title: Characterizing the diversity of enteric neurons using Dopamine Transporter (DAT)-Cre reporter mice

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

institute: McGill University

summary: Dopaminergic (DA) neurons are the predominant cell type in the midbrain that synthesize dopamine, a neurotransmitter implicated in various behavioural processes, including motor function, the reward pathway, and satiety. In diseases affecting these neurons, such as in Parkinson’s disease (PD), there is growing evidence that the gut-brain axis and selective vulnerability of DA neurons plays a crucial role in disease. Most investigations relating to DA neurons in the gut rely on immunoreactivity to tyrosine hydroxylase (TH) - a rate-limiting enzyme in the production of dopamine. However, the reliability of TH staining as a marker of DA neurons has been questioned in recent years. Our aim is to perform a comprehensive characterization of DA neurons in the gut using a well-accepted reporter mouse line, expressing a fluorescent protein under the dopamine transporter promoter (DAT). Our findings confirm a unique localization of DA neurons in the gut, and unveil that there are discrete subtypes of DA neurons in the gut, which we characterized using both immunofluorescence and single-cell transcriptomics. We observed distinct subtypes of DAT neurons expressing co-transmitters and modulators across both plexuses; some of them likely co-releasing acetylcholine, and a smaller population likely releasing nitric oxide; while others were positive for a slew of canonical DA markers (Vmat2, Girk2, Foxa2). Given the clear heterogeneity of DA gut neurons, further investigation is warranted to define their functional signatures and discover their inherent biological differences that predispose these cells to neurodegeneration.

overall_design: Colonic myenteric cells were dissociated, and live tdTomato-positive cells were FACS-collected. Colons were isolated from 2 male and female wild type adult DAT-Cre mice. Wild type C57Bl6/J was used as control for gating.

first: Sherilyn

last: Recinto

first: Shobina

last: Premachandran

first: Sriparna

last: Mukherjee

last: MacDonald

first: Moein

last: Yaqubi

first: Samantha

last: Gruenheid

first: Louis-Eric

last: Trudeau


title: Analysis of skeletal muscle gene expression upon mouse hindlimb unloading and reloading

status: Public on Jul 16 2023

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

type: Expression profiling by high throughput sequencing

summary: To investigate the molecular mechanisms governing the transition of skeletal muscle from atrophy to compensatory regeneration and hypertrophy, we employed a mouse model involving hindlimb unloading and subsequent reloading, conducting a comprehensive analysis of global gene expression using RNA-sequencing (RNA-seq). Gastrocnemius muscle samples were obtained from three groups: control mice, mice subjected to 10 days of hindlimb unloading-induced muscle atrophy, and mice reintroduced to normal cage activity for 1 day following the unloading period (reloading).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse gastrocnemius muscle from model of hindlimb unloading/reloading assessing transitions from atrophy to compensatory regeneration and hypertrophy. Control mice were kept in conventional cages throughout the entire protocol. Experiment was performed in replicates (Control n = 4, Unloading n = 2, Reloading n = 3). Paired-end DNA libraries were prepared using Illumina TrueSeq and sequenced on Illumina HiSeq2000 (.

first: Jorge

middle: C

last: Correia

first: Vicente

last: Martinez-Redondo

first: Paulo

middle: R

last: Jannig

first: Serge

last: Ducommun

first: Stine

middle: M

last: Præstholm

first: Kyle

last: Dumont

first: Daniel

last: Edsgärd

first: Olof

last: Emanuelsson

middle: L

last: Ruas


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [8H and 8K]

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (8H_200903, 8H_200910, 8K_200312).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

middle: G

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Rescue of TDP-43 and neuronal pathologies by peripheral AAV-mediated expression of brain-penetrant progranulin in a mouse model of GRN-linked frontotemporal lobar degeneration

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: Progranulin (PGRN) haploinsufficiency is a major risk factor for Frontotemporal Lobar Degeneration with TDP-43 pathology (FTLD-TDP). Protein replacement therapeutic strategies are currently in clinical development, intended to restore PGRN levels in the central nervous system and slow or halt disease progression. However, such approaches require repeated dosing. Here, we explored the use of adeno-associated virus (AAV) to achieve sustained expression of a brain penetrant PGRN fusion protein, composed of a single chain variable fragment (scFv) recognizing mouse transferrin receptor (TfR) fused to human PGRN (AAV(L):bPGRN). We evaluated this approach for its ability to rescue pathological phenotypes in a double knockout mouse model lacking both PGRN and TMEM106b. A single administration of AAV(L):bPGRN reduced FTLD-TDP associated pathologies including severe motor function deficits, formation of insoluble, abnormally processed and phosphorylated TDP-43, as well as dysfunctional protein degradation, lipid dysregulation and gliosis.

overall_design:
We generated AAV(L):bPGRN (L = liver, b = brain-penetrant), a liver-targeting adenovirus (AAV) encoding a fusion protein (8D3:PGRN) consisting of a single chain fragment variable (scFv) antibody recognizing mouse TfR (transferrin receptor) fused to human PGRN (hPGRN).
To study the effects of AAV(L):bPGRN, we treated 6-week old wildtype or GRN,TMEM106B double knock-out mice with either 1.3 x 10^13 vg/kg AAV or isotonic saline solution (0.9% NaCl) intravenously via tail vain injection.
9-10 weeks after the treatment the animals were sacrificed; they were anesthetized and transcardiacally perfused with PBS. From each animal, one hemibrain (excluding the olfactory bulb, but including cerebellum) was collected, snap frozen on dry ice and pulverized with a pistill.
All animal experiments were performed according to German animal welfare law and approved by the government of upper Bavaria.

first: Marvin

last: Reich

first: Matthew

middle: J

last: Simon

first: Beate

last: Polk

first: Gilbert

last: Di Paolo

first: Christian

last: Haass


title: Expression data of the kidneys from Pkd1 miR Tg mice treated with metformin

status: Public on Jul 15 2023

city: Kueishan

first: Ming-Yang

last: Chang

state: Taoyuan

address: 5 Fu-Shing Street

department: Kidney Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital

summary:
We investigated the effects of metformin treatment on polycystic kidney disease in a mouse model of Pkd1-deficiency.
Kidneys are harvested in postnatal day 63 after 28 days of intraperitoneal injection of metformin (150 mg/kg/day) or saline for control. Total RNA was extracted for microarray analysis. Gene expression profiles were different between treatment and control groups.

overall_design: Kidney RNA samples from three mice treated with saline and three mice treated with metformin were compared using microarray analysis.


title: Rice gene expression profiling in wild type and transgenic rice plants by over-expressing a class I HD-ZIP gene by Agilent custom 8X60K Microarray analysis

city: Singapore

first: Shu-Ye

last: Jiang

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory, National University of Singapore

summary: We designed an array based on the release 7 of Michigan State University (MSU) rice genome annotation database (http://rice.plantbiology.msu.edu). The array was used for investigating the differentially expressed genes after over-expression of the rice gene with locus name LOC_Os02g43330.

overall_design: The expression analysis was carried out using 14-day old whole seedlings from both japonica Nipponbare wild type (WT) and its transgenic plants by over-expressing the rice gene with locus name LOC_Os02g43330.  Two biological replicates were carried out for both WT and transgenic plants.

first: S

middle: Y

first: J

last: Vanitha

first: L

last: Xie

last: Ramachandran


title: Comprehensive gene expression of fibroblasts from idiopathic pulmonary fibrosis patients

city: Kashihara

first: Toshihiro

last: Ito

state: Nara

address: 840 Shijo-cho

country: Japan

institute: Nara Medical University

summary: To investigate the mechanisms underlying disease progression in idiopathic pulmonary fibrosis (IPF), we obtained lung fibroblasts from IPF patients from both non-fibrotic and fibrotic areas, and compared gene expression between these areas by DNA microarray. Forty-two genes were commonly upregulated more than two-fold in fibroblasts from the fibrotic lung region compared with their counterparts from the non-fibrotic region in all three IPF patients.

overall_design: Lung specimens from three patients with lung cancer and IPF were obtained from both the fibrotic and non-fibrotic areas in non-cancerous regions. Comprehensive gene expression of fibroblasts, which were isolated from each region and cultured, were analyzed.

first: Shoichiro

last: Saito


title: RNAseq of the in vitro matured and in vivo matured monkey oocytes

city: Shanghai

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

country: China

institute: Chinese Academy of Sciences

summary: Oocyte quality largely determines the embryo development after fertilization. High-quality oocyte requires the competence of both cytoplasm and nucleus. However, clinically, the treatment of developmentally competent oocytes was limited. Here, in order to improve the embryo development efficiency of developmentally incompetent oocytes, we performed spindle-chromosome complex (SCC) transfer between in vitro matured (IVM) and in vivo matured (IVO) oocytes of the non-human primate. We observed that the blastocyst rate of embryos derived by transferring the SCC of IVM (IVM-SCC) oocytes into enucleated IVO oocytes was comparable with that of embryos derived by IVO oocytes. After transferring the reconstructed embryos into the uterus of surrogate mothers, two live rhesus monkeys were obtained, indicating that the nuclei of IVM oocytes support both the pre-and post-implantation embryo development of non-human primates.

overall_design: RNA-seq for the comparison of gene expression between monkey GV oocytes, in vitro matured oocytes and in vivo matured oocytes.

first: Zhaodi

last: Liao


title: Gene expression profile at single cell level of leukocytes from transplanted syngeneic left lung grafts following treatment with Resolvin D1.

city: Saint Louis

first: Daniel

last: Kreisel

state: Missouri

address: 660 S Euclid Ave

department: Surgery

institute: Washington University

summary: Neutrophils play a pivotal role in the pathogenesis of lung ischemia-reperfusion injury. The effect of pro-resolving lipid mediators, such as Resolvin D1, on early neutrophil trafficking has not been assessed in organ transplantation. We obtained single-cell RNA sequencing of leukocytes from syngeneic left lung grafts to elucidate the genetic changes induced by recipient treatment with Resolvin D1 or vehicle.

overall_design: We obtained single-cell RNA sequencing of sorted CD45+ leukocytes from transplanted B6 mouse left lung grafts that were treated with intravenous Resolvin D1 or vehicle immediately prior to syngeneic transplantation. Lung grafts were exposed to severe ischemia reperfusion injury, including both cold (60 minutes at 4 degrees Celcius) and warm ischemic storage (45 minutes at 28 degrees Celcius) and were collected 2 hours after engraftment. Each condition comprised two pooled lungs.

first: Wenjun

last: Li

first: Hailey

last: Shepherd

first: Yuriko

last: Terada

first: Ashley

middle: E

last: Shay

first: Amit

middle: I

last: Bery

first: Andrew

last: Gelman

first: Kory

last: Lavine

first: Charles

middle: N

last: Serhan


title: The use of human iPSC-derived alveolar organoids to explore SARS-CoV-2 variant infections and host responses

status: Public on Jul 14 2023

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

summary: The apical-in, sheared, and apical-out airway organoids (AOs) were infected with the SARS-CoV-2 WA1 isolate at a multiplicity of infection (MOI) of 0.25 for 72 hours. Subsequently, the total RNA was utilized for next-generation RNA sequencing in order to analyze and characterize the mRNA expression patterns.

overall_design: RNA sequencing analysis of SARS-CoV-2 infected airway organoids

first: Chaoqun

last: Huang

first: Lin

last: Liu

first: Chaitanya

last: Gandikota


title: Loss of Kindlin-1 drives a more aggressive phenotype in cutaneous squamous cell carcinoma

city: Edinburgh

first: Denise Giovana

last: Carrasco Gonzalez

state: --- Select One ---

address: Crewe Road, Western General Hospital Campus (ECRC)

department: ECRC

country: United Kingdom

institute: University of Edinburgh

summary: Kindler syndrome (KS) is a rare genodermatosis resulting from loss-of-function mutations in FERMT1, the gene that encodes Kindlin-1. KS patients have a high propensity to develop aggressive and metastatic cutaneous squamous cell carcinoma (SCC). In this study, we show that loss of Kindlin-1 in a mouse model of cutaneous SCC leads to increased migration, invasion and degradation of collagen. Loss of Kindlin-1 increased tumor growth in vivo and in 3D spheroids, which was associated with the development of a hypoxic tumor environment and increased glycolysis. One of the most highly upregulated genes in Kindlin-1-depleted tumors was Mmp13, and the increased expression of MMP13 was responsible for driving the increased migration and invasion of the Kindlin-1-depleted SCC cells. These results provide evidence that Kindlin-1 loss in SCC can promote migration and invasion through the upregulation of MMP13, and offer novel insights into how Kindlin-1 loss leads to the development of a hypoxic environment that is permissive for tumor growth.

overall_design: RNA samples extracted from tumors derived from cutaneous squamous cell carcinoma expressing Kindlin-1 (wild type-WT) were compared to tumors with Kindlin-1 knockout (Nulls) to assess differences in expression.


title: Effect of NleE effector on gene expression in HCT116 cells

city: Chengdu

first: haiyan

last: ren

address: ren min nan lu san duan 17 hao

institute: sichuan univerisity

summary: To investigate the  function of NleE in the regulation of host transcription, we established HCT116 cell lines stably expressing NleE. We performed toal RNA-seq and compared transcription of HCT116 cells with and without NleE expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  HCT 116 cells expressing NleE and HCT 116 cells with empty vector.

first: Haiyan

last: Ren

first: Xiaoxiao

last: Ouyang

first: Li

last: Zhou


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [8F and 8G]

first: Joseph

last: Ecker

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (8F_190718, 8F_190723, 8G_201029, 8G_201105).

first: Hanqing

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Fetal mesenchymal stem cells promote osteogenesis via Notch signaling

city: Seongnam

first: Hyun-Ju

last: An

address: Seongnam-si, 13496

country: South Korea

institute: CHA university

summary: Comparison of the Osteogenic Differentiation Potential of Stem Cells

overall_design: Comparative gene expression profiling analysis of mRNA-seq data for BM-MSC and Fetal MSC.

first: Soonchul

last: Lee

first: Jong

middle: S

last: Rim


title: KSHV-induced iNOS in Kaposi’s Sarcoma tumors and mouse model

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Kaposi’s Sarcoma (KS) is a heterogenous, multifocal vascular malignancy caused by the human herpesvirus 8 (HHV8), also known as Kaposi’s Sarcoma-Associated Herpesvirus (KSHV). Here, we show that KS lesions express iNOS/NOS2 broadly throughout KS lesions, with enrichment in LANA positive spindle cells. The iNOS byproduct 3-nitrotyrosine is also enriched in LANA positive tumor cells and colocalizes with a fraction of LANA-nuclear bodies. We show that iNOS is highly expressed in the L1T3 tumor model of KS. iNOS expression correlated with KSHV lytic cycle gene expression, which was elevated in late-stage tumors (>4 weeks) but to a lesser degree in early stage (1 week) xenografts. Further, we show that L1T3 tumor growth is sensitive to an inhibitor of nitric oxide, L-NMMA. These finding suggest that iNOS is expressed in KSHV infected endothelial-transformed tumor cells in KS, that iNOS expression depends on tumor microenvironment stress conditions, and that iNOS enzymatic activity contributes to KS tumor growth.

overall_design: RNA-seq of L1T3 tumors with and without inhibitor of nitric oxide, L-NMMA (NG-methyl L-arginine)

first: Olga

last: Vladimirova

first: Paul

last: Lieberman


title: Expression quantitative trait locus (eQTL) mapping with a cross between Tetranychus urticae inbred strains MR-VPi and ROS-ITi

city: Gent

first: Marilou

last: Vandenhole

address: Coupure links 653

department: Department of Plants and Crops

country: Belgium

institute: UGent

summary: We performed expression quantitative trait locus (eQTL) mapping between two strains of Tetranychus urticae (the two-spotted spider mite), a generalist herbivore known for its rapid evolution of acaricide resistance. For parents, we used the inbred strain MR-VPi that is highly resistant to multiple acaricides in different classes, and the inbred strain ROS-ITi that is comparatively susceptible to many acaricides. The eQTL mapping experiment was performed with F3 samples, and thousands of trans and cis eQTL were identified, including for genes in families known (or suspected) to be involved in the metabolism of xenobiotics (plant produced secondary compounds and acaricides). One trans eQTL hotspot was identified that strongly impacted the expression of many detoxification genes in different gene families. Follow up studies using derived near isogenic lines validated the trans eQTL hotspot, and RNA interference (RNAi) knockdown of tandemly duplicated genes encoding products with homology to the ligand binding domains of nuclear hormone receptor 96 genes impacted many of the same detoxification genes controlled by the hotspot.

overall_design: eQTL mapping was performed using F3 mite samples, and subsequently differential gene expression analyses were performed between near isogenic lines (NILs) derived from the parents (MR-VPi and ROS-ITi) and in NILs subjected to RNAi knockdown of candidate genes (the RNAi work was performed with mites on both bean and tomato leaves; otherwise mites on bean leaves were used).

first: Meiyuan

last: Ji

first: Berdien

last: De Beer

first: Sander

last: De Rouck

first: Richard

last: Clark

first: Thomas

last: Van Leeuwen


title: Glycyrrhizic Acid Inhibits Myeloid Differentiation of Hematopoietic Stem Cells and Improves Cognition in Aged Mice by Binding to the S100 Calcium-Binding Protein A8 [scRNA-seq]

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: Glycyrrhizic acid (GA) has numerous biological activities, but the mechanism by which it regulates the immune system and improves cognition in aged mice remains unclear. In this study, we analyzed single-cell sequencing data of peripheral blood mononuclear cells from young mice, aged mice, and GA-treated aged mice, and found that GA reduced senescence-induced increases in macrophages and neutrophils, and increased numbers of lymphoid lineage subpopulations specifically reduced by senescence. In vitro, GA significantly promoted differentiation of Lin-CD117+ hematopoietic stem cells toward lymphoid lineages, especially CD8+ T cells. Moreover, GA inhibited differentiation of CD4+ T cells and myeloid (CD11b+) cells by binding to the S100 calcium-binding protein 8 (S100A8). Overexpression of S100A8 in Lin- CD117+ hematopoietic stem cells enhanced cognition in aged mice and in immune reconstited severely immunodeficient B-NDG mice. Collectively, our results suggest that GA exerts anti-aging effects by binding to S100A8 to remodel the immune system of aged mice.

overall_design: We implemented single cell transcriptomic analyses of PBMC from young, aged and aged mice treatment with GA for 1 month .


title: Glycyrrhizic Acid Inhibits Myeloid Differentiation of Hematopoietic Stem Cells and Improves Cognition in Aged Mice by Binding to the S100 Calcium-Binding Protein A8 [lenti-A8 RNA-seq]

overall_design: We implemented transcriptomic analyses of HSC (Cas9 knockout S100a8).


title: Glycyrrhizic Acid Inhibits Myeloid Differentiation of Hematopoietic Stem Cells and Improves Cognition in Aged Mice by Binding to the S100 Calcium-Binding Protein A8 [OEA8-67-69 RNA-seq]

summary:
Glycyrrhizic acid (GA) has numerous biological activities, but the mechanism by which it regulates the immune system and improves cognition in aged mice remains unclear. In this study, we analyzed single-cell sequencing data of peripheral blood mononuclear cells from young mice, aged mice, and GA-treated aged mice, and found that GA reduced senescence-induced increases in macrophages and neutrophils, and increased numbers of lymphoid lineage subpopulations specifically reduced by senescence. In vitro, GA significantly promoted differentiation of Lin-CD117+ hematopoietic stem cells toward lymphoid lineages, especially CD8+ T cells. Moreover, GA inhibited differentiation of CD4+ T cells and myeloid (CD11b+) cells by binding to the S100 calcium-binding protein 8 (S100A8). Overexpression of S100A8 in Lin- CD117+ hematopoietic stem cells enhanced cognition in aged mice and in immune reconstited severely immunodeficient B-NDG mice. Collectively, our results suggest that GA exerts anti-aging effects by binding to S100A8 to remodel the immune system of aged mice.
We implemented transcriptomic analyses of HSC (Overexpression of S100A8 and Overexpression of S100A8 with point mutation (aa 67 or aa 69) ).

overall_design: Hailiang Liu


title: Transcriptomic data from yeast after heterologous overexpression of human IRAK kinases

city: Madrid

first: Elba

last: del Val

state: Madrid

address: Plaza Ramón y Cajal s/n

department: Microbiología y Parasitología

country: Spain

institute: Universidad Complutense de Madrid

summary: Study of the transcriptional profile of Saccharomyces cerevisiae following overexpression of human IRAK kinases, which are involved in innate immunity signalling, to investigate their phenotypic effects in this eukaryotic model organism.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: The proteins IRAK4, the catalytically inactive version of IRAK4 (named IRAK4(KD)), IRAK1 and IRAK2 were overexpressed from the yeast plasmid pEG(KG). The empty plasmid pEG(KG) was used as a control. Induction of gene expression was performed for 6h by changing the carbon source from raffinose to galactose, as the plasmids are under the control of the GAL1 promoter.  The experiment was performed in biological triplicates.


title: Glycyrrhizic Acid Inhibits Myeloid Differentiation of Hematopoietic Stem Cells and Improves Cognition in Aged Mice by Binding to the S100 Calcium-Binding Protein A8 [HSC+GA RNA-seq]

summary:
Glycyrrhizic acid (GA) has numerous biological activities, but the mechanism by which it regulates the immune system and improves cognition in aged mice remains unclear. In this study, we analyzed single-cell sequencing data of peripheral blood mononuclear cells from young mice, aged mice, and GA-treated aged mice, and found that GA reduced senescence-induced increases in macrophages and neutrophils, and increased numbers of lymphoid lineage subpopulations specifically reduced by senescence. In vitro, GA significantly promoted differentiation of Lin-CD117+ hematopoietic stem cells toward lymphoid lineages, especially CD8+ T cells. Moreover, GA inhibited differentiation of CD4+ T cells and myeloid (CD11b+) cells by binding to the S100 calcium-binding protein 8 (S100A8). Overexpression of S100A8 in Lin- CD117+ hematopoietic stem cells enhanced cognition in aged mice and in immune reconstited severely immunodeficient B-NDG mice. Collectively, our results suggest that GA exerts anti-aging effects by binding to S100A8 to remodel the immune system of aged mice.
We implemented transcriptomic analyses of rHSC treated with GA 24 hours

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  rHSC treated with GA 24 hours.


title: Alternative splicing and DNA methylation interact in linseed (Linum usitatissimum L.) response to different drought stresses

city: Wuhan

first: Wei

last: Wang

address: No.2 Xudong Road

department: Ministry of Agriculture and Rural Affairs Oil Crops Research Institute

institute: Chinese Academy of Agricultural Science

summary:
To investigate changes in genome methylation in flax seedlings under drought stress, we selected a drought-tolerant flax variety (Z141) and a drought-sensitive flax variety (NY-17)
We then performed genome methylation analysis using data obtained from Z141 and NY-17 leaf tissue BS-seq at four different treatments (DS, RW, RD and CK).

overall_design: Comparison of genomic methylation analysis of BS-seq data in leaf tissue of Z141 and NY-17 under CK, DS, RW and RD treatments.

first: Lei


title: Gene expression from microdissected glomeruli and tubulointerstitium of NZM2328 mice

city: Charlottesville

first: Loren

last: Erickson

state: Virginia

address: 345 Crispell Drive

department: Department of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

summary: To characterize molecular profiles through the development of lupus nephritis and identify risk factors for end organ damage, we carried out gene expression analysis of microdissected kidneys from lupus-prone NZM2328 mice. We identified a continuum of inflammatory processes associated with the progression from acute inflammatory to chronic destructuve disease initiated in the glomeruli and progressing to the tubulointerstitium. We examind male mice and the congenic NZM2328.R27 strain, both of which are resistant to the development of chronic nephritis and end organ damage, as a means to define pathogenic processes.

overall_design: RNA was extracted from microdissected kidney glomeruli and tubulointerstitial tissue from female NZM2328 mice with acute (AGN), transitional (TGN), or chronic (CGN) stage glomerulonephritis. NZM2328 male and R27 mice which only develop AGN were also analyzed. For all cohorts, young, non-diseased mice were used as controls. RNA from each sample was then hybridized to Affymetrix arrays for gene expression analysis.

first: Andrea

last: Daamen

first: Peter

last: Lipsky

first: Shu

last: Fu

first: Hongyang


title: Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers [RNA-seq]

city: Memphis

first: Daniel

last: Savic

state: TN

address: 262 Danny Thomas pl.

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: Genes encoding subunits of SWI/SNF (BAF) chromatin remodeling complexes are mutated in >20% of cancers. SWI/SNF complexes exist in three distinct families that each contribute to regulation of transcription, although the functional interactions between the families are not well understood. Rhabdoid tumors constitute an informative model system as these highly aggressive cancers are driven by inactivation of a single SWI/SNF subunit, SMARCB1, which is present in two SWI/SNF families (cBAF and PBAF) but not in the third (GBAF/ncBAF). We and others have shown that BRD9, a therapeutically targetable member of ncBAF, is essential specifically in SMARCB1-deficient cancers, suggesting key functional relationships between SMARCB1-containing complexes and BRD9/ncBAF. However, the mechanistic underpinnings of these relationships are poorly understood. Here, we demonstrate that genomic binding of BRD9 is largely dependent upon SMARCB1 such that the absence of SMARCB1 results in significantly reduced BRD9 binding.  At select sites, however, we show that SMARCB1-loss results in gain of BRD9 binding and BRD9-dependent accessibility. We find that this gain is associated with expression of genes promoting cell migration. Our results define relationships between SWI/SNF complex families, elucidate mechanisms by which SMARCB1 loss drives oncogenesis, and provide mechanistic insight into the synthetic-lethal relationship between SMARCB1 and BRD9.

overall_design: n=3 RNA seq in GFP vs DMARCB1 induced G401 cells treated with DMSO or dBRD9-A for 24hrs

first: Robert

last: Mobley

first: Jacquelyn

middle: A

last: Myers

first: Kendall

last: Wills

first: Hayden

last: Malone

first: Trishabelle

last: Manzano

first: Janet

middle: F

last: Partridge

first: Charles

middle: W

last: Roberts


title: Metabolic control of histone demethylation

city: shanghai

first: li

last: peng

institute: PSC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To analyze whether metabolites regulate histone methylation in plants, we examined genome-wide histone 3 lysine-27 trimethylation (H3K27me3) in an Arabidopsis dehydrogenase mutant (ogdh1/2) by ChIP-seq. We found that the levels of H3K27me3 were reduced at various loci in ogdh1/2 relative to wild type, indicating that metabolites control histone demethylation in Arabidopsis.

overall_design: Nuclei were extracted from 10-d-old WT (Col-0) and ogdh (double mutant) seedlings as previously described (Louwers et al., 2009), followed by chromatin immunoprecipitation with Magna ChIP A/G kit (Millipore). DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), and subsequently were sequenced on NovaSeq 6000 (Illumina). Three biologically independent samples have been analyzed.

first: Fei

last: Huang

first: Yuehui

last: He

first: Yang

last: Ou


title: Gene expression profile at single cell level of whole embryonic (E16.5) and early postantal (P3) mouse liver

city: Solna

first: Emma

last: Andersson

state: Not required for this country

address: Solnav. 9, BioMedicum

institute: Karolinska Institutet

summary: To study molecular differences betweeem wild-type and cholestatic livers of a Jag1Ndr mouse model of Alagille syndrome (Andersson, Chivukula, Hankeova, et al. Gastroenterology, 2018;154(4):1080-1095), we used single cell RNA sequencing (scRNA-seq) of prenatal (E16.5) and early postnatal (P3) livers.

overall_design: Liver cells of Jag1+/+, Jag1Ndr/+ , and Jag1Ndr/Ndr mice (2 individuals per genotype and stage) were enzymatically dissociated,  dead cells removed on MACS, and directly processed for scRNAseq with 10X Genomics, followed by library preparation and sequencing on Illumina NextSeq550, and S4 NovaSeq.

first: Jan

last: Mašek


title: Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers

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

overall_design: Refer to individual Series


title: Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers [ChIP-seq]

overall_design: n=2 MNase ChIP-seq of control vs SMARCB1 induced G401 cells


title: The oncogenic circular RNA circ_63706 is a potential therapeutic target in sonic hedgehog-subtype childhood medulloblastomas.

city: St. Petersburg

first: Ranjan

middle: J.

last: Perera

state: FL

address: 600 Fifth Street S.

department: Department of Oncology,

institute: Johns Hopkins University School of Medicine

summary: To gain further insights into the functional significance of circ_63706, gene expression was measured by RNA-seq in DAOY cells treated with either si-NC (non-targeting control) or si-circ_63706.

overall_design: Gene expression comparison of si-circ_63706 and si-NC (control) using RNA-seq.

first: Rudramani

last: Pokhrel

first: Keisuke

last: Katsushima


title: Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers [ATAC-seq]

first: Daniel

last: Savic

overall_design: n=3 ATAC-seq of control vs SMARCB1 induced G401 cells treated with DMSO or dBRD9-A


title: Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers [CUT & RUN]

overall_design: n=2 SMARCB1 and n=3 BRD9 CUT & RUN in control vs SMARCB1 induced G401 cells

first: Robert

last: Mobley


title: Derivation of embryonic stem cells from wild-derived mouse strains by nuclear transfer using peripheral blood cells

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

summary: The laboratory mouse (Mus musculus domesticus) has long been used in biomedical research due to its easy maintenance and availability of abundant genetic information. However, laboratory mice have an inherent disadvantage of low genetic diversity caused by their origin from a relatively small colony of “fancy mice” in western Europe. Recently captured wild mice (wild-derived mice) are expected to compensate for this shortcoming because of their greater genetic diversity. On the other hand, wild-derived mice often show poor reproductive performance and are difficult animals in which to apply assisted reproductive technologies. In this study, we examined the technical feasibility of derivation of nuclear transfer embryonic stem cells (ntESCs) from wild-derived mouse strains for their safe preservation. We used leukocytes collected from peripheral blood as nuclear donors without sacrificing wild-derived mice. We successfully established 24 ntESC lines from two wild-derived strains of CAST/Ei and CASP/1Nga (11 and 13 lines, respectively), both belonging to Mus musculus castaneus, a subspecies of laboratory mouse. Most (23/24) of these lines had normal karyotype, and all lines examined showed teratoma formation ability (4 lines) and pluripotent marker gene expression (8 lines). Two male lines examined (one from each strain) were proven to be competent to produce chimeric mice following injection into host embryos from laboratory mice. By natural mating of these chimeric mice, the CAST/Ei male line was confirmed to have germline transmission ability. Our results demonstrate that intersubspecific ntESCs derived from peripheral leukocytes could provide a strategy for preserving genetic resources of wild-derived mouse strains.

sample_organism:
Mus musculus castaneus
Mus musculus domesticus

overall_design: Gene expression analysis of inter-subspecies ntESCs lines established from leukocyte SCNT blastocysts.

first: Naomi

last: Watanabe

first: Atsuo

last: Ogura


title: Glycyrrhizic Acid Inhibits Myeloid Differentiation of Hematopoietic Stem Cells and Improves Cognition in Aged Mice by Binding to the S100 Calcium-Binding Protein A8

first: Hailiang

last: Liu


title: Tissue-level transcriptome response to local and distal chilling reveals potential chilling survival mechanisms in maize

city: Changchun

first: Chunmei

last: Xue

state: Jilin Province

address: No. 5333 Xi’an Road, Lvyuan District

institute: Jilin University

summary: Chilling is a major stress to plants of subtropical and tropical origins including maize. To reveal molecular mechanisms underlying chilling tolerance and chilling survival, we investigated maize transcriptome responses to chilling stress in differentiated leaves and roots as well as in crowns with meristem activity for survival. Chilling stress on maize shoots and roots is found to each contribute to seedling lethality in maize. Comparison of maize lines with different chilling tolerance capacity reveals that chilling survival in maize is highly associated with upregulation in leaves and crowns of abscisic acid response pathway, transcriptional regulators and cold response as well as downregulation of heat response in crowns. Comparison of chilling treatment on whole and part of the plants reveals that response to distal-chilling is very distinct from, and sometimes opposite to, response to local- or whole-plant chilling in both leaves and roots, suggesting a communication between shoots and roots in environmental perception. In sum, this study details chilling responses in leaves, roots and crowns and reveals potential chilling survival mechanism in maize, which lays ground for further understanding survival and tolerance mechanisms under low but non-freezing temperatures in tropical and subtropical plants.

overall_design: Examination of 48 samples in maize B73 on three-leaf stage, including four tissues (leaf, root, top-crown and bottom-crown) under four conditions (normal condition, whole-plant chilling, shoot-only chilling and root-only chilling) with three biological repeats. The four tissues under normal condition were the control group and the others were experimental group.

first: Yuan

last: Jiang

first: Yaping

last: Yuan

first: Jian

last: Hua


title: Essential roles of RNA cap-proximal ribose methylation in mammalian embryonic development and fertility

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

summary: Eukaryotic RNA pol II transcripts are capped at the 5′ end by the methylated guanosine (m7G) moiety. In higher eukaryotes, CMTR1 and CMTR2 catalyse cap-proximal ribose methylations on the first (cap1) and second (cap2) nucleotides, respectively. These modifications mark RNAs as ‘self’, blocking the activation of the innate immune response pathway. Here we show that loss of mouse Cmtr1 or Cmtr2 leads to embryonic lethality, with non-overlapping sets of transcripts being regulated, without activation of the interferon pathway. In contrast, Cmtr1 mutant adult mouse livers exhibit a chronic activation of the interferon pathway, with multiple interferon-stimulated genes (ISGs) being expressed. Conditional deletion of Cmtr1 in the male germline leads to infertility, while global translation is unaffected in the Cmtr1 mutant mouse liver and human cells. Thus, mammalian cap1 and cap2 modifications have an essential role in embryonic gene regulation that is independent of their established role in evading the innate immune system.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA sequencing was applied to study the gene expression differences between Cmtr1+/+ and Cmtr1-/- mouse embryos (E6.5 and E7.5), Cmtr1+/loxP; AlbCreERT2+/- (control) and Cmtr1-/loxP; AlbCreERT2+/- (Cmtr1 cKO) mouse livers, CMTR1+/+ and CMTR1-/- HAP1 cells, Cmtr2+/+ and Cmtr2-/- mouse embryos (E6.5 and E7.5). Ribosome profiling was used to assess translation efficiency differences between Cmtr1+/loxP; AlbCreERT2+/- (control) and Cmtr1-/loxP; AlbCreERT2+/- (Cmtr1 cKO) mouse livers, CMTR1+/+ and CMTR1-/- HAP1 cells.

first: Michaela

last: Dohnalkova

first: Kyrylo

last: Krasnykov

first: Mateusz

last: Mendel

first: Lingyun

last: Li

first: Olesya

last: Panasenko

first: Fabienne

last: Fleury-Olela

first: Cathrine

middle: B

last: Vågbø

first: David

last: Homolka


title: Long non-coding RNAs contribute to DNA damage resistance in Arabidopsis thaliana

city: Vienna

first: Aleksandra

last: Kornienko

state: Vienna

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

summary: Efficient repair of DNA lesions is essential for faithful transmission of genetic information between somatic cells and for genome integrity across generations. Plants have multiple, partially redundant and overlapping DNA repair pathways, probably due to the less constricted germline and the inevitable exposure to light including higher energy wavelengths. Many proteins involved in DNA repair and their mode of actions are well described. In contrast, a role for DNA damage-associated RNA components, evident from many other organisms, is less well understood. Here, we have challenged young Arabidopsis thaliana plants with two different types of genotoxic stress and performed de novo assembly and transcriptome analysis. We identified three long non-coding RNAs (lncRNAs) that are lowly or not expressed under regular conditions but up-regulated or induced by DNA damage. To address whether they have a potential role in DNA repair, we generated CRISPR/Cas deletion mutants and found that the absence of the lncRNAs impairs the recovery capacity of the plants from genotoxic stress. The genetic loci are highly conserved among world-wide distributed Arabidopsis accessions and within related species in the Brassicaceae group. Together, these results suggest that the lncRNAs have a conserved function in connection with DNA damage and provide a basis for a mechanistic analysis of their role.

overall_design: To identify lncRNAs specifically involved in repair of DNA double strand breaks, we perfomed a transcriptomic analysis combined with de novo transcriptome assembly of Arabidopsis seedlings challenged with two different genotoxic treatments (zeocin and UV-C)

first: Nathalie

last: Durut

first: Heiko

last: Schmidt

first: Nicole

last: Lettner

first: Mattia

last: Donà

first: M

last: Nordborg

first: Ortrun

last: Scheid


title: Evolutionarily conserved effects of Notch signaling drive intestinal graft-versus-host disease in mice and non-human primates

city: Seattle

first: Scott

last: Furlan

address: 1100 Fairview Ave N

institute: CRD

summary: Notch signaling promotes T-cell pathogenicity and graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation (allo-HCT) in mice, with a dominant role for the Delta-like ligand DLL4. To assess if Notch’s effects are evolutionarily conserved and identify key mechanisms, we studied antibody-mediated DLL4 blockade in a non-human primate (NHP) model similar to human allo-HCT. Short-term DLL4 blockade improved post-transplant survival with striking, durable protection from gastrointestinal GVHD, out of proportion to other disease sites. Unlike prior immunosuppressive strategies tested in the NHP GVHD model, anti-DLL4 interfered with a T-cell transcriptional program associated with intestinal infiltration. In cross-species investigations, Notch inhibition decreased surface abundance of the gut-homing integrin α4β7 in conventional T-cells while preserving α4β7  in regulatory T-cells, with findings suggesting increased 1 competition for 4 binding in conventional T-cells. Secondary lymphoid organ fibroblastic reticular cells emerged as the critical cellular source of Delta-like Notch ligands for Notch-mediated up-regulation of α4β7  integrin in T-cells after allo-HCT. Altogether, DLL4/Notch blockade decreased effector T-cell infiltration into the gut, with increased regulatory to conventional T-cell ratios early after allo-HCT. Our results identify a conserved, biologically unique and targetable role of DLL4/Notch signaling in GVHD.

overall_design: Microarray Data for CD3 T cells from 107 samples taken from animals after HCT and controls

first: Leslie

last: Kean


title: HDAC3 is critical in tumor development and therapeutic resistance in Kras-mutant non-small cell lung cancer [ChIP-seq GEMM tumors]

city: La Jolla

first: Reuben

last: Shaw

address: 10010 N Torrey Pines Rd

department: Molecular and Cell Biology Laboratory

institute: Salk Institute for Biological Studies

summary: HDAC3 is one of the main targets of Histone Deacetylase (HDAC) inhibitors in clinical development as cancer therapies, yet the in vivo role of HDAC3 in solid tumors is unknown.  Here, we identified a critical role for HDAC3 in KRAS mutant lung cancer.  Using genetic engineered mouse models (GEMM), we found that HDAC3 is required for lung tumor growth in vivo.  HDAC3 was found to direct and enhance the transcription effects of the lung cancer lineage transcription factor NKX2-1 to mediate expression of a common set of target genes.  We identified FGFR1 as a critical new target of HDAC3.  Leveraging this, we identified that an HDAC3-dependent transcriptional cassette becomes hyperactivated as KRAS/LKB1 mutant cells develop resistance to the MEK inhibitor trametinib, and this can be reversed by treatment with the HDAC1/HDAC3 inhibitor entinostat.  We found that the combination of entinostat plus trametinib treatment elicits therapeutic benefit in the KRAS/LKB1 GEMM.

overall_design: ChIP-seq for Hdac3 in KL and KP primary tumors.

first: Lillian

last: Eichner


title: HDAC3 is critical in tumor development and therapeutic resistance in Kras-mutant non-small cell lung cancer [ChIP-seq KL LJE1 cells]

overall_design: ChIP-seq for Hdac3 and H3K27ac in KL cells.


title: Single-cell transcriptional sequencing of whole mouse lung cells

city: Nanjing

first: Chao

last: Jie

state: Jiangsu

address: 87 Dingjiaqiao Rd

department: Department of Physiology

institute: Southeast University

summary: We report the main cell types and molecular mechanisms involved in pulmonary fibrosis based on single-cell sequencing.

overall_design: Examination of mouse lung sample of NS-7d, SiO2-7d, NS-7d, SiO2-56d

first: Mengling

last: Chen

first: Jie

last: Chao


title: Activity-Dependent Transcriptional Program in NGN2+ Neurons Enriched for Genetic Risk for Brain-Related Disorders

city: New York City

first: Jaroslav

last: Bendl

state: New York

address: One Gustave L. Levy Place, Department of Genetics and Genomics Sciences, Box 1210

department: Genetics and Genomics Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: We generated human-induced pluripotent stem cell (hiPSC) derived neurons isolated from six childhood-onset schizophrenia (COS) cases and five healthy controls. To measured the transcriptional and epigenomic changes following neuronal activation with KCl, we harvested these cells one and six hours after stimulation with 50mM KCl and under non-stimulating conditions, followed by RNA-seq and ATAC-seq profiling. We comprehensively characterized activity-dependent changes in gene expression and gene regulatory element activity (chromatin accessibility) in hiPSC-derived neurons. After one hour of KCl induced depolarization, neurons invoked substantial activity-dependent changes in the expression of genes regulating synaptic functions, some of which are known to be perturbed in neuropsychiatric diseases, including schizophrenia and autism spectrum disorder. By capturing changes in chromatin accessibility, we extended our analysis to activity-dependent gene regulatory elements, captured by changes in chromatin accessibility, and also found significant heritability enrichment for schizophrenia variants in the activity-induced enhancers. Our framework not only offers an alternative approach to study the mechanisms of COS but also adds to converging evidence that activity-induced expression changes mediated by the activity of regulatory elements might contribute to schizophrenia risk.

overall_design: Gene expression (RNA-seq) and open chromatin (ATAC-seq assay) profiles in hiPSC neurons in unstimulated and KCl-stimulated conditions (measured after 1hr and 6hr following membrane depolarization).

first: Panos

last: Roussos

first: Brennand

last: Kristen

first: John

last: Fullard

first: Ma

last: Yixuan

first: Bendl

last: Jaroslav


title: Modeling incomplete penetrance in arrhythmogenic cardiomyopathy by human induced  pluripotent stem cell derived cardiomyocytes

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary: Human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) are  commonly used to model arrhythmogenic cardiomyopathy (ACM), a heritable cardiac  disease characterized by severe ventricular arrhythmias, fibrofatty myocardial  replacement and progressive ventricular dysfunction. Although ACM is inherited as an  autosomal dominant disease, incomplete penetrance and variable expressivity are  extremely common, resulting in different clinical manifestations. Here, we propose  hiPSC-CMs as a powerful in vitro model to study incomplete penetrance in ACM.  Six hiPSC lines were generated from blood samples of three ACM patients carrying a  heterozygous deletion of exon 4 in the PKP2 gene, two asymptomatic (ASY) carriers of  the same mutation and one healthy control (CTR), all belonging to the same family.  Whole exome sequencing was performed in all family members and hiPSC-CMs were  examined by ddPCR, western blot, Wes™ immunoassay system, patch clamp,  immunofluorescence and RNASeq.  Our results show molecular and functional differences between ACM and ASY hiPSC_x0002_CMs, including a higher amount of mutated PKP2 mRNA, a lower expression of the  connexin-43 protein, a lower overall density of sodium current, a higher intracellular  lipid accumulation and sarcomere disorganization in ACM compared to ASY hiPSC_x0002_CMs. Differentially expressed genes were also found, supporting a predisposition for a  fatty phenotype in ACM hiPSC-CMs. These data indicate that hiPSC-CMs are a suitable model to study incomplete penetrance in ACM.

overall_design: Gene expression profiles of total RNA extracted from human induced pluripotent stem cell-derived cardiomyocites from ACM patients and asymptomatic family members. Cells were cultivated either in basal medium condition or in conditions stimulating adipogenic differentiation. Differential expression analysis was carried out using DESeq2 comparing gene expression data between ACM and asymptomatic samples in basal or adipogenic medium.

first: Marzia

last: De Bortoli

first: Viviana

last: Meraviglia

first: Katarina

last: Mackova

first: Laura

last: Frommelt

first: Eva

last: König

first: Chiara

last: Volani

first: Maja

last: Schlittler

first: Giada

last: Cattelan

first: Benedetta

last: Motta

first: Claudia

last: Volpato

first: Werner

last: Rauhe

first: Andrea

last: Barbuti

first: Serena

last: Zacchigna

first: Peter

middle: P

last: Pramstaller

first: Alessandra

last: Rossini


title: Transcriptional effects of LXR nuclear receptors on GM-CSF-derived macrophages

first: Miguel

last: Vega

address: Ramiro de Maeztu 9

institute: CIB (CSIC)

summary:
Analysis of the role of LXR transcriptions factors on the transcriptional signature of human GM-CSF-dependent monocyte-derived macrophages.
Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were treated with LXR agonist GW3965 (1 uM, Tocris), LXR antagonist GSK2033 (1 uM, Tocris), GW3965 and GSK2033, or dimethyl sulfoxide (DMSO) as vehicle. In the dual condition, the antagonist was added 1-hour prior to agonist treatment.
Then, monocytes were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 7 days in the presence of 1000 U/ml GM-CSF, with cytokine addition every two days.

overall_design: mRNA profiles of human GM-CSF-derived macrophages treated modulators of LXR nuclear receptors

first: Arturo

last: González de la Aleja

first: Angel

last: Corbí


title: Cannabinoids act as H3k27ac Epigenetic Modifiers  of Genes Regulating MHC-I Antigen Processing and Presentation that Induce Cytolytic T Lymphocyte Recognition of Metastatic Cancers

city: Vancouver

first: Wilfred

last: Jefferies

state: BC

address: 2260 Oak st

department: Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

overall_design: Twenty-four hours after seeding, cells were cultured at the optimum concentrations of Cannabigerol 0.055umol, or 5.832x10-6 nmol IFN gamma or 1% DMSO vehicle for 48 hours. Cells were harvested using trypsin, and were pelleted at 200g for 5 mins before being resuspended in PBS. Cell viability was determined using Trypan Blue dye (Catalog# 15250061, Gibco) and cell counting slides (Catalog#1450015, Biorad) with Biorad TC20 automated cell counter. Once the viability was above 90%, the cells were quantified and 130K live cells were transferred into a new tube

first: Jefferies

last: Wilfred

first: Lack

last: Nathan

first: Morova

last: Tunc


title: Mutations in MAFB that cause Multicentric Carpo Tarsal Osteolysis (MCTO) affect the transcriptome of M-MØ

city: Madrid

summary: Macrophage phenotypic and functional heterogeneity derives from tissue-specific transcriptional signatures shaped by the local microenvironment. Most studies addressing the molecular basis for macrophage heterogeneity have focused on murine cells, while the factors controlling the functional specialization of human macrophages are less known. M-CSF drives the generation of human monocyte-derived macrophages with a potent anti-inflammatory activity upon stimulation. The contribution of MAFB to the homeostatic/anti-inflammatory macrophage profile is further supported by the skewed polarization of monocyte-derived macrophages from Multicentric Carpo Tarsal Osteolysis (OMIM#166300), a pathology caused by mutations in the MAFB gene.

overall_design: mRNA profiles of human macrophages differentiated with M-CSF from peripheral blood monocytes from one patient with MCTO and two healthy donors.

first: Angeles

last: Dominguez-Soto


title: Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation

status: Public on Jul 13 2023

city: Invergowrie / Dundee

first: Raul

last: Huertas

state: Perth and Kinross

address: Errol Road

department: Environmental and Biochemical Sciences

institute: The James Hutton Institute

summary: Knowing how switchgrass (Panicum virgatum L.) responds and adapts to phosphorus (P)-limitation will aid efforts to optimize P acquisition and use in this species for sustainable biomass production. This integrative study investigated the impacts of mild, moderate, and severe P-stress on genome transcription and whole-plant metabolism, physiology and development in switchgrass. P-limitation reduced overall plant growth, increased root/shoot ratio, increased root branching at moderate P-stress, and decreased root diameter with increased density and length of root hairs at severe P-stress. RNA-seq analysis revealed thousands of genes that were differentially expressed under moderate and severe P-stress in roots and/or shoots compared to P-replete plants, with many stress-induced genes involved in transcriptional and other forms of regulation, primary and secondary metabolism, transport, and other processes involved in P-acquisition and homeostasis. Amongst the latter were multiple miRNA399 genes and putative targets of these. Metabolite profiling showed that levels of most sugars and sugar alcohols decreased with increasing P stress, while organic and amino acids increased under mild and moderate P-stress in shoots and roots, although this trend reversed under severe P-stress, especially in shoots.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from switchgrass plants grown under optimal nutritional conditions or with different phosphorus limitation regimes (mild, moderate and severe) for four weeks.

last: Ding

first: Ivone

last: Torres-Jerez

first: Nick

last: Krom

first: Yuhong

last: Tang

first: Wolf

last: Scheible

first: Michael

last: Udvardi


title: Cardiac Remodeling During Pregnancy With Metabolic Syndrome: Prologue of Pathological Remodeling

city: Philadelphia

first: Yijun

last: Yang

address: 3500 North Broad St., MERB 1007

institute: Temple University School of Medicine

summary: The heart undergoes physiological hypertrophy during pregnancy in healthy individuals. Metabolic syndrome (MetS) is now prevalent in women of child-bearing age and might add risks of adverse cardiovascular events during pregnancy. The present study asks if cardiac remodeling during pregnancy in obese individuals with MetS is abnormal and whether this predisposes them to a higher risk for cardiovascular disorders. The idea that MetS induces pathological cardiac remodeling during pregnancy was studied in a long-term (15 weeks) Western diet–feeding animal model that recapitulated features of human MetS. Pregnant female mice with Western diet (45% kcal fat)–induced MetS were compared with pregnant and nonpregnant females fed a control diet (10% kcal fat). Pregnant mice fed a Western diet had increased heart mass and exhibited key features of pathological hypertrophy, including fibrosis and upregulation of fetal genes associated with pathological hypertrophy. Hearts from pregnant animals with WD-induced MetS had a distinct gene expression profile that could underlie their pathological remodeling. Concurrently, pregnant female mice with MetS showed more severe cardiac hypertrophy and exacerbated cardiac dysfunction when challenged with angiotensin II/phenylephrine infusion after delivery. These results suggest that preexisting MetS could disrupt physiological hypertrophy during pregnancy to produce pathological cardiac remodeling that could predispose the heart to chronic disorders.

overall_design:
The idea that MetS induces pathological cardiac remodeling during pregnancy was studied in a long-term (15 weeks) Western diet–feeding animal model that recapitulated features of human MetS. Pregnant female mice with Western diet (45% kcal fat)–induced MetS were compared with pregnant and nonpregnant females fed a control diet (10% kcal fat).
***Please note that the raw data have been lost and thus are not provided****

first: Justin

last: Kurian


title: Analysis of early transcriptomic response of Arabidopsis seedlings under priming and heat shock

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRAE

summary: We evaluated the effect of a pre-treatment at 38°C on the early response (30 min) of Arabidopsis thaliana seedlings to a 43°C treatment

overall_design: Comparative gene expression analysis (nuclear and organellar RNAs) between pre-treated and non pre-treated Arabidopsis seedlings

first: Elise

last: Réthoré

first: David

last: Macherel


title: HDAC3 is critical in tumor development and therapeutic resistance in Kras-mutant non-small cell lung cancer [RNA-seq GEMM tumors]

first: Reuben

last: Shaw

state: California

overall_design: RNA-seq on primary NSCLC tumors from Kras, KL, KP, KPL genotypes.

first: Lillian

last: Eichner


title: A novel TOX3-WDR5-ABCG2 signaling axis regulates the progression of colorectal cancer by accelerating stem-like traits and chemoresistance

city: Dalian

first: Jiaojiao

last: Hao

address: No.9 West Section of Lvshun South Road, Dalian City, Liaoning Province, China

institute: Dalian Medical University

summary: To further explore the molecular characteristics of these formed cCSCs, mRNA profile analysis was performed and compared between cCSCs and the corresponding adherent cells.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of2 different cells at two forms(adherent and spheroids ).
Comparative gene expression profiling analysis of RNA-seq data for HCT116 and LOVO cells and their different forms.

first: Wei

last: Guo


title: ChIP-seq analyis of SVG-p12 human fetal glial cells with exogenous expression of wildtype SOX10 or schwannoma-derived mutant isoforms

city: Urbana

first: Jun

last: Song

email: songj@illinois.edu, jssong137@gmail.com

state: IL

address: 1110 West Green Street, MC 704

institute: University of Illinois, Urbana-Champaign

summary:
To investigate the chromatin binding patterns of wildtype SOX10 versus schwannoma-derived mutant isoforms, we established SVG-p12 cell lines stably expressing either FLAG epitope tagged wildtype SOX10 or two different mutant isoforms of SOX10.
We then performed chromatin immunoprecipitation-DNA sequencing on these SVG-p12 cell lines stably transduced with wildtype or mutant SOX10 isoforms using an anti-FLAG epitope antibody.

overall_design: Comparative chromatin binding analysis of ChIP-seq data for SVG-p12 cells following stable transduction wildtype SOX10 or two different tumor-derived mutant isoforms of SOX10.

last: Solomon

first: Joseph

last: Costello


title: The transcriptional landscape of Nicotiana benthamiana and Verticillium dahliae interaction

city: Tübingen

first: Chenlei

last: Hua

address: Auf der Morgenstelle 32

department: Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP)

country: Germany

institute: University of Tübingen

summary: Verticillium dahliae is a soil-borne fungus with a broad host range, including the model plants Nicotiana benthamiana and Arabidopsis thaliana. The plant immunity can be activated by Vd-derived patterns while V. dahliae secreted effectors. We report here the RNAseq analyses of samples from N. benthamiana infected by V. dahliae strains 592 and 171 at different time points. The data showed dynamic expression patterns of genes not only from plant defense signaling but also plant developmental signaling.

sample_organism:
Nicotiana benthamiana
Verticillium dahliae

overall_design: We used two V. dahliae strains 592 and 171 to inoculate N. benthamiana seedlings followed by RNA isolation from infected seedlings at 3, 6, 9 12 days after inoculation.

first: Lisha

last: Zhang


title: HDAC3 is critical in tumor development and therapeutic resistance in Kras-mutant non-small cell lung cancer [RNA-seq HDAC3 KO p65 KO]

overall_design: RNA-seq in KL cells transduced with sgNT (non-targeting), sgHdac3, or sgp65.


title: HDAC3 is critical in tumor development and therapeutic resistance in Kras-mutant non-small cell lung cancer [RNA-seq trametinib entinostat treatment]

overall_design: RNA-seq in KL cells treated with Trametinib, Entinostat for 3 or 13 days.


title: Regulation of host antiviral factors expression by TET2-mediated DNA demethylation

city: Hangzhou

first: Yixiang

last: Hu

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

institute: Zhejiang University

summary:
Host antiviral innate immune response is regulated by epigenetic mechanisms. TET2 oxidizes the methyl group of 5-methylcytosine (5mC)  to 5-hydroxymethylcytosine (5hmC) in a process that activates demethylation of CpG DNA. Here, we characterize the genome-wide distribution of 5hmC in both wild-type and TET2-knockout THP-1 cells infected with the influenza A virus (IAV) using DNA immunoprecipitation by anti-5hmc antibody coupled with high-throughput DNA sequencing. 5hmC marks signature genes associated with host innate immune response against IAV infection. Moreover, TET2 expression is inhibited by IAV infection via viral endoribonuclease PA-X . Deletion of the TET2 gene in THP-1 cells decreased expression of genes related to interferon signaling. We further verified that TET2 plays a critical role in the expression of STAT1 and some interferon-stimulated genes through demethylation. Collectively, our findings demonstrate a key role of TET2-mediated active DNA demethylation in anti-IAV immunity.
Hydroxymethylated DNA immunoprecipitation-sequencing (hMeDIP-Seq) in IAV-infected wild-type and TET2-knockout THP-1 cells.

overall_design: Yixiang, Hu

first: Xinru

last: Chen

first: Yuehuan

last: Ling

first: Kun

last: Zhou

first: Yan

last: Li


title: Oxidative stress induces lysosomal membrane permeabilization and ceramide accumulation in retinal pigment epithelial cells

first: Kevin

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Oxidative stress has been implicated in the pathogenesis of age-related macular degeneration, the leading cause of blindness in older adults, with retinal pigment epithelium (RPE) cells playing a key role. To better understand the cytotoxic mechanisms underlying oxidative stress, we used a mouse model of iron overload, as iron can catalyze reactive oxygen species formation in the RPE. In a liver-specific Hepc (Hamp) knockout murine model of systemic iron overload, RPE cells accumulated lipid peroxidation adducts and lysosomes, developed progressive hypertrophy, and underwent cell death. Proteomic and lipidomic analyses revealed accumulation of lysosomal proteins, ceramide biosynthetic enzymes, and ceramides. The proteolytic enzyme cathepsin D had impaired maturation. A large proportion of lysosomes were galectin-3 positive, suggesting cytotoxic lysosomal membrane permeabilization. RNA sequencing was performed and did not show evidence of upregulation of CLEAR network genes, suggesting that the lysosomal accumulation was due to decreased lysosomal turnover and not increased lysosomal biogenesis. Collectively, these results demonstrate that iron overload induces lysosomal accumulation and impairs lysosomal function, likely owing to iron-induced lipid peroxides that can inhibit lysosomal enzymes.

overall_design: To determine whether liver-specific hepcidin knockout (LS-HepcKO) mice had increased lysosomal biogenesis, we performed an RNA sequencing experiment using isolated RPE cells from 12 month old control and LS-HepcKO mice. There were two control and 3 LS-HepcKO mice.

first: Joshua

last: Dunaief


title: 9-Butyl-Harmol Exerts Antiviral Activity against Newcastle Disease Virus through Targeting GSK-3β and HSP90β

city: Yangling

first: Chongyang

last: Wang

address: Xinong road

department: College of veterinary medicine

institute: Northwest Agriculture and Forestry University

summary: To investigate the potential function and target of 9-butyl-harmol, DF-1 cells were treated with 9-butyl-harmol or DMSO.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 9-butyl-harmol- or DMSO- treated DF-1 cells.

first: Ting

first: Ruochen

first: Liuyuan

last: Duan

first: Qili

last: Hou

first: Yu

last: Han

first: Jiangkun

last: Dai

first: Wenbin

first: Shanhui

last: Ren

first: Haijin

last: Liu

first: Xinglong

first: Sa

last: Xiao

first: Junru

first: Zengqi

last: Yang


title: ChIP-seq analysis of OGDH1 occupancy in the Arabidopsis genome

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

summary: To determine which loci are bound by OGDH1, we performed ChIP-seq experiment using a functional OGDH1:Flag line. We found that in the Arabidopsis genome most of the OGDH1 target loci carry histone methylation marks (e.g. H3K4me3, H3K27me3 etc.). This suggests that the function of nuclear OGDH1 is linked with histone-methylation control  in Arabidopsis.

overall_design: Nuclei were extracted from 11-d-old OGDH1:FLAG seedlings as previously described (Louwers et al., 2009), followed by chromatin immunoprecipitation with anti-FLAG M2 magnetic beads (Sigma). DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), and subsequently were sequenced on NovaSeq 6000 (Illumina).

first: Yang

last: Ou

first: Z

first: Y

last: He


title: Transcriptomic analyis of SVG-p12 human fetal glial cells with overexpression of wildtype SOX10 or schwannoma-derived mutant isoforms

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

summary:
To investigate the gene expression changes caused by wildtype versus schwannoma-derived mutations in SOX10, we established SVG-p12 cell lines stably expressing either empty pCDF1 vector, wildtype SOX10, or two different mutant isoforms of SOX10.
We then performed gene expression profiling analysis using RNA-seq for these SVG-p12 cell lines stably transduced with wildtype or mutant SOX10 isoforms.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SVG-p12 cells following stable transduction with empty pCDF1 vector, wildtype SOX10, or two different tumor-derived mutant isoforms of SOX10.


title: The tumor suppressor CREBBP and the oncogene MYCN cooperate to induce malignant brain tumors in mice

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

summary: The tumor suppressor CREBBP (CREB binding protein) and the MYCN proto-oncogene are critically involved in brain development. Both genes are frequently mutated in the same tumor entities, including high-grade glioma and medulloblastoma. Therefore, we hypothesized that alterations in both genes cooperate to induce brain tumor formation. For further investigation, hGFAP-cre::CrebbpFl/Fl::lsl-MYCN mice were generated, which combine a Crebbp deletion with an overexpression of MYCN in neural stem cells (NSCs). Within eight months, these animals developed aggressive forebrain tumors that resulted in tumor-related death with a penetrance of 75 percent. The earliest tumors were detectable in the olfactory bulbs of seven-day-old mice. In order to examine the cellular biology of these tumors, single-cell RNA sequencing (scRNA-seq) was performed, which revealed high intratumoral heterogeneity. Data comparison with reference CNS cell types indicated the highest similarity of tumor cells with transit-amplifying or activated NSCs of the ventricular-subventricular zone (V-SVZ). Consequently, we analyzed V-SVZ NSCs of our mouse model with the aim of confirming that the tumors originate from this stem cell niche. Mutant V-SVZ NSCs showed significantly increased cell viability and proliferation as well as reduced glial and neural differentiation in vitro compared to control cells. In summary, we demonstrate the oncogenic potential of a combined loss of function of CREBBP and overexpression of MYCN  in this cell population. This mouse model thus provides a valuable tool to study tumor-driving mechanisms in a key neural stem/progenitor cell niche.

overall_design: We investigated the transcriptomes of two tumors from a conditional knockout mouse model (hGFAP-cre::CrebbpFl/Fl::lsl-MYCNFl/Fl, tumors extracted from a 90 day old male and 100 days old female). This model combines a homozygous deletion of murine Crebbp and biallelic expression of exogenous human MYCN. Single-cell suspensions were generated from both tumors and further processed for  single-cell RNA sequencing (scRNA-seq) using 10x Genomics technology.

first: Melanie

last: Schoof

first: Gefion

middle: D

last: Epplen

first: Annika

last: Ballast

first: Dörthe

last: Holdhof

last: Göbel

first: Sina

last: Neyazi

first: Thomas

last: Albert

first: Kornelius

last: Kerl

first: Ulrich

last: Schüller


title: A novel co-culture model for investigation of the effects of systemic inflammation on brain endothelial cells

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

summary: To investigate the mechanisms underlying the blood-brain barrier dysfunction caused by systemic inflammation. We establish a co-culture system consisting of bEnd.3 cells and LPS-treated Raw 246.7 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bEnd.3 cells co-cultured with PBS- and LPS-treated Raw 246.7 cells group.

first: Junling

first: Ken-ichiro

last: Fukuchi

first: Mark

last: Maienschein-Cline


title: IL-7 receptor signaling drives human B-cell precursor differentiation and expansion

city: Leiden

first: Mirjam

last: van der Burg

address: Albinusdreef 2

country: Netherlands

institute: LUMC

summary: Whereas absence of interleukin 7 (IL-7) signaling completely abrogates T and B lymphopoiesis in mice, severe combined immunodeficiency patients with mutations in the IL-7 receptor α chain still generate peripheral blood B cells. Consequently, human B lymphopoiesis has been thought to be independent of IL-7 signaling. Using flow cytometric analysis and single-cell RNA sequencing of bone marrow samples of IL-7 receptor α chain-deficient patients and healthy controls in combination with in vitro modeling of human B-cell differentiation, we demonstrate that IL-7 receptor signaling has a crucial role in human B lymphopoiesis. IL-7 drives proliferation and expansion of early B-cell progenitors, but not of pre-BII large cells. In addition, IL-7 has a limited role in the prevention of cell death. Furthermore, IL-7 guides cell fate decisions by enhancing the expression of BACH2, EBF1, and PAX5, which jointly orchestrate specification and commitment of early B-cell progenitors. In line with this observation, early B-cell progenitors of IL-7Rα-deficient patients still expressed myeloid-specific genes. Collectively, our results unveil a thus-far unknown role for IL-7 signaling in promoting the B-lymphoid fate and expanding early human B-cell progenitors, while defining important differences between mice and humans. Our results have implications for hematopoietic stem cell transplantation strategies in patients with T- B+ severe combined immunodeficiency and provide insights into the role of IL-7 receptor signaling in leukemogenesis.

overall_design: Sorted mononuclear cells from bone marrow of two healthy donors and two patients with IL7RA deficiency were stained with CITEseq antibodies (IL7RA, CD34, CD19 and IgM) and analyzed using scRNAseq

first: Fabian

last: Kaiser

first: Iga

last: Janowska

first: Roberta

last: Menafra

last: de Gier

first: Jakov

last: Korzhenevich

first: Ingrid

last: Pico-Knijnenburg

first: Indu

last: Khatri

first: Ansgar

last: Schulz

first: Taco

last: Kuijpers

first: Arjan

last: Lankester

first: Lukas

last: Konstantinidis

first: Mirian

last: Erlacher

first: Susan

last: Kloet

first: Pauline

last: van Schouwenburg

first: Marta

last: Rizzi


title: HDAC3 is critical in tumor development and therapeutic resistance in Kras-mutant non-small cell lung cancer

city: La Jolla

first: Reuben

last: Shaw

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

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

overall_design: Refer to individual Series


title: HDAC3 is critical in tumor development and therapeutic resistance in Kras-mutant non-small cell lung cancer [RNA-seq HDAC3 KO NKX2-1 KO]

summary: HDAC3 is one of the main targets of Histone Deacetylase (HDAC) inhibitors in clinical development as cancer therapies, yet the in vivo role of HDAC3 in solid tumors is unknown.  Here, we identified a critical role for HDAC3 in KRAS mutant lung cancer.  Using genetic engineered mouse models (GEMM), we found that HDAC3 is required for lung tumor growth in vivo.  HDAC3 was found to direct and enhance the transcription effects of the lung cancer lineage transcription factor NKX2-1 to mediate expression of a common set of target genes.  We identified FGFR1 as a critical new target of HDAC3.  Leveraging this, we identified that an HDAC3-dependent transcriptional cassette becomes hyperactivated as KRAS/LKB1 mutant cells develop resistance to the MEK inhibitor trametinib, and this can be reversed by treatment with the HDAC1/HDAC3 inhibitor entinostat.  We found that the combination of entinostat plus trametinib treatment elicits therapeutic benefit in the KRAS/LKB1 GEMM.

overall_design: RNA-seq in KL and KP cells transduced with sgNT, sgHdac3, or sgTTF1/NKX2-1.

first: Lillian

last: Eichner


title: Epigenome analysis of schwannomas

first: David

last: Solomon

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of 22 schwannomas belonging to three different genotypes (NF2-mutant, SOX10-mutant, and HTRA1-fused). The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of 22 schwannomas.

overall_design: Bisulfite converted genomic DNA extracted from the 22 schwannoma tumor samples was hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips


title: FACT maintains pluripotency factor expression through gene-distal regulation in embryonic stem cells [RNA-seq]

city: Pittsburgh

middle: Charles

last: Klein

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

summary: The mammalian FACT complex is a highly conserved histone chaperone with essential roles in transcription elongation, histone deposition, and maintenance of stem cell state. FACT is essential for viability in pluripotent cells and cancer cells, but otherwise dispensable for most mammalian cell types. FACT deletion or inhibition can block reprogramming of fibroblasts to induced pluripotent stem cells, yet the molecular mechanisms through which FACT regulates cell fate decisions remain unclear. To determine the mechanism by which FACT regulates stem cell identity, we used the auxin-inducible degron systems to deplete murine embryonic stem cells of FACT subunit SPT16 and subjected depleted cells to genome-wide factor localization, nascent transcription analyses, and genome-wide nucleosome profiling. Inducible depletion of SPT16 reveals a critical role in regulating targets of the master regulators of pluripotency: OCT4, KLF4, MYC, NANOG, and SOX2. Depletion of SPT16 leads to increased nucleosome occupancy at genomic loci occupied by these transcription factors, as well as gene-distal regulatory sites defined by DNaseI hypersensitivity. This heightened occupancy suggests a mechanism of nucleosome filling, wherein the sites typically maintained in an accessible state by FACT are occluded through loss of FACT-regulated nucleosome spacing. 20% of transcription arising from gene-distal regions bound by these factors is directly dependent on FACT, and putative gene targets of these non-coding RNAs are highly enriched for pluripotency in pathway analyses. Upon FACT depletion, transcription of Pou5f1 (OCT4), Sox2, and Nanog are downregulated, suggesting that FACT not only co-regulates expression of the encoded proteins’ targets, but also the pluripotency factors themselves. We find that FACT maintains cellular pluripotency through a complex regulatory network of both coding and non-coding transcription.

overall_design: 12 traditional RNA-seq libraries, with two replicates per condition in two independently-targeted cell lines (SPT16-V5-AID C-terminal tag). Control samples were treated with EtOH, while experimental samples were treated with IAA.

middle: C

first: Santana

middle: M

last: Lardo

first: Sarah

last: Hainer

first: Kurtis

last: McCannell


title: RNA-Seq of HUVEC

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Determination of basal expression levels of protein-coding and lncRNA genes in human umbilical vein endothelial cells.

overall_design: 4 replicates of untreated HUVEC

first: Matthias

last: Leisegang


title: PU.1-driven gene regulation in HSPC under chronic inflammatory conditions

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus


title: Gene Expression Signature in Rat Pituitary MMQ Cells Treated With DRD2 agonist UNC9994

city: Wuhan

first: Zhoubin

last: Tan

state: Hubei province

institute: Tongji Hospital, Wuhan, China

summary: DRD2 agonists are effective in treating pituitary tumors. To fathom the β-arresin-dependent mechanisms underlying DRD2-mediated pituitary tumor growth suppression,we applied RNA-seq analysis to rat pituitary MMQ cells treated with a DRD2 β-arresin-biased agoinst, UNC9994.MMQ cells were treated with UNC9994(15μM) or vehecle control for 12 h or 24 h and then subject to RNA-seq analysis.We found oxidative-stress-related genes such as Nqo1 and Hmox1 were upregulated by UNC9994, revealing oxidative stress may be the basis of UNC9994-induced tumor growth suppression. Our study represents the first detailed analysis of transcriptomes in rat pituitary MMQ cells treated with DRD2 β-arresin-biased agonist.The significance of altered expression of specific transcripts will enhance our understanding of DRD2 signaling in pituitary tumor cells.

overall_design: MMQ cells were treated with UNC9994 (15μM) or vehicle control (DMSO) for 12h or 24h


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [7E and 7F]

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (7E_201029, 7E_201105, 7F_200723).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

middle: G

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: STAT5 occupancy profiling in GSCs (CUT&Tag)

status: Public on Jul 12 2023

first: Wei

last: Wang

state: Hubei

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology Tongji Medical College

summary: We investigated  the  STAT5 genomic binding regulated by EGFR signaling in GSCs

overall_design: CUT&Tag using antibody against STAT5 in  GSC456 cells untreated (UT) or treated with erlotinib

first: Xuhui

last: Qin


title: The role of EGFR-STAT5 signaling in GSCs


title: Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states [scRNA-Seq]

city: Philadelphia

first: Sam

last: Reffsin

address: 415 Curie Blvd

summary: The ability of a virus to infect a cell type is partly determined by host factors required for the viral life cycle. However, not every cell of a given type is equally susceptible, suggesting that our knowledge of the full spectrum of factors that promote infection is incomplete. Profiling the susceptible subsets of cells could reveal additional host factors, but viral infection dramatically alters the state of the cell, obscuring the state of these cells prior to infection. We used single-cell clone tracing to retrospectively identify cells that were highly susceptible to infection with SARS-CoV-2. Our approach revealed candidate factors playing roles in viral entry and regulation of the infectable cell state itself. Patient samples revealed heterogeneous expression of these factors in vivo, with heightened expression in particular inflammatory pathologies. Thus, variable expression of intrinsic cell states is a major determinant of whether individual cells can be infected by SARS-CoV-2.

overall_design: Comparative gene expression profiling analysis of single-cell RNA-seq data for Calu-3 cells. Biological and technical replicates are included and indicated. Technical replicates refer to same biological replicate split amongst multiple lanes of the 10x chromium chip.

last: Miller

first: Kasirajan

last: Ayyanathan

first: Margaret

last: Dunagin

first: Naveen

last: Jain

first: David

last: Schultz

first: Sara

last: Cherry

first: Arjun

last: Raj


title: Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states


title: Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states [bulkRNA-Seq]

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for Calu-3 cells sorted on ACE2 and TIG1 expression. Biological replicates are included and indicated.


title: Analysis of global transcriptomic response of lettuce seedlings (Lactuca sativa L.) to microalgae extract used as biostimulant agents

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

institute: University of Catania

summary: The use of new natural eco-sustainable products is becoming an interesting option in order to reduce the use of chemical fertilizers and increase crop yields. Seaweed extracts are gained major attention as plant biostimulants due to their positive effect on plant-growth as well as on improving plants’ tolerance against abiotic stresses. Among the horticulture crops, lettuce (Lactuca sativa L.) is a major fresh vegetable crop in the Mediterranean area, which often requires the use of natural biostimulants to improve both the quantity and quality of production. The aim of this work was to assess the effect of either Chlorella vulgaris or Scenedesmus quadricauda extracts on lettuce seedlings (Lactuca sativa L.) by motoring the induced transcriptomic modifications using a RNASeq approach. The results showed that both C. vulgaris and S. quadricauda extracts positively influence the growth of lettuce seedlings. However, a higher reprogramming of the gene expression occurred in the case of C. vulgaris treatment than in S. quadricauda extract. Considering the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional enrichments, the main KEGG terms are in the “Biosynthesis of secondary metabolites”, “Metabolic pathways”, “Carbon metabolism” and “Biosynthesis of amino acids” categories. This study lays the basis for understanding the mechanisms and processes triggered by the use of microalgal extracts, which can represent an easier-to-handle and cheaper method for an eco-sustainable cultivation of lettuce plants than the application of chemicals.

overall_design: Lettuce seedlings (Lactuca sativa L.) were provided by a local nursery and 10 seedlings at the “four true leaves” stage were transplanted in each box in a completely random design, performing five biological replicates for treatments. The seedlings were grown for 6 days in a growth chamber at 25 ± 2°C, with a 16-h photoperiod and they were irrigated every day with 100 mL distilled water. After this period of acclimatization (6 days),  the treatment was performed by irrigating the inert substrate with Hoagland solution (500 mL) containing either Chlorella vulgaris (LsCv sample) or Scenedesmus quadricauda (LsSq sample) extracts at the concentration of 1 mg of organic carbon per liter (Corg L-1), whereas the untreated plants (LsCK) received only 500 mL of Hoagland solution.

first: Danilo

last: Santoro

first: Ivana

last: Puglisi

first: Angelo

last: Sicilia

first: Andrea

last: Baglieri

first: Emanuele

last: La Bella

first: Angela


title: Multi-omics analysis explores the effect of chronic exercise on liver metabolic reprogramming in mice

first: Jianxin

last: Wu

address: No. 2, Yabao Road, Chaoyang District

institute: Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics

summary: The effect of exercise on human metabolism is obvious. However, the effect of chronic exercise on liver metabolism in mice is less well described. The healthy adult mice running for 6 weeks as exercise model and sedentary mice as control were used to perform transcriptomic, proteomic, acetyl-proteomics, and metabolomics analysis. In addition, correlation analysis between transcriptome and proteome, and proteome and metabolome was conducted as well. This dataset is transcriptomic data.

overall_design: We used healthy adult mice running for 6 weeks as exercise model, and sedentary mice as control.

first: Zhaoxu

last: Lu

first: Ping

last: Qian

first: Jiahui

last: Chang

first: Xuejia

last: He

first: Haifeng

last: Zhang

first: Jian

first: Ting


title: Enhanced nitrogen removal via Yarrowia lipolytica-mediated nitrogen and related metabolism of Chlorella pyrenoidosa from wastewater

city: Guangzhou

first: Danni

last: Lin

address: 388 Guangxin Road, Baiyun District

institute: Zhongkai University of Agriculture and Engineering

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the mechanism by which the microalgae-yeast co-culture system promotes wastewater denitrification. We concluded that microalgae and yeast exhibit a mutually beneficial relationship in the co-culture system. Microalgae nitrogen metabolism can be influenced by both miRNA and mRNA, and the presence of yeast stimulates gene expression in microalgae.

sample_organism:
Auxenochlorella pyrenoidosa
Yarrowia lipolytica

overall_design: We investigated mRNA/microRNA (miRNA) expression in the C. pyrenoidosa and Y. lipolytica co-culture after 3 and 5 days.

first: Yuming

last: Zhong

first: Huifan

last: Liu

first: Sufen

last: Li


title: Global mouse gene expression data from NUP98-NSD1/FLT3-ITD  AML samples and Normal Wild Type whole bone marrow and Normal Wild Type lineage negative bone marrow samples assessed by Bulk RNA-Seq.

city: Bethesda

first: Peter

last: Aplan

state: Maryland

address: 37 convent drive

department: Genetics

institute: CCR-NCI-NIH

summary: Acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy driven largely by gene mutations and epigenetic modifications. The Nucleoporin 98kDa (NUP98) gene is a component of the nuclear pore complex that also plays a role as an intranuclear transcription scaffold.  Fusion genes involving NUP98 have been recognized in a wide array of hematologic malignancy, most commonly AML4. Among over 30 partner genes known to be fused to NUP98 in human leukemia, NSD1 (for Nuclear receptor-binding SET Domain protein 1) (NSD1) is the most common. Patients with NUP98::NSD1 gene fusions have a poor prognosis, and the leukemic blasts frequently have an internal tandem duplication (ITD) of the FMS-related tyrosine kinase 3 gene (FLT3) gene accompanying the NUP98::NSD1 fusion. Previous reports have utilized BM transduction with retroviral vectors followed by transplantation into recipient mice to model AML driven by a NUP98::NSD1 fusion.  Given that  genetically engineered mice offer certain advantages over retroviral transduction models, such as consistent transgene expression and integration effects, lack of  ionizing radiation, and transferability between investigators, we generated NUP98::Nsd1 transgenic mice.

overall_design: We compared expression profiles of  AML derived from bone marrow tissue of NUP98-NSD1/FLT3-ITD transgenic mouse(N=7) with normal wild type mouse whole bone marrow (N=4) or normal wild type mouse lineage negative bone marrow (N=4).

first: Toshihiro

last: Matsukawa

first: Vijay

last: Negi

first: Nupur

last: Nigam


title: Probing the direct differences in TREX1 gene modification in mice.

city: fuzhou

first: yangfan

last: zhang

address: Fujian Normal University Qishan Campus, College Town, Fuzhou, Fujian Province

institute: FJNU

summary: We constructed Trex1-/-, Trex1D18N, Trex1p212fs mice by CRISPR-Cas9 technology. Four genotypes of MEFS, WT, Trex1-/-, Trex1D18N, Trex1p212fs were obtained by isolating 13.5-day mouse embryos, and then second generation MEFs were collected for RNA-seq analysis to explore the differences between cells.

first: Hekang

last: Du

first: Yangfan

first: Nanyang

last: Xiao


title: Expression data from adult Drosophila melanogaster virgin males

city: Aarhus C

first: Mads

middle: Fristrup

last: Schou

address: Nu Munkegade 114

department: Biology

country: Denmark

institute: Aarhus University

summary:
We used microarrays to investigate the transcriptome of male flies exposed to either a rich or a poor nutrient environment during development. Further we investigated transcriptome of their offspring and grand-offspring also developed at poor or rich diet.
The ability of organisms to cope with poor quality nutrition is essential for their persistence. For species with short generation time, the nutritional environments can transcend generations, making it beneficial for adults to prime their offspring to particular diets. However, our understanding of potential adaptive generational effects, including those of diet quality, is still very limited. Here we use the vinegar fly, Drosophila melanogaster, to investigate if females developing as larvae on a nutritionally poor diet produce offspring that are primed for nutrient deficiencies in the following generations. We found that females developed at low quality diets produced offspring, which at similarly low-quality diets had both increased egg-to-adult viability and starvation tolerance compared to females experiencing a nutrient rich diet in the previous generation. When testing the persistence of such generational priming, we found that just one generation of high-quality diet is sufficient to return performance to initial levels. A global transcriptomic profile analysis suggests that the observed phenotypic priming is not a constitutive transcriptomic adjustment, instead offspring appear primed to initiate an adaptive response only when exposed to low quality diets. Our results show that generational priming is likely an important adaptive mechanism of coping with transient nutritional fluctuations.

overall_design: Ten experimental groups were analysed in triplicate, in total 30 Affymetrix Drosophila Gene 1.0 arrays

first: Jesper

last: Sørensen

first: Torsten

middle: N

last: Kristensen

first: Volker

last: Loeschcke

first: Lucy

last: Davies