayer (atrial and ventricular) and two organoid (also atrial and ventricular) differentiation protocols. Cells from multiple samples at differentiation day 15 (wild type cell lines) and day 30 (all cell lines) were isolated, multiplexed using the MULTI-seq approach; subsequently library preparation (10X platform) and sequencing was performed.

overall_design: Single cell sequencing of wild type and Nkx2-5 genetically modified hiPSC derived cells using monolayer and organoid systems at day15 and day30

first: Guang

first: Wei

last: Feng

first: Hannah

last: Schriever

first: Abha

last: Bais


title: The role of mitochondrial calcium in embryonal rhabdomyosarcoma

city: Singapore

first: Reshma

last: Taneja

address: 2 Medical Drive, MD9

department: Physiology

country: Singapore

institute: National University of Singapore

summary: Rhabdomyosarcoma (RMS), the most common paediatric soft-tissue sarcoma, is characterized by cells of skeletal muscle origin that fail to both irreversibly exit the cell cycle and complete skeletal muscle differentiation. Embryonal rhabdomyosarcoma (ERMS) is the most prevalent subtype of RMS and its molecular signatures has been associated with metabolism defects and increased oxidative stress. However, the details of the contributing factors or molecules have not been studied. Both metabolism and oxidative stress are associated with mitochondrial functions and an important molecule that regulates mitochondrial functions is calcium. Till date, there has been no studies that examine the role of mitochondrial calcium in ERMS. In addition, the molecular component of mitochondrial calcium uniporter complex, which is responsible for the uptake of mitochondrial calcium was only discovered in 2012. Since then, there has been an increasing interest in investigating the role of mitochondrial calcium and mitochondrial calcium uniporter complex in various cancers. Mitochondrial calcium uniporter (MCU), the main channel forming protein is often found to be dysregulated in various cancers. Our preliminary data has shown that mitochondrial calcium is dysregulated in ERMS due to overexpression of MCU. This dysregulation of mitochondrial calcium has led to multiple mitochondrial dysfunctions and oncogenic phenotypes. Hence, we would like to investigate the downstream targets of MCU in order to identify the mechanism through which MCU regulates oncogenic phenotypes in ERMS.

overall_design: Examination of downstream targets of MCU through transient MCU knockdown in RD cell line. Triplicates of MCU knockdown cells and control cells were analysed.

first: Hsin

middle: Y

last: Chiu


title: BRB-seq analysis of PFOS disruption of key developmental pathways during hiPSC-derived cardiomyocyte differentiation

status: Public on May 03 2022

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary: Exposure to per- and polyfluoroalkyl substances (PFASs) such as perfluorooctanesulfonic acid (PFOS) has been associated with congenital heart disease (CHD) and decreased birth weight. PFAS exposure can disrupt signaling pathways relevant for cardiac development in stem cell derived cardiomyocyte assays, including PFOS-induced disruption to in vitro cardiac differentiation into contracting spheroids of cardiomyocytes; the PluriBeat assay. Notably, cell line origin can affect how the assay respond to PFAS exposure. Herein, we examine the effect of PFOS on cardiomyocyte differentiation by transcriptomics profiling of two different human induced pluripotent stem cell (hiPSC) lines, to see if they exhibit a common pattern of disruption. Two stages of differentiation, the cardiac progenitor stage (early) and the cardiomyocyte stage (late), were investigated.

overall_design:
Medium from hiPSC-derived cardiomyocyte at day 3 (early stage) and day 7 (late stage) in the human cell line BIONi010-C or IMR90-1 was mixed with either DMSO (vehicle)  6.25 µM, 12.5 µM or 25µM of PFOS.

>>>Submitter states: For patient privacy concerns we can't make the raw data fully public in GEO<<<

first: Frederic

first: Nichlas

last: Davidsen

first: Indusha

last: Kugathas

first: Terje

last: Svingen


title: Genome-wide DNA methylation profiling of GCTB, ABC, CB, NOF, BT, MSC, OB

city: Ulm

first: Julian

middle: Philipp

last: Giesche

address: Albert-Einstein-Allee 23

department: Institute of Pathology

country: Germany

institute: University Hospital Ulm

summary: Genome wide DNA methylation profiling of 16 GCTB tissue samples, 7 GCTB cell lines, 3 chondroblastomas, 3 aneurysmal bone cysts, 3 non-ossifying fibromas, 2 hyperparathyroidism-associated brown tumours, 5 mesenchymal stem cell samples, 6 osteoblast samples. The Illumina Infinium MethylationEPIC BeadChip arrays were used to obtain DNA methylation profiles across approximately 850,000 CpGs.

overall_design: Bisulphite converted DNA from the 45 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChips

first: J

middle: P

first: T

middle: E

last: Barth


title: Investigating the Relationships between Hormones and Critical Substances in Tea Leaves During Withering

city: Hangzhou

first: Xu

last: Ping

state: Zhejiang

address: 866 Yuhangtang Road

department: Tea Research Institute

country: China

institute: Zhejiang University

summary: To investigate the relationships between hormones and critical components in tea leaves during withering process, we detected the alterations of abscisic acid (ABA), salicylic acid (SA), and jasmonic acid (JA), catechins, theanine, and caffeine in tea leaves withered at different time points from 0 to 24 hours. The content of ABA increased from 0h to 9h and decreased thereafter and JA content continuous increased, however, SA content was no significantly changes during withering process. Except for gallocatechin (GC) and epicatechin (EC), the contents of other critical components were significantly reduced at 24h. Transcriptome analysis shown that compared with 0h, a total of 2,256, 3,654, and 1,275 differentially expressed genes (DEGs) were identified at 9h, 15h, and 24h, respectively. The pathways of“Phenylalanine, tyrosine and tryptophan biosynthesis”, and “Phenylalanine metabolism” involved in biosynthesis of catechins were enriched significantly with DEGs of all comparisons. Weighted correlation network analysis (WGCNA) of co-expression genes indicated that many of modules were correlated with a specific trait only, however, the darkolivegreen module were correlated with two traits ABA and theanine during withering process. Our study indicates that withering induced dramatic alteration of the gene transcription, hormones (ABA, JA, and SA) and important components, and ABA may regulate theanine matebolism during this process.

overall_design: The expression profiles of mRNAs during withering process


title: Profiles of Differentially Expressed Long-Noncoding RNAs and mRNAs in Non-alcoholic Fatty Liver Disease Mice

city: Weifang

first: Fengqi

address: Baotong Street

institute: Weifang Medical University

summary: Non-coding RNAs (ncRNAs), including piwi-interacting RNA (piRNAs), circular RNAs (circRNAs) and long ncRNAs (lncRNAs), have been recently emerged as key regulators of pathological process of metabolic diseases. Since previous studies have reported that piRNAs and circRNAs involve in non-alcoholic fatty liver disease (NAFLD), this study was designed to explore more potential regulators of lncRNAs in NAFLD. A NAFLD mouse model was successfully constructed by providing high-fat diet (HFD) for 16 weeks as determined by immunohistology and serology assay. The lncRNAs expression profile including 549 upregulated lncRNAs and 108 downregulated lncRNAs was observed using microarray analysis, which was further confirmed by quantitative real-time Polymerase Chain Reaction (qRT-PCR). Moreover, we identified 308 differentially expressed mRNAs in the NAFLD group. Importantly, the sphingolipid signaling pathway may be significantly enriched pathways closely related to NAFLD using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Further study revealed that lncRNAs and their interacting mRNAs may participate in the pathophysiological process of NAFLD by regulating sphingolipid signaling pathway. Taken together, the current study demonstrated more potential regulators of lncRNAs and the interacting pathways between lncRNAs and mRNAs, which may provide new insights into the pathogenesis of NAFLD.

overall_design: A NAFLD mouse model was successfully constructed by providing high-fat diet (HFD) for 16 weeks as determined by immunohistology and serology assay. The lncRNAs expression profile was observed using microarray analysis, which was further confirmed by quantitative real-time Polymerase Chain Reaction (qRT-PCR). Moreover, we identified differentially expressed mRNAs in the NAFLD group. A pathway was shown closely related to NAFLD using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis.

first: F

first: C

last: Xue

first: X

last: Qiao

first: Y

last: Wang


title: Auricularia auricula polysaccharides reduce obesity in mice through gut commensal Papillibacter cinnamivorans [liver]

first: Luoyi

last: Zhu

address: 866 Yuhang Tang Road

summary: Auricularia auricula is a well-known traditional edible and medicinal fungus with high nutritional and pharmacological values, as well as metabolic and immunoregulatory properties. However, the exact mechanisms underlying the effects of Auricularia auricula polysaccharides (AAP) on obesity and related metabolic endpoints, including the role of the gut microbiota, remain insufficiently understood. To determine the mechanistic role of the gut microbiota in observed anti-obesogenic effects AAP, faecal microbiota transplantation (FMT) and pseudo germ-free mice model treated with antibiotics were also applied, together with 16S rRNA genomic-derived taxonomic profiling. HFD murine exposure to AAP thwarted weight-gains, reduced fat depositing, together with upregulating thermogenesis proteomic biomarkers within adipose tissue. These effects were associated with diminished intestine/bloodstream-borne lipid transportation, together with enhanced glucose tolerance. FMT administered in tandem with antibiotic treatment demonstrated the intestinal microbiota was necessary in deploying AAP anti-obesogenic functions. Intestine-dwelling microbial population assessments discovered AAP to enhance (in a selective manner) Papillibacter cinnamivorans, a commensal bacterium having reduced presence within HFD mice. Notably, HFD mice treated with oral formulations of Papillibacter cinnamivorans diminished obesity and was linked to decreased intestinal lipid transportation. Datasets from the present study show that AAP thwarted dietary-driven obesity and metabolism-based disorders through regulating intestinal lipid transportation, a mechanism that is dependent on the gut commensal Papillibacter cinnamivorans. These results indicated AAP and Papillibacter cinnamivorans as newly identified pre- and probiotics that could possibly serve as novel countermeasure against obesity.

overall_design: Forty-five 6-week-old C57BL/6 mice were randomly divided into 3 groups (15 per group), namely control group (C group), high-fat diet group (HFD group), high-fat diet with gavage of Papillibacter cinnamivorans group (HB group), respectively.

first: Xin

last: Zong

first: Hao

last: Zhang

first: Hui

last: Yang

first: Yizhen

first: Mingliang

last: Jin


title: Auricularia auricula polysaccharides reduce obesity in mice through gut commensal Papillibacter cinnamivorans

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

overall_design: Refer to individual Series


title: Auricularia auricula polysaccharides reduce obesity in mice through gut commensal Papillibacter cinnamivorans [colon]

overall_design: Forty-five 6-week-old C57BL/6 mice were randomly divided into 3 groups (15 per group), namely control group (C group), high-fat diet group (HFD group), high-fat diet with gavage of Papillibacter cinnamivorans group (HB group) , respectively.


title: Integrated analysis of mRNA and miRNA expression in response to interleukin-6 in hepatocytes

city: Brisbane

first: Samuel

last: Lukowski

state: Queensland

address: 306 Carmody Road, St Lucia

country: Australia

institute: Institute for Molecular Bioscience

type: Non-coding RNA profiling by high throughput sequencing

summary:
The interactions between miRNAs and the genes that they regulate during the acute phase response have not been investigated. We examined the effects of IL-6 stimulation on the transcriptome and miRNome of human and mouse primary hepatocytes and the HepG2 cell line.
Using an integrated analysis, we identified differentially expressed miRNAs whose seed sequences are significantly enriched in the 3′ untranslated regions of differentially expressed genes, many of which are involved in inflammation-related pathways.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Integrated analysis of mRNA and miRNA expression (RNAseq and small RNAseq) in response to interleukin-6 in human and mouse primary hepatocytes and the HepG2 cell line

middle: W

first: Marguerite

last: Neerman-Arbez


title: GS ablation leads to elevated mTORC1 activation in mouse livers harboring c-Met/ΔN90-β-catenin

city: piscataway

first: Junrong

last: Yan

state: NJ

address: 164 frelinghuysen road

department: Chemical Biology

institute: Rutgers University

summary: Hepatic GS loss leads to increased mTORC1 signaling and ribosome biogenesis in response to β-catenin activation

overall_design: Seven-week-old GS WT and KO male mice were injected with vehicle or c-Met/ΔN90-β-catenin/SB10 plasmids, and livers were harvested 0, 2 or 3 weeks after the injection for RNA-sequencing analysis

first: Wei-Xing

first: Weiwei

last: Dai

first: Jianliang

last: Shen

first: Yongbo


title: Single-Cell RNA Sequencing Reveals the Impact of Macrophage on Mesangial Cells in Lupus Nephritis Kidney Injury

city: Natong

first: Xi'an

last: Ni

address: Qixiu Road No.19

institute: Nantong University

summary: Single-Cell RNA Sequencing provides a potential solution for exploring the heterogeneity of LN, helping to identify potential biomarkers and drug targets. We analyzed various cell types at the injury site of kidneys by scRNA-seq technology in a mouse LN model and identified different kinds of cell types

overall_design: Isolation of renal cortex of MRL/lpr and C57BL/6 mice ,preparation of cell suspension and analyzed using scRNAseq.

first: Zhanyun

last: Da


title: Generation and gene expression profiles of Grevy’s zebra iPSCs

city: Kyoto Sakyo

first: Yoshinori

last: Endo

state: Kyoto

address: 2-24 Tanaka Sekidencho

country: Japan

institute: Kyoto University

summary: Induced pluripotent stem cells (iPSCs) can provide biological resource for functional and conservation research for various species. However, the understanding of species variations of mammalian iPSCs is still limited. Here, we report the first generation of iPSCs from the endangered species Grevy's zebra (Equus grevyi; gz-iPSCs). We reprogram primary fibroblasts with human reprogramming transcription factors, OCT3/4, SOX2, KLF4, and c-MYC, with the retroviral method and confirmed the pluripotency and differentiation potential. In light of RNA sequencing analysis, generated gz-iPSCs robustly express genes associated with pluripotency and reprogramming processes, including epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions (EMT-MET). Comparative transcriptomics with other species reveals patterns of gene expressions among mammalian PSCs and detects evolutionary conservation of pluripotency-associated genes and plausible importance of translation process. This work will aid in providing biological resource for this endangered species and enables new insight into the evolution of the mammalian PSCs.

overall_design: We analyzed gene expression to characterize Grevy’s zebra iPSCs reprogrammed from primary fibroblasts. Total RNA from Grevy’s zebra iPSCs and fibroblasts, each at three different generations, and RNA-seq were performed using Oxford Nanopore Technologies long-read cDNA sequencing. The sequence reads were mapped to the horse reference genome, EquCab3.0, because reference genome is lacking in the Grevy’s zebra at the time of analysis. The differentially expressed genes were estimated between iPSCs and fibroblasts, and Grevy’s zebra transcriptome was further compared with other mammalian PSCs.

first: Ken-ichiro

last: Kamei

first: Kouichi

last: Hasegawa

first: Keisuke

last: Okita

first: Hideyuki

last: Ito

first: Shiho

last: Terada

first: Miho

last: Inoue-Murayama


title: Bulk RNA-seq profiles of primary AML samples corresponding to existing scRNA-seq data from GSE116256

city: Toronto

first: Andy

last: Zeng

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

summary: The treatment landscape of AML is evolving with promising therapies entering clinical translation, yet patient responses remain heterogeneous and biomarkers for tailoring treatment are lacking. To understand how disease heterogeneity links with therapy response, we determined the leukemia cell hierarchy make-up from bulk transcriptomes of over 1000 patients through deconvolution using single-cell reference profiles of leukemia stem, progenitor, and mature cell types. Leukemia hierarchy composition was associated with functional, genomic, and clinical properties and converged into four overall classes, spanning Primitive, Mature, GMP, and Intermediate. Critically, variation in hierarchy composition along the Primitive vs GMP or Primitive vs Mature axes were associated with response to chemotherapy or drug sensitivity profiles of targeted therapies, respectively. A 7-gene biomarker derived from the Primitive vs Mature axis was predictive of patient response to 105 investigational drugs. Thus, hierarchy composition constitutes a novel framework for understanding disease biology and advancing precision medicine in AML.

overall_design: RNA sequencing was performed on bone marrow aspirates from four AML patients collected at diagnosis (D0). All four AML samples were previously profiled by scRNA-seq in van Galen et al (Cell 2019), thus these data represent matched bulk RNA-seq profiles for scRNA-seq data from GSE116256.

middle: G

first: Peter

last: van Galen

first: John

last: Dick


title: RNA sequencing of patient-derived AML xenografts treated with Selinexor (KPT-330)

overall_design: RNA sequencing was performed on 6 AML patient-derived xenograft samples from 3 AML patients, each treated with either Selinexor (KPT-330) or Vehicle control. Treatment data for these samples was originally reported in Etchin et al (Leukemia 2015).


title: RNA sequencing of patient-derived AML xenografts treated with Fedratinib

overall_design: RNA sequencing was performed on 26 AML patient-derived xenograft samples from 13 AML patients, each treated with either Fedratinib or Vehicle control. Treatment data for these samples was originally reported in Chen et al (Cancer Research 2016). Each patient sample is annotated based on in vivo response to Fedratinib, based on the relative reduction (RR) in leukemic engraftment in drug-treated compared to vehicle-treated mice. Samples were classified as either Responder: RR >50% in injected right femur (RF); Partial-Responder: RR 20%-50% in RF or >20% in non-injected bone marrow (BM) only; Non-Responder: RR <20% in both RF and BM.


title: The molecular response of two Brassica napus cultivars to short-term hypoxia in the root zone

city: Bayreuth

first: Angelika

last: Mustroph

address: Universitaetsstr. 30, NWI

department: Plant Physiology

institute: University Bayreuth

summary: Waterlogging is one major stress for crops and causes multiple problems for plants, for example low gas diffusion, reducing conditions in the soil and accumulation of toxic metabolites. Brassica napus is an important oil crop with high waterlogging sensitivity, which may cause severe yield losses. Its reactions to the stress are not fully understood. In this work the transcriptional response of rapeseed to one aspect of waterlogging, hypoxia in the root zone, was analyzed, including two rapeseed cultivars from different origin, Avatar from Europe and Zhongshuang 9 from Asia. Both cultivars showed a high number of differentially expressed genes in roots after 4 and 24 h of hypoxia. The response included many well-known hypoxia-induced genes such as genes coding for glycolytic and fermentative enzymes. Leaves hardly responded to the root stress after a 24-h-stress treatment, and photosynthesis seemed to be not affected by the stress applied to roots. There was no clear difference in either gene expression or tolerance to waterlogging between the two genotypes used in this study.

overall_design: two Brassica napus cultivars (Avatar, Zhongshuang 9), two timepoints (4 and 24 h), two organs (root, leaf), two treatments (aeration, nitrogen gassing), three replicates


title: RNA sequencing of paired AML samples at diagnosis and relapse

overall_design: RNA sequencing was performed on 22 AML peripheral blood samples collected from 11 AML patients, once at diagnosis and once at relapse following induction of remission by chemotherapy. Samples from patient LDXRX0004 were collected before and after a second remission (“diagnostic” sample was collected after exposure to previous treatment), while samples from all other samples corresponded to the first remission (diagnostic samples are pre-treatment). These samples, with the exception of LDXRX0004, were originally profiled in Shlush et al (Nature, 2017) and annotated for relapse origin class as per the original Shlush et al study.


title: Energy starvation in Daphnia magna from exposure to a lithium cobalt oxide nanomaterial

city: Milwaukee

first: Rebecca

middle: D

last: Klaper

state: WI

address: 600 E Greenfield Ave

department: School of Freshwater Sciences

institute: University of Wisconsin - Milwaukee

summary: We determined lithium cobalt oxide LCO’s effects on pathways in the model organism Daphnia magna through RNA-Seq global gene expression analysis.

overall_design: Examination of LCO exposure effect on gene transcription after 48 hr exposure. 5 replicates each of: no treatement control, LCO 1 mg/L, LCO 10 mg/L, and ion control equivelent to Li and Co released from 10 mg/L LCO at 48 hrs.

first: Nicholas

middle: J

last: Niemuth

first: Becky

last: Curtis

first: Elizabeth

last: Laudadio

first: Jelena

last: Sostare

first: Evan

middle: A

last: Bennett

first: Nicklaus

last: Neureuther

first: Aurash

last: Mohaimani

first: Angela

last: Schmoldt

first: Eric

last: Ostovich

first: Mark

middle: R

last: Viant

first: Robert

last: Hamers


title: RPAP2 regulates a transcription initiation checkpoint by inhibiting assembly of pre-initiation complex

city: Shanghai

first: Aixia

last: Song

address: Dong'an Road

institute: Fudan University

type: Genome binding/occupancy profiling by high throughput sequencing


title: Lysophosphatidylserines derived from microbiota in Crohn’s disease elicit pathological Th1 response

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Microbiota alteration and IFN-γ-producing CD4+ T cell overactivation are implicated in Crohn's disease (CD) pathogenesis. However, it remains unclear how dysbiosis enhances Th1 responses, leading to intestinal inflammation. Here, we identified key metabolites that are derived from dysbiotic microbiota and induce enhanced Th1 responses and severe colitis in mouse models. Patients with CD showed elevated lysophosphatidylserine (LysoPS) concentration in their feces, accompanied with a higher relative abundance of microbiota possessing a gene encoding the phospholipid-hydrolyzing enzyme phospholipase A. LysoPS induced metabolic reprograming, thereby eliciting aberrant effector responses in both human and mouse IFN-?-producing CD4+ T cells. Administration of LysoPS into T cell-dependent mouse colitis models induced severe inflammation. LysoPS-induced aggravation of colitis was impaired in mice lacking P2ry10 and P2ry10b, and their CD4+ T cells were hypo-responsive to LysoPS. Thus, our findings elaborate on the mechanism by which metabolites elevated in patients with CD harboring dysbiotic microbiota induce intestinal pathology.

overall_design:
RNA sequencing was performed on Illumina NovaSeq 6000 for naive_T_cells and HiSeq 2500 platforms for PMA_Iono_LysoPS cells and in 101 and 75-base single-end mode, respectively.
Colonic CD4+ T cells, such as naive T cells, effector T cells, and regulatory T cells were performed RNA sequence analysis.

first: Yuriko

last: Otake

first: Hisako

last: Kayama


title: RNA sequencing of functionally validated LSC fractions in AML

first: Andy

last: Zeng

overall_design: RNA sequencing was performed on 111 AML fractions from 62 primary AML patient samples, sorted on the basis of CD34 and CD38. Each fraction was functionally annotated for LSC activity based on engraftment capability in xenotransplantation experiments, constituting 70 LSC+ (AML engrafting) fractions, 40 LSC- (non-engrafting) fractions, and 1 fraction which initiated normal (non-leukemic) multi-lineage grafts.

first: John

last: Dick


title: Identification of IVIg regulated genes in human peripheral blood B cells by gene expression analysis before and after IVIg infusion in CVID patients [CD20]

city: Madrid

first: Angeles

last: Domínguez Soto

address: Ramiro de Maeztu

country: Spain

institute: CSIC

overall_design: Human peripheral blood B cells from independent CVID patients were isolated by anti-CD20-labeled magnetic microbeads before and after IVIg treatment.Total RNA from each condition was extracted and purified using the RNA isolation kit (Macheray-Nagel). Labelled RNA was used as hybridization probes on human Agilent-072363 SurePrint G3 Human Gene Expression v3 8x60K (G4851C). All experimental procedures were performed following manufacturer instructions. Microarrays were scanned on an Agilent G2539A scanner. Scanned images and raw data were pre-processed with GeneSpring GX (Agilent).

last: Soto

first: Miguel

last: Vega

first: Angel

middle: L

last: Corbí


title: Identification of IVIg regulated genes in human peripheral blood monocytes from Common Variable Immunodeficiency patients (CVID) [CD14+]

summary: Identification of IVIg regulated genes in human peripheral blood monocytes by gene expression analysis before and after IVIg infusion in CVID patients

overall_design: Human peripheral blood monocytes from three independent CVID patients were isolated by anti-CD14-labeled magnetic microbeads before and after IVIg treatment.Total RNA from each condition was extracted and purified using the RNA isolation kit (Macheray-Nagel). Labelled RNA was used as hybridization probes on human Agilent-072363 SurePrint G3 Human Gene Expression v3 8x60K (G4851C). All experimental procedures were performed following manufacturer instructions. Microarrays were scanned on an Agilent G2539A scanner. Scanned images and raw data were pre-processed with GeneSpring GX (Agilent).


title: A cellular hierarchy framework for understanding heterogeneity and predicting drug response in acute myeloid leukemia


title: Identification of IVIg regulated genes in human peripheral blood monocytes by gene expression analysis before and after IVIg infusion in CVID patients [CD3]

overall_design: Human peripheral blood T cells from independent CVID patients were isolated by anti-CD3-labeled magnetic microbeads before and after IVIg treatment.Total RNA from each condition was extracted and purified using the RNA isolation kit (Macheray-Nagel). Labelled RNA was used as hybridization probes on human Agilent-072363 SurePrint G3 Human Gene Expression v3 8x60K (G4851C). All experimental procedures were performed following manufacturer instructions. Microarrays were scanned on an Agilent G2539A scanner. Scanned images and raw data were pre-processed with GeneSpring GX (Agilent).


title: Optimization of the TeraTox assay for preclinical teratogenicity assessment

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

summary: Stem-cell-based in vitro systems are promising tools to predict human teratogenicity. However, current in vitro assays are limited because they either capture effects on a certain germ layer or focus on a subset of predictive markers. Here we report the characterization and critical assessment of TeraTox, a newly developed multi-lineage differentiation assay using 3D human induced pluripotent stem cells. TeraTox probes stem-cell-derived embryoid bodies with two endpoints, one quantifying cytotoxicity and the other inferring the teratogenicity potential with gene expression as a molecular phenotypic readout. To derive teratogenicity potential from gene expression profiles, we applied both unsupervised machine-learning tools including factor analysis, and supervised tools including classification and regression. To identify the best predictive model for the teratogenicity potential that is explainable, we systematically tested 64 machine-learning model architectures and identified the optimal model, which uses the expression of 77 representative germ-layer genes, summarized by 10 latent germ-layer factors, as input for random-forest regression. We combined measured cytotoxicity and inferred teratogenicity potential to predict concentration-dependent teratogenicity profiles of 33 approved pharmaceuticals and 12 proprietary drug candidates with known in vivo data. Compared with the mouse embryonic stem cell test, which has been in routine use for more than a decade, the TeraTox assay shows higher sensitivity, particularly towards teratogens impairing ectodermal development or stem-cell renewal, and a more balanced prediction performance. We envision that further refinement and development of TeraTox has the potential to reduce and replace animal research in drug discovery and to improve preclinical assessment of teratogenicity.

overall_design: Commercial and proprietary compounds are tested in two batches (Run1 and Run2, respectively). Each compound is tested in dose-response (six or twelve points each), and each concentration is tested in two independent biological replicates. Samples are treated in 96-well plates, each containing DMSO controls (up to twelve replicates) and samples treated with one or more compounds.

first: Manuela

last: Jaklin

first: Nicole

last: Schäfer

first: Erich

last: Küng

first: Jitao


title: RNA sequencing of primary AML samples prior to in vivo treatment with Fedratinib

overall_design: RNA sequencing was performed on primary AML samples from 15 AML patients, prior to xenotransplantation and in vivo Fedratinib treatment. Treatment data for these samples was originally reported in Chen et al (Cancer Research 2016). Each patient sample is annotated based on in vivo response to Fedratinib, based on the relative reduction (RR) in leukemic engraftment in drug-treated compared to vehicle-treated mice. Samples were classified as either Responder: RR >50% in injected right femur (RF); Partial-Responder: RR 20%-50% in RF or >20% in non-injected bone marrow (BM) only; Non-Responder: RR <20% in both RF and BM. These samples partially overlap with primary AML RNA-seq profiles from GSE156914.


title: Time-course cellular interactome analysis by single-cell RNA-seq in bleomycin-induced pulmonary fibrosis

status: Public on May 02 2022

city: Kashiwa

first: BIN

last: WU

state: Chiba

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

department: Research

institute: ImmunoGeneTeqs

summary: Pulmonary fibrosis (PF) is an intractable disorder with a poor prognosis. Although multiple cell subsets contribute to the pathogenesis of PF, the entiety of the changes of cell-cell interaction remain unclear. To identify PF pathology-associated changes in cell-cell interaction network, we performed time-course single-cell transcriptome analysis of the single cell suspensiton obtained from the lungs of bleomycin-treated mice.

overall_design: To clarify changes of cellular interactome throughout PF initiation and progression, we isolated lung single cell suspension at 0, 3, 7, 10, 14,and 21 days post-bleomycin administration and performed single-cell RNA-seq by using an BD Rhapsody platform and a Novaseq6000 sequencer.

first: Shigeyuki

last: Shichino

first: Shinichi

last: Hashimoto

first: Shungo

last: Deshimaru

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima


title: Gene expression data from normal endometrium (NE), endometrium with endometriosis (EE) and ovarian endometrioma (OE)

city: Kyoto

first: Toshiyuki

last: Minami

address: 465 Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine,

summary: This study aimed to identify an essential gene in NE, EE and OE.

overall_design: mRNA profiles of 2 patients with NE, 2 patients with EE and 2 pathients with OE

first: Yukiko

last: Tanaka

first: Jo

last: Kitawaki

first: Taisuke

last: Mori


title: mouse retina 10x Genomics Multiome ATAC+RNA data

city: Houston

first: Katy

last: Rezvani

address: Zayed Building, 5th floor 6565 MD Anderson Blvd. Unit 1061 Houston, TX 77030

department: Stem Cell Transplantation & Cellular Therapy department

institute: MD Anderson Cancer Center

summary: Mouse retina is heterogeneous, composed of multiple neuronal and non-neuronal cell types. Among them, bipolar cells (BC), which connect photoreceptors (cones and rods) to inner retina, are traditionally dissected into rare subtypes of subtle functional and morphological differences. While high-resolution single-cell transcriptomic profiles of BCs are availabl, little is known about the corresponding single-cell chromatin landscapes. Although it is now possible to directly generate multiome data, there are often restrictions on cost, feasibility, and data quality. Therefore, integrating single-cell ATAC and RNA profiles obtained independently from the same retina sample may provide an exciting opportunity to comprehensively characterize these rare cell subtypes and discover transcription factors (TFs) important in establishing or maintaining the cell identities

overall_design: We generated coassayed snRNA-seq and snATAC-seq data using the 10x Genomics Multiome ATAC+RNA kit from an adult mouse retina sample.

first: Rui

last: Chen

first: Ken

first: Jinzhang

last: Dou


title: Next generation sequencing transcriptome analysis of patient-derived macrophages after SARS-CoV-2 mRNA vaccination

city: Cologne

first: Richard

middle: James

last: Acton

state: North Rhine-Westphalia

address: CECAD Cluster of Excellence at the University of Cologne, Joseph-Stelzmann-Straße 26

department: Bioinformatics Core

institute: CECAD

summary: Innate immunity triggers responsible for viral control or hyperinflammation in COVID-19 are largely unknown.  Recently we could show that the SARS-CoV-2 spike protein (S-protein) primes inflammasome formation and release of mature interleukin-1β (IL-1β) in macrophages derived from COVID-19 patients but not in macrophages from healthy SARS-CoV-2 naïve individuals (Theobald et al. EMBO Mol Med. 2021). Further analysis revealed that SARS-CoV-2 infection causes profound and long-lived reprogramming of macrophages resulting in augmented immunogenicity of the SARS-CoV-2 S-protein, a major vaccine antigen and potent driver of adaptive and innate immune signaling. In this project we want to focus on novel mRNA vaccines, which are exploiting S-protein driven immunogenicity for protection against SARS-CoV-2. Transcriptome analyses of macrophages might reveal differences in innate immune-associated pathways between vaccinated and unvaccinated individuals after prime-boost. Thus, our project could help to gain a better understanding of vaccine-induced immunity including underlying molecular mechanisms in the interaction of the innate and adaptive immune system after mRNA-based SARS-CoV-2 vaccination.

overall_design: Macrophages of vaccinated (n = 6) and unvaccinated (n = 6) individuals were stimulated with SARS-CoV-2 spike protein (S-protein), lipopolysaccharide (LPS) or left unstimulated. All experiments were performed in technical triplicates. In total 36 samples are provided (3 conditions (unstimulated, LPS and S-protein) from 12 different individuals (6 vaccinated; 6 unvaccinated). LPS is a classical PAMP, known for its strong activation of inflammasome/inflammation-associated pathways and it's used in our experiments as control for activation of the inflammation-associated genes and pathways. Recombinant SARS-CoV-2 spike protein is used in our experiments to mimic reexposition with SARS-CoV-2 mRNA vaccine, which is based on the spike protein production by the host or SARS-CoV-2 infection. To get a deeper understanding of spike protein induced immunity we would like to analyze differences in gene expression of macrophages from vaccinated vs unvaccinated inidividuals exposed to the different stimuli (unstimulated, LPS, S-protein). Moreover we would like to compare differences within the two groups (vaccinated or unvaccinated) in response to LPS or S-protein.

first: Jan

last: Rybniker

first: Alexander

last: Simonis

first: Julie

last: Mudler

first: Sebastian

last: Theobald


title: Single cell RNA sequencing of in vitro generated monocyte-derived macrophage subsets

city: Biberach an der Riss

first: Madhura

middle: Meghsham

last: Modak

address: Birkendorfer Strasse 65

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

summary: Analysis of three subsets of monocyte-derived macrophage generated using various differentiation cocktails: M1 (IFN-γ+LPS), M2a (IL-4+IL-13) and M2c (IL-10).

overall_design: Untouched monocytes were isolated from the PBMC of two healthy donors. Monocytes were then differentiated to M0 macrophages upon culturing monocytes with M-CSF (100ng/ml) for 6 days. On day 6 M0 macrophages were further stimulated with differentiation cocktail for 24 hour to obtain three different subsets of monocyte-derived macrophages namely M1 (stimulated with IFN-γ+LPS), M2a (stimulated with IL-4+IL-13) and M2c (stimulated with IL-10).

first: Ann-Kathrin

last: Mattes

first: Daniela

last: Reiss

first: Wioletta

last: Skronska-Wasek

first: Rebecca

last: Langlois

first: Nicolas

last: Sabarth

first: Renate

last: Konopitzky

first: Fidel

last: Ramirez

first: Katharina

last: Lehr

first: Tobias

last: Mayr

first: David

last: Kind

first: Coralie

last: Viollet

first: Lee

middle: K

last: Swee

first: Jutta

last: Petschenka

first: Karim

middle: C

last: El Kasmi

first: Elfriede

last: Noessner

first: Kerstin

last: Kitt

first: Stefan

last: Pflanz


title: BMDC treated with I-BET151 and sitmulated with IgG immune complex

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

summary: Bone marrow derived dendritic cells were cultured and stimulated with I-BET151 or DMSO control, and stimulated with Ovalbumin-IgG immune complex or Ovalbumin control.

overall_design: BMDC from wild-type C57BL/6 mice

first: Colin

last: Lee

first: Gemma

last: Banham

first: Menna

last: Clatworthy


title: Whole genome sequencing of WT, ccrZ deletion, and overexpressed ccrZ in Bacillus subtilis

city: Ann Arbor

first: Lyle

middle: A.

last: Simmons

state: MI

address: 1105 N. University Ave.

department: Molecular, Cellular, & Developmental Biology

institute: University of Michigan

summary: We obtained whole genome sequencing data as a measure of chromosome replication to see if deletion or overexpression of ccrZ altered replication initiation

first: Katherine

last: Wozniak


title: A male pheromone that improves quality of the oogenic germline

city: Medford

last: Angeles-Albores

state: MA

address: 61 Locust St

institute: Northwestern University

summary: Pheromones exchanged by conspecifics are a major class of chemical signals that can alter behavior, physiology, and development. In particular, males and females communicate with potential mating partners via sex pheromones to promote reproductive success. Physiological and developmental mechanisms by which pheromones facilitate progeny production remain largely enigmatic. Here we describe how a C. elegans male pheromone, ascr#10, improves the oogenic germline. Before most signs of aging become evident, C. elegans hermaphrodites start producing lower quality gametes characterized by abnormal morphology, increased rates of chromosomal nondisjunction, and higher penetrance of deleterious alleles. We show that exposure to the male pheromone substantially ameliorates all of these defects and reduces embryonic lethality. ascr#10 stimulates proliferation of germline precursor cells in adult hermaphrodites. Greater precursor supply increases physiological germline cell death, which is required to improve oocyte quality in older mothers. The hermaphrodite germline is sensitive to the pheromone only during a time window, comparable in duration to a larval stage, used by the pre-reproductive adults to assess suitability of the environment for reproduction. Our results identify developmental events that occur in the oogenic germline in response to a male pheromone. They also suggest that the opposite effects of the pheromone on gamete quality and organismal longevity arise from a competition over resource allocation between soma and the germline.

overall_design: The study is a two-factor design (two animal ages, and exposure to placebo or ascaroside) sequenced using single-end Illumina reads. Three samples are provided for the each of the 50hr placebo/ascr conditions; there are a total of six  samples for each of the 58hr placebo/ascr conditions; half  of these were collected concurrently along with the 50hr timepoints, but due to insufficient sequencing depth the 58hr samples were collected and sequenced again

first: Erin

middle: Z

last: Aprison

first: Svetlana

last: Dzitoyeva

first: Ilya

last: Ruvinsky


title: An intersegmental single-cell profile reveals aortic heterogeneity [aorta]

city: Jinan

first: Liwen

last: Yu

state: Shandong province

address: No.107, Wen Hua Xi Road

institute: Shandong University

summary: The continuous inter-segmental aortic profile has been rarely reported at the single-cell level. To reveal aortic heterogeneity, we identified 15 cell subtypes from five continuous aortic segments by marker genes and functional definitions. In conclusion, our study provides a more comprehensive segmental single-cell transcriptome of the aorta at the physiological level, inspiring new ideas for diagnosis and intervention targets in the pathogenesis of aortic diseases. Furthermore, a novel construction system of VSMCs was proposed to replace the traditional classification.

overall_design: a segmental transcriptome of aortic cells from five male wild-type C57BL/6 mice

first: Meng

last: Zhang


title: mRNA bisulfite-sequencing of pancreatic cancer cells

city: Tainan City

first: Po-Hsien

last: Huang

address: No.1, University Road

department: Biochemistry and Molecular Biology

institute: National Cheng Kung University

type: Methylation profiling by high throughput sequencing

summary: 5-methylcytosine sites of mRNA in BxPC-3, PANC1, and MiaPaCa-2 pancreatic cancer cells  at the single-base resolution by whole-transcriptome bisulfite sequencing.

overall_design: Mapping of mRNA 5-methylcytosine sites by bsRNA-seq in the NSUN2 knockdown versus the control cells.

first: Szu-Ying

last: Chen


title: Identification of IVIg regulated genes in human peripheral blood mononuclear cells from Common Variable Immunodeficiency patients (CVID) [PMBC]

first: Angeles

last: Domínguez Soto

summary: Identification of IVIg regulated genes in human PBMC by gene expression analysis before and after IVIg infusion in CVID patients.

overall_design: Human peripheral blood mononuclear cells  from four independent CVID patients were isolated before and after IVIg treatment.Total RNA from each condition was extracted and purified using the RNA isolation kit (Macheray-Nagel). Labelled RNA was used as hybridization probes on human Agilent-072363 SurePrint G3 Human Gene Expression v3 8x60K (G4851C). All experimental procedures were performed following manufacturer instructions. Microarrays were scanned on an Agilent G2539A scanner. Scanned images and raw data were pre-processed with GeneSpring GX (Agilent).

last: Soto

first: Miguel

last: Vega

first: Angel

last: Corbí


title: Data

city: London

first: Kerri

last: Kinghorn

state: London

address: Gower Street

department: Genetics, Evolution and Environment

institute: University College London (UCL)

summary: data

overall_design: data

first: Magda

last: Dias Pereira Atilano


title: Identification of temperature-sensitive (TS) p53 mutations and potassium antimony tartrate (PAT)-treatable p53 mutations in mammalian U937 (free of endogenous p53) cells using a systematic p53 mutation library

first: Yigang

last: Tang

address: No 197 RUIJIN ER RD

institute: Shanghai Jiaotong University

summary: To identified TS p53 mutations and PAT-treatable p53 mutations in mammalian U937 cells.

overall_design: 827 plasmids encoding p53 with either 815 frequent missense mutations, 6 truncation mutations (E11stop, P98stop, P151stop, P152stop, A159stop, P177stop), or 6 synonymous mutations (P151P, G154G, A159A, P177P, G244G, R282R) were stably expressed in U937 cells. This cell library was treated with 0, 5, 10 μM PAT or sub-physiological temperature (32 ℃) for 7 days, followed by p53 variant abundance using next-generation sequencing.

first: Huaxin

last: Song

first: Min

last: Lu


title: RNA-seq profiling of tubulointerstitial tissue reveals a potential therapeutic role of dual anti-phosphatase 1 in kidney diseases

city: Seoul

first: Sehoon

last: Park

address: Daehak-ro 101

country: South Korea

institute: Seoul National University Hospital

summary: We profiled manually microdissected tubulointerstitial tissue from 43 IgA nephropathy, 3 diabetes mellitus nephropathy, 3 focal segmental glomerulosclerosis, 3 lupus nephritis, 4 membranous nephropathy, and 9 minimal change disease biopsy cores and 22 nephrectomy controls by RNA sequencing. The 3 outliers which were not included in our main analysis were also uploaded in this database.

overall_design: RNA-seq profiling for manulaly microdissected tubulointerstitial tissue from 90 kidney samples.

first: Hajeong

last: Lee

first: Seung

last: Yang

first: Dong

last: Kim

first: Sangmoon

first: Jeongha

first: Murim

last: Choi


title: Single-Cell RNA-Sequencing of potassium antimony tartrate (PAT)-treated PBMCs with p53-V272M  derived from an AML patient

summary: The goals of this study are to compare transcriptome of  p53-V272M rescued by PAT in primary AML PBMCs

overall_design: PBMCs with predominant p53-V272M clones treated with or without 5 μM PAT for 24 hr in vivtro

first: Feng

last: Liu


title: CTCF blocks anti-sense transcription initiation at divergent gene promoters [ChIP-Seq]

city: Philadelphia

first: Jing

last: Luan

address: 3615 Civic Center Blvd, ARC 315

institute: University of Pennsylvania

summary: Transcription is typically divergent, initiating at closely spaced oppositely oriented core promoters to produce sense and unstable upstream antisense transcripts (uasTrx). How antisense transcription is regulated and coordinated with sense transcription is largely unknown. Here by combining acute degradation of the multi-functional transcription factor CTCF and nascent transcription measurements, we find that CTCF specifically suppresses antisense but not sense transcription at hundreds of divergent promoters, the great majority of which bear proximal CTCF binding sites. Genome editing, chromatin conformation studies and 5’ transcript mapping revealed that CTCF directly suppresses uasTrx initiation in manner independent of its chromatin architectural function. Primary transcript RNA FISH revealed co-bursting of sense and anti-sense transcripts is disfavored, suggesting CTCF-regulated competition for transcription initiation. In sum, CTCF shapes the noncoding transcriptional landscape by suppressing upstream antisense transcription.

overall_design: Transient endogenous CTCF/Nipbl depletion coupled with genome wide RNA Pol II binding profiling (ChIP-seq) and nascent transcription quantification (PRO-seq)

first: Gerd

last: Blobl


title: CTCF blocks anti-sense transcription initiation at divergent gene promoters

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

overall_design: Refer to individual Series


title: BMDM treated with I-BET151 and sitmulated with IgG immune complex

first: John

last: Ferdinand

summary: Bone marrow derived macrophages were cultured and stimulated with I-BET151 or DMSO control, and stimulated with Ovalbumin-IgG immune complex or Ovalbumin control.

overall_design: BMDM from wild-type C57BL/6 mice

first: Colin

middle: Y

first: Gemma

last: Banham

first: Menna

last: Clatworthy


title: Antibody-mediated blockade of the IL-23 receptor destabilizes intratumoral regulatory T cells and enhances immunotherapy

city: Boston

first: Andrew

last: Wight

address: 450 Brookline Ave

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

summary: Regulatory T cells (Treg) can impede anti-tumor immunity and currently represent a major obstacle to effective cancer immunotherapy. Targeting tumor-infiltrating regulatory Treg while sparing systemic Treg represent optimal approaches to this problem. Here, we provide evidence that the interleukin 23 receptor (IL23R) expressed by tumor-infiltrating Treg promotes suppressive activity. Disruption of the IL23R results in increased responsiveness of destabilized Treg to the IL-12 cytokine, production of g-interferon (IFNg) and recruitment of CD8 T cells that inhibit tumor growth. Since the Treg destabilization pathway that is initiated by IL23R blockade is distinct and independent from the destabilization pathway coupled to Glucocorticoid-Induced TNFR-Related protein (GITR) activation, we examined the impact of coordinate induction of the two destabilization pathways on anti-tumor immune responses. Combined GITR and IL23R antibody treatment of mice inoculated with MC38 tumors resulted in robust and synergistic anti-tumor responses. These findings indicate that delineation of independent Treg destabilization pathways may allow improved approaches to the development of combination immunotherapy for cancers.

overall_design: 4 replicates of spleen and tumor-infiltrating Treg from WT (IL23RWT/WT FoxP3Cre) and 3 replicates of Treg-specific KO (IL23RFlox/Flox FoxP3Cre) (14 samples total). In all cases, comparisons are between Flox and WT samples within the same tissue type.

first: Harvey

middle: I

last: Cantor


title: Murine Kras mutant or Kras wildtype cancer cell lines

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

summary: Comparison of gene expression in murine Kras mutant (LLC, AE17, MC38, FULA1)  and Kras wildtype cell lines (B16F10, PANO2, CULA). First gene expression of benign cells and tissue ( BMDM, TEC, LUNG, BMMC) was subtracted from both Kras mutant or Kras wildtype gene expression profiles. Second Kras mutant gene expression was compared to Kras wildtype gene expression. Cell lines expressing genetically modified Kras gene were included in the analysis. Genetic modification was either done by overexpression of mutant KRAS harboring a G12C mutation  or silencing with shRNA targeting Kras. shControl cell lines were used also as wildtype samples in different analysis presented in the manuscript except MC38 ( run on chip MoGene_1.0).

overall_design: Compare differential gene expression between mouse cancer cells with Kras mutation and mouse cancer cells without Kras mutation.

first: Kristina

last: Arendt

first: Mario

last: Pepe

first: G


title: An intersegmental single-cell profile reveals aortic heterogeneity [AAA]

first: Liwen

last: Yu

summary: According to the new scRNA-seq data after batch correction, we obtained 22, 975 cells totally isolated from aortic tissues of three groups including healthy abdominal aorta group (AA group), Ang II+ DMSO group (D_A group) and Ang II+ Inhibitor group (IN_A group)

overall_design: Single-cell analysis of Ang II-induced AAA with DMSO or inhibitor

first: Meng

last: Zhang


title: Identification of N6-methyladenosine (m6A) modification in sweet sorghum under salt stress

last: Sui

state: Shandong

address: Wenhua East Road

department: College of Life Sciences

institute: Shandong normal university

summary: The N6-methyladenosine (m6A) modification is the most common internal post-transcriptional modification, with important regulatory effects on RNA export, splicing, stability，and translation. However, the effects of m6A modifications on the resistance of sweet sorghum to salt stress remain unclear. In this study, we mapped the m6A modifications in two sorghum inbred lines (salt-tolerant M-81E and salt-sensitive Roma) that differ regarding salt tolerance. Dynamic changes to m6A modifications in sweet sorghum were identified in response to salt stress. Our data suggest that the differences in the m6A modifications between salt-tolerant and salt-sensitive sweet sorghum might contribute to the diversity in salt tolerance.

overall_design: m6A modifications in two sweet sorghum strains were identified in response to salt stress

first: Hong

middle: X

last: Zheng

first: Xi

last: Sun


title: AML1-ETO induced leukemia stem cell self-renewal depends on Plcg1

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

institute: Charité Universitätsmedizin Berlin

summary: Leukemia stem cells are characterized by aberrant self-renewal capacity. Targeting oncogenic fusions that mediate this aberrant self-renewal capacity remains a therapeutic challenge. The t(8;21) translocation, resulting in the oncogenic fusion AML1-ETO (AE, RUNX1-RUNXT1) is among the most common chromosomal rearrangements found in acute myeloid leukemia (AML). By conducting high-resolution proteomic analysis on myeloid leukemia stem cells we identified Phospholipase C- and Ca++-signaling pathways to be differentially regulated in AE/t(8;21) AML. Phospholipase C gamma 1 (Plcg1) was specifically, and highly expressed in t(8;21) AML and could be identified as a direct target of the AML1(RUNX1)-ETO fusion. Genetic inactivation of Plcg1 resulted in abrogation of disease initiation by AE, reduction of intracellular Ca++ release and loss of AE-driven self-renewal programs. Plcg1 deletion after onset of AE-induced leukemia significantly reduced disease penetrance, number of leukemia stem cells and resulted in abrogation of leukemia development in secondary recipients. Inactivation of Plcg1 in human AE-positive AML cells by RNAi reduced colony formation and AML development in vivo. In contrast, Plcg1 was dispensable for steady state hematopoiesis and maintenance of murine and human hematopoietic stem cells (HSC). Translationally, we used pharmacologic inhibition of Ca++ signaling downstream of Plcg1 in AE-driven AML and this resulted in impaired proliferation and self-renewal capacity. The Plcg1 pathway represents a novel, specific vulnerability of AE-driven leukemia and represents an important new therapeutic target.

overall_design: mRNA profiles of Plcg1 -/- in AML1-ETO9a stem cells (LCSs) were generated using SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) and Nextera XT Kit (Illumina) followed by sequencing with 50 bp single-end reads on HiSeq 2000.

first: Florian

last: Heidel

first: Lars

last: Bullinger

first: Tina

last: Schnöder


title: KMT2C methyltransferase domain regulated INK4A expression suppresses prostate cancer metastasis

city: Vienna

first: Tanja

last: Limberger

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

summary: Frequent truncating mutations of the histone lysine N‑methyltransferase KMT2C have been detected by whole exome sequencing studies in various cancers, including malignancies of the prostate. However, the biological consequences of these alterations in prostate cancer have not yet been elucidated. To investigate the functional impact of these mutations we deleted the C-terminal catalytic core motif of KMT2C specifically in the prostate epithelium of mice. We show here that impaired KMT2C methyltransferase activity drives proliferation and, when combined with loss of the tumour suppressor PTEN, triggers metastatic dissemination and reduces life expectancy. In our model system and human prostate cancer samples we show that KMT2C-mutated tumours activate the proliferative MYC signalling axis and fail to express the oncogene-induced cell cycle repressor p16INK4A. In addition, we observe a striking reduction in disease-free survival of patients with KMT2C-mutated prostate cancer. Thus, we identify truncated KMT2C as a driver of aggressive prostate cancer.

overall_design: mRNA expression profiles of prostate epithelial cells derived from 19-week-old mice with prostate specific deletion of Pten (P), Kmt2c SET domain (K), both (D) or neither (W).

first: Lukas

last: Kenner


title: Transcriptome analysis of mutant p53 rescued by potassium antimony tartrate (PAT)

city: Shanghai

first: Yigang

last: Tang

summary: The goals of this study are to compare transcriptome of mutant p53 rescued by PAT.

overall_design: Treat isogenic U937 (p53-/-) cells (infected with p53-V272M, p53-R273H) with PAT. U937 cells infected with wild-type p53 and vector are as positive and negative control, respectively.

first: Min

last: Lu


title: CTCF blocks anti-sense transcription initiation at divergent gene promoters [PRO-Seq]

first: Jing

last: Luan

first: Gerd

last: Blobl


title: Ultraviolet light induces HERV expression to activate RIG-I signaling pathway in keratinocytes

status: Public on May 01 2022

city: Changsha

first: Xiaoli

last: Min

state: Hunan

address: Nor.139 of Furong street

department: Second Xiangya Hospital

institute: Central South University

summary: Skin inflammation and photosensitivity are common in lupus erythematosus (LE) patients, and Ultraviolet (UV) light is a known trigger of skin and possibly systemic inflammation in systemic lupus erythematosus (SLE) and discoid lupus erythematosus (DLE) patients. Type I interferons (IFN) are upregulated in LE skin after UV exposure, however, the mechanisms to explain UVB-induced inflammation remain unclear. Here we performed RNA-seq to HaCat cells with UVB irradiation to characterize gene expression and resolve differential responses of keratinocytes, in order to understand how the keratinocyte response contributes to the disease. Our data showed that HERVs and RIG-I pathway were activated in keratinocytes after UVB exposure and indicate that RIG-I pathway and HERVs are involved in proinflammatory by activating the I-IFN pathway, which provide a novel insight into how UVB promotes and aggravate skin lesion of LE patients.

overall_design: mRNA prifules of HaCat cells exposed with or without UVB

first: Meiling

first: Yaqian

first: Jiali

last: Wu

first: Qiqi

last: Kuang

first: Zhi

last: Hu

first: Lianlian

last: Ouyang

first: Shuang

first: Ming

last: Zhao


title: MOZ and Menin-MLL Complexes are Complementary Regulators of Chromatin Association and Transcriptional Output in Gastrointestinal Stromal Tumor

city: Worcester

first: Matthew

last: Hemming

address: 364 Plantation Street

institute: UMass Medical School


title: Adaptive immune response that restrains ALV

city: Houston

first: Ningbo

last: Zheng

state: Texas

address: 3455 Cullen Blvd

institute: University of Houston

summary: To determine the underlying mechanism within tumor-specific TMV cells that eliminates solid tumors with antigen heterogeneity, we used RNA-seq to analyze the global RNA expression of tumors

overall_design: B16 cells were s.c. injected both flanks of the mice. Indicated treatments were administrated on day 7 when tumors reached ~7×6 mm. Adjuvant CTX (i.p.) was administered to mice one day before ACT. In group 3, free MV was intratumorally injected only into the left tumors [refers to ‘MV (L. i.t.)’], and right tumors did not receive intratumorally injection [refers to ‘remote tumor (no MV)’]. Tumor tissues (~100 mg/mice, 12 days after ACT) were harvested. Total RNA was extracted from the tumor tissues for RNA-Seq (n=2).

first: Yong


title: RNAsequence study of gene expression in lymph nodes after treatment of C57BL/6j mice with vitamin D3-hydroxyderivatives

city: Birmingham

first: Andrzej

last: Slominski

state: AL

address: 1720 2nd Avenue South

department: Dermatology

institute: UAB

summary: The goal of the study was comparison of the gene expression profile in lymph nodes of the C57BL/6j female and male mice treated in vivo with vitamin D3-hydroxyderivatives in relation to the ethanol treated control

overall_design: Methods: RNA sequence was performed by BGI company using RNA isolated from lymph nodes of female and male C57BL/6j mice treated with 20(OH)D3 and 25(OH)D3 at a dose of 4 µg/kg b.w./daily for 1 week. The control female and male mice were treated with EtOH for 1 week as a vehicle.

first: Xu

last: Hui

first: Joanna

last: Stefan

first: David

last: Crossman


title: Concurrent stem- and lineage-affiliated chromatin programs precede hematopoietic lineage restriction

city: Lund

first: Göran

last: Karlsson

state: Scania

address: Kilinkgatan 26 BMC B12

department: Division of Molecular Hematology

country: Sweden

institute: Lund University

summary: The emerging notion of hematopoietic stem- and progenitor cells (HSPCs) as a low-primed cloud without sharply demarcated gene expression programs raises the question on how cellular fate options emerge, and at which stem-like stage lineage priming is initiated. Here we investigated single-cell chromatin accessibility of Lineage-, cKit+, Sca1+ (LSK) HSPCs spanning the early differentiation landscape. Application of a signal-processing algorithm to detect transition points corresponding to massive alterations in accessibility of 521 transcription factor-motifs revealed a population of LSK FMS-like tyrosine kinase 3(Flt3)intCD9high cells that concurrently display stem-like and lineage-affiliated chromatin signatures pointing to simultaneous gain of both Lympho-Myeloid and Megakaryocyte-Erythroid programs. Molecularly and functionally, these cells position between stem cells and committed progenitors, display multi-lineage capacity in vitro and in vivo, but lack self-renewal activity. This integrative molecular analysis resolves the heterogeneity of cells along hematopoietic differentiation trajectories, and permits investigation of chromatin-mediated transition between multipotency and lineage restriction.

overall_design: Single-cell ATAC-Seq and single cell RNA-Seq

first: Fatemeh

last: Safi

first: Parashar

last: Dhapola

first: Ram Krishna

last: Thakur


title: An alternatively spliced variant of METTL3 mediates tumor suppression in hepatocellular carcinoma

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

summary: Many steps of post-transcriptional mRNA processing have shown crucial roles in the tumorigenesis and progression of cancers, such as the N6-methyladenosine (m6A) modification and alternative splicing. Up-regulation of METTL3, the catalytic core of the m6A methyltransferase complex, increases the m6A levels and results in significant effects on the progression of hepatocellular carcinoma (HCC). However, alternative splicing of METTL3 has not been fully investigated and functions of its splice variants remain unclear. Here, we first analyze online and our transcriptomic data and obtain 13 splice variants of METTL3 besides the canonical full-length METTL3-A in HCC cell lines and tissues. Validated by RT-qPCR, we find that METTL3-D, one of the splice variants expressing a truncated METTL3 protein, exhibits higher levels than the METTL3-A in normal human livers but lower levels in HCC tumor tissues and cell lines. Further functional assays demonstrate that expression of METTL3-D decreases the cellular m6A modification, inhibits the proliferation, migration and invasion of HCC cells, and is negatively associated with the malignancy of patient tumors, exhibiting an opposite function as the full-length METTL3-A does. Analyses of TCGA data also show that HCC patients with higher levels of METTL3-D have longer survivals. This study demonstrates that the METTL3-D splice variant is a tumor suppressor, and it could be used as a potential target for the therapy of HCC.

overall_design: mRNA sequence of HepG2 cell line

first: Rui-Yao

last: Xu

first: Wei

last: Shao


title: Expression data from ORC1 or ORC2 mutant cell lines

city: Charlottesville

first: Anindya

last: Dutta

state: Virginia

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: Analysis of ORC mutant HCT116 p53-/- cell lines. Results identify the involvment of ORC protein in the regulation of gne expression

overall_design: RNA was extracted from ORC mutant cell lines and  hybridized to Affymetrix microarrays

first: Etsuko

last: Shibata

first: Yoshiyuki


title: MOZ and Menin-MLL Complexes are Complementary Regulators of Chromatin Association and Transcriptional Output in Gastrointestinal Stromal Tumor [RNA-seq]

first: Matthew

summary: Gastrointestinal stromal tumor (GIST) is commonly characterized by activating mutations in the receptor tyrosine kinase KIT. Tyrosine kinase inhibitors are the only approved therapy for GIST, and other complementary treatment strategies are urgently needed. As GIST both lacks oncogene amplification and relies upon an established network of transcription factors, we hypothesized that unique chromatin modifying enzymes are essential in orchestrating the GIST epigenome. Here, we identified through genome-wide CRISPR screening that MOZ and Menin-MLL chromatin regulatory complexes are cooperative and unique dependencies in GIST. These complexes were enriched at GIST-relevant genes and regulated their transcription. Inhibition of MOZ and Menin-MLL complexes decreased GIST cell proliferation by disrupting interactions with transcriptional regulators, such as DOT1L. Menin inhibition caused significant reductions in tumor burden in xenograft models, with superior effects observed in combination with imatinib. These results define unique chromatin regulatory dependencies in GIST and identify therapeutic strategies for clinical application.

overall_design: RNAseq of GIST cell lines and xenografts


title: Zfp335 establishes neonatal immune tolerance through safeguarding effector Treg lineage commitment and maintenance

city: Xi'an

first: baojun

last: zhang

state: --- Select One ---

address: No.76, West Yanta Rd

institute: xi'an jiaotong university

summary: Regulatory T (Treg) cells are crucial for maintaining peripheral immune tolerance and preventing destructive autoreactive responses, but how heterogeneous Treg populations establish tolerant status remains unclear. Here, we found that Zinc finger protein 335 (Zfp335) is indispensable for the differentiation and maintenance of effector Treg (eTreg) population and immunological self-tolerance in neonates.Mice with Zfp335 deletion in Treg cells exhibit early-onset autoimmune disease with severe inflammation in multiple organs and unrestricted activation and expansion of conventional T cells.

overall_design: Examination of CD4+CD25+ Tregs from the spleens of WT and Zfp335 deficient mice

first: Baojun

last: Zhang

first: Xin

last: Wang

first: Lina

last: Sun

first: Cangang


title: RNA sequencing of tumor tissue from DAOY xenograft study

city: Stockholm

first: Malin

last: Wickström

address: Tomtebodavägen 18a

department: Department of Women's and Children's health

institute: Karolinska institutet

summary: The embryonic brain tumor medulloblastoma is a highly malignant tumor of the cerebellum and the most common CNS malignancy of childhood and multimodal treatment has improved the survival rates considerably. Unfortunately, the intense treatment often leads to neurological morbidity and the risk of a resistant relapse is significant and therefore improvement of the treatment regiments is needed to increase the survival rates and reduce the late side effects. Our study shows that the ω3-fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) decreased medulloblastoma cell viability and colony forming ability dose-dependently and furthermore, treatment with DHA-oil reduced tumor growth in a medulloblastoma xenograft study. Additionally, DHA decreased prostaglandin E2 (PGE2) production from medulloblastoma cells in vitro and PGE2 and prostacyclin were significantly decreased in tumor tissue from ω3-fatty acid treated mice compared to control animals. RNA sequencing showed 10 commonly downregulated genes (CRYAB, CASQ1, MYH13, ATP2A1, POTEI, APOBEC2, CKM, TNNC2, MYLPF, PVALB) in tumors from mice revieving treatment with DHA alone or in combination with EPA.

overall_design: Medulloblastoma cell line DAOY were implanted on the flank of nude mice and randomized into three groups: treatment with docosahexaenoic acid (DHA)- or a combination of DHA and Eicosapentaenoic acid (EPA) or control eating ordinary chow. Bulk RNA sequencing was performed on fresh frozen tumors from the study. The Illumina TruSeq Stranded mRNA sample preparation protocol was used to construct libraries suitable for Illumina sequencing and then sequenced on the Illumina Nextseq 550 for a 75-cycle v2 sequencing run generating 75 bp single-end reads.

first: Linda

last: Ljungblad

first: Thale

last: Olsen


title: 2-arachidonoyl glycerol (2-AG) modulated miRNAs expression in human cholangiocarcinoma

city: Guangzhou

first: Li

last: Huang

state: Guangdong

address: Zhongshan NO.2 Road

department: Pancreatobiliary surgery

institute: The first affiliated hospital, Sun Yat-sen University

summary: The endocannabinoid system (ECS) is dysregulated in various liver diseases. Biliary tract cancers (BTCs) encompass gallbladder carcinoma, intrahepatic, perihilar and distal cholangiocarcinoma. Previously we have shown that the two major endocannabinoids (ECs), anandamide (AEA) and 2-arachidonoyl glycerol (2-AG) exerted opposing effects on BTCs cell lines in which 2-AG promoted tumor proliferation. The underlying mechanism and regulation of 2-AG on miRNAs expression in BTCs remain inconclusive.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In the presented study, human cholangiocarcinoma cell line RBE were treated with 2-AG(10μM) or DMSO respectively for 14 days and reagents were replaced every 48 hours.


title: Transcriptional profiling of primary prostate tumor in metastatic hormonesensitive prostate cancer and association with clinical outcomes: correlative analysis of the E3805 CHAARTED study

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

summary: Gene expression study of the ECOG 3805 randomized controlled trial

overall_design: Retrospective analysis of 160 tumor transcriptomes from ECOG 3805.

first: A

last: Hamid

first: H-C

first: V

first: Y-H

last: Chen

first: F

middle: F

last: Felix

first: B

last: Robert

first: G

last: Attard

first: E

middle: M

last: Van Allen

first: P

last: Tran

first: D

middle: E

last: Spratt

first: R

last: Dittamore

last: Liu

last: DiPaola

first: M

last: Carducci

first: C

last: Sweeney


title: Bone metabolism-related serum miRNAs to diagnose postmenopausal osteoporosis in middle-aged and elderly women

first: Shengli

last: Zhao

address: No.58, Zhong Shan Er Lu.

department: Department of Spine Surgery

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

summary: Serum miRNAs could be powerful classifiers for the detection of patients with postmenopausal osteoporosis.

overall_design: Circulting miRNA profiles of 10 samples consisted of 6 postmenopausal osteoporosis patients and 4 postmenopausal without osteoporosis controls.

first: Bailing


title: Bulk RNA sequencing of chow diet mouse hepatocytes treated with iron chelator (DFO) and chow diet mouse hepatic stallete cells treated with iron

city: SAN DIEGO

first: gaowei

last: wang

state: CALIFORNIA

address: 3393 Lebon DR, APT 202

institute: University of California San Diego

summary: The goals of this study are to compare transcriptome profiling (RNA-seq) on iron of hepatocytes and stellate cells. Methods:  mRNA profiles of wild-type (WT) NCD hepatocytes treated with or without DFO (100 uM) (n=6) and WT chow diet stellate cells treated with or without iron were generated by deep sequencing,

overall_design: Samples for analysis were obtained from chow diet mouse and seeded into plates as indicated. 24 hours later, mediums were changed with the indicated treatment. Cells were collected after 24 hour treatment for RNA isolation.

first: Hong

last: Gao

first: Wei

last: Ying


title: A human blood-derived microRNA facilitates flavivirus infection in fed mosquitoes [S0]

city: Beijing

first: Yibin

last: Zhu

address: Tsinghua, Beijing, China

institute: Tsinghua University

summary: We report that the mosquito small RNA expression level  in mosquitoes following a sugar meal

overall_design: To exclude potential interference with feeding-induced mosquito miRNAs with a high identity to human ones, we exploited the mosquitoes that were fed on sugar syrup as mock controls. The engorged mosquitoes were reared for snRNA sequencing at 1 hr  following a sugar meal

first: Gong

last: Cheng


title: A Gene expression profiling study of ossification of ligamentun flavum

city: yinchuan

first: yufei

last: zhang

state: ningxia

address: ningxia medicine university

institute: ningxia medicine university

summary: To investigate the genes abnormally expressed in TOLF and their related biological processes and metabolic pathways through differential expression analysis and enrichment analysis by high-throughput sequencing of peripheral blood samples from TOLF patients and healthy people using human whole genome expression profile chip technology.To explore the mechanism of osteogenesis in OLF cells at the molecular level, and to provide molecular theoretical basis for the pathogenesis of OLF in clinical practice.

overall_design: Gene expression was measured in 5 OLF and 5 normal human blood .

first: Yufei

last: Zhang


title: Adoptive cell therapy [Fig.4]

city: cleveland

first: Yong

last: Lu

address: 9500 euclid avenue, NB40

institute: Cleveland Clinic

summary: We performed an RNA-Seq analysis comparing CAR-T cells and Tat-Beclin1-treated SKOV3 cells.

overall_design: RNA-Seq analysis comparing CAR-T and Tat-Beclin1-treated SKOV3 cells. PBS, MV, CAR-T, MV loaded CAR-T or Tat-Beclin1 were cocultured with SKOV3 cells.

first: Ningbo

last: Zheng


title: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

first: TAIWEI

last: ZHANG

address: 180 Fenglin Rd

institute: Zhongshan Hospital Fudan University

summary: The objective of this study was to compare the expression of the transcriptome in healthy and degenerative intervertebral discs. According to the standard of Pfirrmann Grading, the patients with Pfirrmann Grade III and above were divided into the degeneration group and the rest were the control group. During the operation, the nucleus pulposus tissue of patients were collected and sequenced in Illumina HiSeq 4000. Sequencing results were further calculated using Cufflinks, Deseq and Clusterprofiler.

overall_design: Nucleus pulppsus of Degenerated IVD and normal IVD identified by MRI.

first: Libo

last: Jiang

first: Shenglong

last: Ding

first: Taiwei

first: Qichen


title: MTG16 regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors

city: Nashville

first: Christopher

last: Williams

state: Tennessee

address: 1075 MRBIV/Light Hall, 22 Garland Ave.

department: Medicine/Gastroenterology

institute: Vanderbilt University Medical Center

summary: Aberrant epithelial differentiation and regeneration contribute to colon pathologies, including inflammatory bowel disease (IBD) and colitis-associated cancer (CAC). Myeloid translocation gene 16 (MTG16, also known as CBFA2T3) is a transcriptional corepressor expressed in the colonic epithelium. MTG16 deficiency in mice exacerbates colitis and increases tumor burden in CAC, though the underlying mechanisms remain unclear. Here, we identified MTG16 as a central mediator of epithelial differentiation, promoting goblet and restraining enteroendocrine cell development in homeostasis and enabling regeneration following dextran sulfate sodium–induced (DSS-induced) colitis. Transcriptomic analyses implicated increased Ephrussi box–binding transcription factor (E protein) activity in MTG16-deficient colon crypts. Using a mouse model homozygous for a point mutation that attenuates MTG16:E protein interactions (Mtg16P209T), we showed that MTG16 exerts control over colonic epithelial differentiation and regeneration by repressing E protein–mediated transcription. Mimicking murine colitis, MTG16 expression was increased in biopsies from patients with active IBD compared with unaffected controls. Finally, uncoupling MTG16:E protein interactions partially phenocopied the enhanced tumorigenicity of Mtg16-null colon in the azoxymethane (AOM) /DSS-induced model of CAC, indicating that MTG16 protects from tumorigenesis through additional mechanisms. Collectively, our results demonstrate that MTG16, via its repression of E protein targets, is a key regulator of cell fate decisions during colon homeostasis, colitis, and cancer.

overall_design: Mtg16-null mice (C57/BL6 background) and homozygous P209T (T/T) mice (C57/BL6 background) were bred using heterozygous x heterozygous breeding schemes in independent colonies. All mice were at least 8 weeks old. WT and Mtg16-null or WT and T/T mice were appropriately littermate-matched in each analysis. For baseline analyses, RNA-sequencing was performed on proximal (5 cm from cecum) and distal (5 cm from anus) murine colon crypt isolates (chelation and RNA extraction protocol described below) from untreated mice. Independent experiments and differential expression analyses: 2 Mtg16-null vs. 2 WT proximal homeostatic colon crypt isolates, 4 Mtg16-null vs. 4 WT homeostatic distal colon crypt isolates, 2 T/T vs. 2 WT homeostatic proximal colon crypt isolates, and 4 T/T vs. 3 WT homeostatic distal colon crypt isolates. As a secondary analysis, WT samples were pooled from these experiments to compare baseline gene expression in distal vs. proximal homeostatic colon. For analyses post-DSS injury-repair, mice were treated with DSS for 5 days and allowed to recover for 4 days as described below. RNA-sequencing was performed on distal colon crypts isolated following sacrifice. Independent experiments and differential expression analyses: 4 Mtg16-null vs. 3 WT distal colon crypt isolates post-DSS injury-repair, 3 T/T vs. 3 WT distal colon crypt isolates post-DSS injur-repair. As a secondary analysis, distal colon crypt isolates from WT mice matched to P209T mice post-DSS injury-repair were compared to homeostatic distal colon crypt isolates from WT mice matched to P209T mice. For AOM/DSS tumor analyses, mice were treated with AOM followed by 3 cycles of DSS injury repair as described below. Distal tumors were harvested at sacrifice. RNA-sequencing was performed on 3 T/T vs. 3 WT distal colon tumors.

first: Rachel

last: Brown

first: Justin

last: Jacobse

middle: S


title: Single-cell transcriptomics analysis of the repair process of ligament breaks

city: Qingdao City

first: Haibo

address: No. 16, Jiangsu Road, Shinan District

institute: Qingdao University Hospital

summary: The healing of ligaments is a complex and highly regulated process, including an early stage, a repair stage, and a remodeling stage. Increasing concerns have been attached to the concept of cell heterogeneity which is of great significance for understanding the complicated biological functions of tissues. Meanwhile, it also provides important insights for the development of novel therapies for disease management. Single-cell RNA sequencing (scRNAseq) is a technique employed to identify the molecular heterogeneity of a single cell in tissue by detecting its transcriptome. The current paper conducted in-depth research on the anterior cruciate ligament tissues of three patients and three healthy individuals who were injured one week, three weeks, and six months later using the scRNAseq technique. A profound and unbiased analysis was performed on the gene expression of 83 195 single cells in vitro collected from the 6 cases, to identify potential cells or genes that may be related to tissue recovery. Additionally, immunohistochemistry was adopted to verify the findings of scRNAseq approach. In this research, we formally distinguish between tenocytes and fibroblasts for the first time. In addition to fibroblasts, macrophages, endothelial cells, stromal cells, epithelial cells, T cells, B cells, chondrocytes, and monocytes, the anterior cruciate ligament tissues have at least additional 10 types of tendon cell populations, including tenocytes A, B, C, D, and E, fibroblasts, astrocytes, monocytes, myeloid cells, and stromal cells. These findings indicated the existence of a wide variety of specialized tenocytes and opened up a new way for subsequent investigations on cell therapy of tendon diseases.

overall_design: Single-cell transcriptome sequencing of injury and normal tendon tissue

first: Jinli

last: Chen

first: Tianrui

last: Wang

first: Zewen

last: Sun

first: Xia

first: Tengbo

last: Yu

first: Yingze


title: ZFP423 Controls EBF2 Co-activator Recruitment and PPARgamma Occupancy to Determine the Thermogenic Plasticity of Adipocytes

city: Durham

first: Rana

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

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

overall_design: Refer to individual Series


title: A Diagnostic Classifier for Gene Expression-Based Identification of Early Lyme Disease

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

summary: Lyme disease is a tickborne illness that causes an estimated 476,000 infections annually in the United States. New diagnostic tests are urgently needed, as existing antibody-based assays lack sufficient sensitivity and specificity. Using transcriptome profiling by RNA-Seq, targeted RNA sequencing, and machine learning (ML)-based classification of 218 subjects, we identified a 31-gene Lyme disease classifier (LDC) to discriminate early Lyme patients from “non-Lyme” controls infected with influenza, bacteremia, or tuberculosis or uninfected asymptomatic controls. Among the 31 classifier genes, 23 (74.2%) had previously been described in association with clinical investigations of Lyme disease patients or in vitro cell culture and rodent studies of Borrelia burgdorferi infection. Evaluation of the LDC using an independent test set of samples from 63 subjects (16 Lyme seropositive patients, 14 Lyme seronegative patients, and 33 controls) yielded an overall sensitivity of 90.0%, specificity of 100%, and accuracy of 95.2%. The LDC was positive in 85.7% of seronegative patients and persisted for ≥3 weeks in available longitudinal samples from 9 of 12 (75%) patients. These results highlight the potential clinical utility of a gene expression classifier for diagnosis of early Lyme disease.

overall_design:
A total of 31 samples were analyzed in this set which include 6 uninfected controls, 6 influenza, 6 bacteremia, and 13 Lyme samples.
>>> Submitter declares that raw data will be submitted to dbGaP due to patient privacy concerns.<<<

first: Venice

last: Servellita

first: Jerome

last: Bouquet

first: Alison

last: Rebman

first: Ting

last: Yang

first: Mark

last: Soloski

first: John

last: Aucott


title: ZFP423 Controls EBF2 Co-activator Recruitment and PPARgamma Occupancy to Determine the Thermogenic Plasticity of Adipocytes_ChAP-seq

summary: Energy-storing white adipocytes maintain their identity by suppressing the gene program defining energy-burning thermogenic brown/beige adipocytes. Here, we reveal that the protein-protein interaction between the transcriptional co-regulator ZFP423 and brown/beige cell determination factor, EBF2, is essential for restraining the thermogenic phenotype of white adipose tissue (WAT). Disruption of the ZFP423-EBF2 protein interaction through CRISPR-Cas9 gene editing triggers widespread “browning” of WAT in adult mice. Mechanistically, adipocyte Zfp423 deficiency induces an EBF2 NuRD-to-BAF co-regulator switch and a shift in PPARgamma occupancy to thermogenic genes. This shift in PPARgamma occupancy increases the anti-diabetic efficacy of the PPARgamma agonist rosiglitazone in obesity while diminishing the unwanted weight-gaining effect of the drug. These data indicate that ZFP423 controls EBF2 co-activator recruitment and PPARgamma occupancy to determine the thermogenic plasticity of adipocytes and raise the concept of targeting transcriptional brakes in adipocyte gene expression as a therapeutic strategy to induce thermogenic adipocyte biogenesis in obesity.

overall_design: Chromatin Affinity Purification (ChAP)-seq experiment to analyze ZFP423 DNA binding sites in differentiated adipocytes.

first: Mengle

last: Shao


title: Intergenerational hormesis is regulated by heritable 18S rRNA methylation  18S rRNA methylation is heritably transmitted to regulate intergenerational hormesis

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

summary: Heritable non-genetic information can regulate a variety of complex phenotypes. However, what specific non-genetic cues are transmitted from parents to their descendants are unknown. Here, we perform metabolic methyl-labelling experiments to track the heritable transmission of methylation from ancestors to their descendants in the nematode Caenorhabditis elegans. We find that methylation is transmitted to descendants in proteins, RNA, DNA and lipids. We further find that in response to parental starvation, naïve progeny display reduced fertility, increased heat stress resistance, and extended longevity. This intergenerational hormesis is accompanied by a heritable increase in N6’-dimethyl adenosine (m6,2A) on the 18S ribosomal RNA at adenosines 1735 and 1736. We identified DIMT-1 as the m6,2A methyltransferase in C. elegans and find that dimt-1 is required for the intergenerational hormesis phenotypes. Together this study provides the first labeling and tracking of heritable non-genetic material across generations and demonstrates the importance of rRNA methylation for regulating the heritable response to starvation

overall_design: Matched mRNAseq and Ribo-seq (ribosome profiling). Two experiments: Fed vs. Starved (6 replicates each); Empty vector vs two targeted knockdowns (4 replicates each)

first: Noa

last: Liberman

middle: V

first: Eric

last: Greer


title: Defining the Transcriptional and Epigenetic Basis of Organotypic Endothelial Diversity in the Developing and Adult Mouse II

city: Houston

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Significant phenotypic differences exist between the vascular endothelia of different organs, including cell size, shape, and mural cell coverage. These organ-specific morphological features ultimately manifest as different functional capacities, as demonstrated by the dramatic differences in capillary permeability between the leaky vessels of the liver compared to the almost impermeable vasculature found in the brain. While these morphological and functional differences have been long appreciated, the molecular basis of endothelial organ specialization remains unclear. To determine the epigenetic and transcriptional mechanisms driving this functional heterogeneity, we profiled accessible chromatin, as well as gene expression, in six different organs, across three distinct time points, during murine development. After identifying both common, and organ-specific, DNA motif usage and transcriptional signatures, we then focused our studies on the endothelium of the central nervous system. Using single cell RNA-seq, we identified key gene regulatory networks governing brain blood vessel maturation, including TCF/LEF and FOX transcription factors. Critically, these unique regulatory regions and gene expression signatures are evolutionarily conserved in humans. Collectively, this work provides a valuable resource for identifying the transcriptional regulators governing organ-specific endothelial specialization and provides novel insight into the gene regulatory networks governing the maturation and maintenance of the cerebrovasculature.

overall_design: Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq of brain microvascular endothelial cells (ECs) from the hCMEC/D3 cell line.

last: Gutierrez

first: Matthew

last: Hill

first: Gabrielle

last: Largoza

first: James

last: Martin

first: Joshua

middle: D

last: Wythe


title: Studying the gene expression of FOXM1- depleted SCLC cell lines by RNA-seq

city: Hsinchu

first: Chia-Chan

last: Hsu

address: 101, Section2, Kuan-Fu Road

department: Institute of Biotechnology

institute: National Tsing Hua University

summary:
Purpose: Small cell lung cancer (SCLC) continues to cause poor clinical outcomes due to limited advances in sustained treatments for rapid cancer cell proliferation and progression. The transcriptional factor Forkhead Box M1 (FOXM1) regulates cell proliferation, tumor initiation and progression in multiple cancer types. However, its biological function and clinical significance in SCLC remain to be established. Hence, the goals of this study are to decipher if FOXM1 is crucial to SCLC cells.
Methods: NCI-H1688 stable cells, which contain shFOXM1 or shControl inducible expressing cassette based on pInducer20, plated as triplicates in 60-mm dishes for culturing overnight were induced by doxycycline for 48 hours. Total RNAs were collected by NucleoSpin RNA mini kit and sent for RNA-seq by Novogene. Bioanalyzer 2100 was used to analyze the RNA integrity and cDNA library was constructed with NEBNext UltraTM RNA Library Prep Kit for Illumina. Differential expression gene (DEG) analysis was performed using DESeq2 R package. DEGs were then subjected to ClusterProfiler R package for GO and KEGG enrichment analysis.
Results: 1809 downregulated genes and 1781 upregulated genes were enriched in FOXM1-depleted NCI-H1688 cells. SCLC related KEGG pathway was found to be repressed, while multiple cell adhesion and junction associated GOs were induced in FOXM1-depleted NCI-H1688 cells. Furthermore, Foxm1 knockout inhibited SCLC formation in the Rb1fl/flTrp53fl/flMycLSL/LSL (RPM) mouse model associated with increased levels of neuroendocrine markers, Ascl1 and Cgrp, and decrease in Yap1. Consistently, FOXM1 depletion in NCI-H1688 SCLC cells reduced migration and enhanced apoptosis and sensitivity to cisplatin and etoposide. SCLC with high FOXM1 expression (N=30, 57.7%) was significantly correlated with advanced clinical stage, extrathoracic metastases and decrease in overall survival (OS), compared with the low-FOXM1 group (7.90 vs. 12.46 months). Moreover, the high-FOXM1 group showed shorter progression-free survival (PFS), compared with the low-FOXM1 group (3.90 vs. 8.69 months). Our collective findings support the utility of FOXM1 as a prognostic biomarker and potential molecular target for SCLC.

overall_design: Analysis of RNA expression in 3 shControl and 3 FOXM1-depleted NCI-H1688 cell lines.

first: I-Ching

last: Wang

first: Sheng-Kai

last: Liang


title: Genome-wide distribution analysis of RNA Helicase Maleless (MLE) in Drosophila Melanogaster early male embryo, before (0-2 Hr) and after (2-4 Hr) maternal to zygotic transition (MZT) and in absence of CLAMP

city: Providence

first: Erica

last: Larschan

state: RI

address: 164 Angell St

institute: Brown University

summary:
Purpose: Study how maternal Pioneer Transcription factor CLAMP affects sex-specifc splicing during initial embryonic development by regulating occupancy of spliceosome component Maleless (MLE), a RNA helicase on chromatin
Method: Cut and Run (CUT&RUN) DNA libraries (Uyehara and McKay 2019) using anti-MLE antibody were generated from male embryos at 0-2 Hr pre-MZT and 2-4 hr post-MZT stages in presence and absence of maternal CLAMP. Maternal CLAMP was depleted by driving UAS-CLAMPRNAi in the ovaries using MTD-GAL4 maternal triple driver. As a control UAS-GFPRNAI was driven using the MTD-GAL4. Embryos were sexed using the meiotic drive system that produces sperm with  only Y chromosomes (Reider et al 2017), resulting in progeny of only male genotypes.
Results: We identified regions on chromatin where MLE binds during 0-2 Hr pre-MZTand 2-4 Hr post-MZT embryonic stages in males. In 0-2 Hr and 2-4 Hr old control embryos 28,279 and  24,910 MLE peaks were detected. After depletion of maternal CLAMP, 41.97% of 0-2 Hr peaks (22183 remaining, 6096 lost) and 59.1% of 2-4 Hr peaks (15735 remaining, 9175 lost) are lost. We also found loss of maternal CLAMP resulted in 26% and 35.25% new MLE peaks at 0-2 hr pre-MZT and 2-4 Hr post-MZT embryonic stages. Our motif search shows presence of putative motifs for MLE binding on chromatin which needs further validation.
Conclusion: This is the first study showing genome-wide MLE occupancy in sexed embryos during 0-2 hr pre-MZT and 2-4 hr post-MZT stages. We show that the maternally deposited transcription factor CLAMP affects MLE occupancy on chromatin in early embryos. Thus, we conclude that maternal transcription factors can affect spliceosome function by regulating occupancy of their components on chromatin.

overall_design: Male embryos with maternal CLAMP (control, MTD-GAL4>GFPRNAi mothers) and depleted maternal CLAMP (experimental, MTD-GAL4>CLAMPRNAi mothers) at two time points-1)0-2 Hr pre-MZT and 2) 2-4 Hr post-MZT collected. Using anti-MLE antibody the DNA fragments bound to MLE protein captured (Cut and Run protocol) and DNA libraries made. Pair-end sequencing of DNA libraries in a Hi-seq illumina platform with average 7-10 million reads per sample. Multiple batches of crosses were set and embryos collected from multiple timed egg-layings used to make DNA libraries, 2 replicates for each genotype and time point.

first: Ashley

last: Conard

first: Mukulika

last: Ray


title: Dihydrocoumarin, an extract of Melilotus officinalis, inhibits IgE-dependent mast cell activation in vitro and in vivo

city: Shenzhen

first: Hui

address: Taoyuanjiedao

institute: Shenzhen University

summary: In summary, dihydrocoumarin could suppress MC activation in vitro and in vivo through inhibiting the MAPKs and NF-kB pathways.

overall_design: RBL-2H3 mRNA profiles of DHC treated mast cell and untreated mast cell

first: Jiajie

last: Chen

first: Kunmei

last: Ji


title: RNA Sequencing Facilitates Quantitative Analysis of LINC00901 knockout and Control MIA PaCa-2 Cell Transcriptomes

city: Jackson

first: Yin-Yuan

last: Mo

state: MS

address: 2500 N State Street, G652

institute: Univ of Mississippi Medical Center

summary: Total RNA sequencing of LINC00901 KO and vector control cells

first: Wan-Xin

last: Peng

first: Liu

last: Yang


title: RNA Sequencing Facilitates Quantitative Analysis of LINC00901 overexpression and Control MIA PaCa-2 Cell Transcriptomes

overall_design: Total RNA sequencing of LINC00901 overexpression and vector control cells


title: Identification of mosquito genes regulated after blood meal with hsa-miR-150-5p antagomir

first: Yibin

last: Zhu

summary: We report the RNA-seq based analyses of the transcriptional changes in the Aedes aegypti transcriptome 4 days after blood feeding with 2 μM hsa-miR-150-5p antagomir or mock.

overall_design: Comparison of the transcriptome of Aedes aegypti after blood feeding with  2 μM hsa-miR-150-5p antagomir or mock.

first: Gong

last: Cheng