title: Genome profiling of WDR5, P53, H3K4Me3 binding in mouse embryonic bodies using SFEBq differetiation methods

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

summary: This study describes the binding profile of  WDR5, p53 and H3K4Me3 in mouse embryonic bodies at day 2 (WT, Wdr5 KO, Wdr5 and p53 double knockout)

overall_design: Cut & Run profile of WDR5, P53, H3K4Me3 binding in day2 embryonic embryoid bodies  (WT, Wdr5 KO, Wdr5 and p53 double knockout)

first: Rajesh

last: Rao


title: Single-cell gene expression analyses reveal distinct self-renewing and proliferating subsets in the leukemia stem cell compartment in murine acute myeloid leukemia

status: Public on Nov 25 2019

city: Minneapolis

first: Zohar

last: Sachs

state: MN

address: 420 Delaware Street SE MMC 480

department: Department of Medicine, Division of Hematology, Oncology and Transplantation

country: USA

institute: University of Minnesota Twin Cities

type: Expression profiling by high throughput sequencing

summary: Standard chemotherapy for acute myeloid leukemia (AML) targets proliferative cells and efficiently induces complete remission; however, many patients relapse and die of their disease. Relapse is caused by leukemia stem cells (LSCs), the cells with self-renewal capacity. Self-renewal and proliferation are mutually exclusive in normal hematopoietic stem cells (HSCs) in steady state conditions. If these functions are also mutually exclusive in LSCs, then antiproliferative therapies may fail to target self-renewal, allowing for relapse. We investigated whether proliferation and self-renewal are mutually exclusive in LSCs as they often are in HSCs. Using single-cell RNA sequencing, we identified distinct transcriptional profiles within LSCs of Mll-AF9/NRASG12V murine AML. We used single-cell qPCR and found that these genes were also differentially expressed in primary human LSCs and normal human HSPCs. A smaller subset of these genes was upregulated in LSCs relative to HSPCs; this smaller subset of genes constitutes “LSC-specific” genes in human AML. To assess the differences between these profiles, we identified cell surface markers, CD69 and CD36, whose genes were differentially expressed between these profiles. Using in vivo mouse reconstitution assays, we found that only CD69High LSCs were capable of self-renewal and were poorly proliferative. In contrast, CD36High LSCs were unable to transplant leukemia but were highly proliferative. These data demonstrate that the transcriptional foundations of self-renewal and proliferation are distinct in LSCs as they often are in normal stem cells and suggest that therapeutic strategies that target self-renewal, in addition to proliferation, are critical to prevent relapse and improve survival in AML.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Our study uses single-cell RNA sequencing to identify transcriptional heterogeneity within LSCs and define the self-renewing subset within this compartment. We performed single-cell RNA sequencing on the LSC-enriched compartment of our murine leukemia model. As we previously demonstrated that self-renewal is dependent on NRASG12V activity in this model, we also performed single-cell RNA sequencing on the LSC-enriched compartment after turning off NRASG12V transgene expression. To identify the functional contribution of each single-cell transcriptional profile, we performed in vivo assays of proliferation (using CellTrace labeling) and self-renewal (using in vivo leukemia reconstitution assays). We also performed single-cell qPCR on primary human LSCs and normal bone marrow HSPCs to determine whether these cells express components of this single-cell self-renewal signature. Finally, we analyzed the TCGA gene expression data to determine whether elements of the single-cell self-renewal gene expression signature that we identified are associated with survival in AML.

first: Yoonkyu

last: Lee


title: Paternal nicotine enhances fear memory, reduces nicotine administration and alters hippocampal genetic and neural function in offspring [RNA-seq]

city: University Park

first: Lisa

last: Goldberg

state: Pennsylvania

address: 130 Biobehavioral Health Bldg, Penn State University

department: Biobehavioral Health

institute: Penn State University

summary: We tested the effects of chronic paternal nicotine exposure in C57BL6/J mice on hippocampal RNA expression in F1 offspring.

overall_design: Examination of differential gene expression in the hippocampus of offspring from males treated chronically with nicotine or males treated chronically with saline.

middle: R

first: Thomas

middle: J

last: Gould


title: Anaerobic degradation of syringic acid by an adapted strain of Rhodopseudomonas palustris

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: Rhodopseudomonas palustris strain SA008.1.07 can use syringic acid as sole organic carbon source anaerobically. Grew all anaerobically in various carbon sources: syringic acid, succinate, and p-hydroxybenzoic acid.

overall_design: Strain comparison of R. palustris during anaerobic growth on various carbon sources.

first: J

middle: Z

last: Oshlag

first: Yanjun

last: Ma

first: Kaitlin

last: Morse

first: Brian

last: Burger

first: Rachelle

last: Lemke

first: Stephen

middle: D

last: Karlen

first: Timothy

last: Donohue

first: Daniel

last: Noguera


title: CD4 T cell response in AKI

city: Baltimore

first: Sanjeev

last: Noel

address: Broadway

institute: Johns Hopkins

summary: CD4+ T cells mediate the pathogenesis of ischemic and nephrotoxic acute kidney injury (AKI), as well as acute injury to other organs. However, the underlying mechanisms of CD4+ T cell-mediated pathogenesis are largely unknown. We therefore conducted unbiased RNA-sequencing to discover novel mechanistic pathways of kidney CD4+ T cells post-ischemia compared to normal mouse kidney. Unexpectedly, lipocalin-2 (Lcn2) gene, which encodes neutrophil gelatinase-associated lipocalin (NGAL) had the highest (~60)-fold increase. The NGAL increase in CD4+ T cells during AKI was confirmed at the mRNA level with real-time PCR and at the protein level with ELISA. NGAL is a potential biomarker for the early detection of AKI and has multiple potential biological functions during organ injury. However, the role of NGAL produced by CD4+ T cells has not been investigated. We found that ischemic AKI in NGAL knockout (KO) mice had worse renal outcomes compared to wild type (WT) mice. Adoptive transfer of NGAL-deficient CD4+ T cells from NGAL KO mice into CD4 KO or WT mice led to worse renal function than transfer of WT CD4+ T cells. In vitro simulated ischemia reperfusion showed that NGAL-deficient CD4+ T cells express higher levels of IFN-γ mRNA compared to WT CD4+ T cells. In vitro differentiation of naive CD4+ T cells to Th17, Th1 and Th2 cells led to significant increase in Lcn2 expression. Human kidney CD4+ T cell NGAL also increased significantly post-ischemia. These results demonstrate an important role for CD4+ T cell NGAL as a mechanism by which CD4+ T cells mediate AKI and extend the importance of NGAL in AKI beyond diagnostics.

overall_design: C57BL6/J WT and CD4Keap1 KO mice were assigned to control and ischemia reperfusion injury (IRI) groups. RNA was isolated 24h after the surgery and kidney CD4 T cells flow sorted for RNA-seq analysis. There were 12 samples comprising 4 biologic classes of three replicates each, and experimental samples were compared to controls.

first: Hamid

last: Rabb

first: Sul

middle: A


title: Deep Characterization of the Human Antibody Response to Natural Infection Using Longitudinal Immune Repertoire Sequencing

status: Public on Nov 26 2019

city: Stanford

first: Erin

last: Mitsunaga

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University School of Medicine

summary: Human antibody response studies are largely restricted to periods of high immune activity (e.g., vaccination). To comprehensively understand the healthy B cell immune repertoire and how this changes over time and through natural infection, we profiled the antibodies of a single individual over 11 months through two periods of natural viral infection.  We found that 1) a baseline of healthy variable (V) gene usage in antibodies exists and is stable over time, but antibodies in memory cells consistently have a different usage profile relative to earlier B cell stages; 2) a single complementarity-determining region 3 (CDR3) is potentially generated from more than one VJ combination; and 3) IgG and IgA antibody transcripts are found at low levels in early human B cell development, suggesting that class switching may occur earlier than previously realized.  These findings provide insight into immune repertoire stability, response to natural infections, and human B cell development.

overall_design: Targeted RNA sequencing of flow cytometry-sorted human B cell receptors through two periods of natural viral infection over an 11 month period

middle: M


title: Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain

status: Public on Nov 27 2019

city: Dresden

first: Fabian

last: Rost

address: Pfotenhauerstraße 108

country: Germany

institute: MPI-CBG

summary: Zebrafish display widespread and pronounced adult neurogenesis, which is fundamental for their regeneration capability after central nervous system injury. However, the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas.  Here, we used short-term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia, newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically, we detected 2 separate newborn neuron types, which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain, identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon.  Thus, we prospectively isolated adult newborn neurons from the adult zebrafish forebrain, identified markers for newborn and mature neurons in the adult brain, revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types.

overall_design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain

first: Christian

last: Lange

first: Anja

last: Machate

first: Susanne

last: Reinhardt

first: Matthias

last: Lesche

first: Anke

last: Weber

first: Veronika

last: Kuscha

first: Andreas

last: Dahl

first: Steffen

last: Rulands

first: Michael

last: Brand


title: Genome-wide maps of CTCF in glioblastoma

city: Cleveland

first: Peter

last: Scacheri

state: OH

address: 2109 Adelbert Road

department: Genetics and Genome Sciences

institute: Case Western Reserve University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here we have used CTCF ChIP-seq in glioblastoma to understand CTCF elements in the context of chromatin topology genome-wide.

overall_design: Examination of CTCF in 2 glioblastoma cell models.

middle: C

first: Andrew

last: Morton


title: Genome-wide maps of active chromatin in Wilms tumor

summary: Here we have used H3K27ac ChIP-seq in primary Wilms tumors to identify active promoter and enhancer elements genome-wide.

overall_design: Examination of H3K27ac in 5 primary human Wilms tumors


title: Human iPSC-derived microglia assume a primary microglia-like state after transplantation into the neonatal mouse brain [Bulk RNAseq]

city: Cambridge

first: Devon

last: Svoboda

email: svobodadevon@gmail.com, barc@wi.mit.edu

address: 455 Main St

institute: Whitehead Institute

summary: iPSC derived microglial precursors were transplanted into the brains of neonatal mice, FACS sorted out based on GFP+ following 2 months, and compared to in vitro differentiated iPSC derived microglia from the same precursors.

overall_design: Microglial Precursors were either transplanted into neonatal mice, plated for in vitro differentiation, or FACS sorted for RNA collection.  All samples in the study came from the same batch of differentiated iPSCs of cell line 657-GFP.  Transplanted GFP+ cells and in vitro differentiated cells were collected for FACS sorting and RNA extraction following 10 days and 60 days, resulting in a total of 5 sample groups, n=6 for each group.  For mice, n=one mouse.  For in vitro differentiated microglia, n=3 pooled well of a 6-well plate.  For precursors, n=floating cells from two pooled t75 flasks.

first: George

last: Bell

first: Rudolf

last: Jaenisch


title: Chromosome topology of the EGFR locus in glioblastoma

summary: Here we have used 4C-seq to interrogate the toplogy of the EGFR locus in glioblastoma models that are EGFR unamplified (GSC23) and amplified (GBM3565).

overall_design: 4C-seq in two different glioblastoma with 5 anchor points


title: RNAseq of 3T3L1 cells undergoing differentiation

middle: K

last: Jackson

address: 279 Campus Dr., CCSR 3230

institute: Stanford University

summary: Confluency-arrested, undifferentiated 3T3-L1 cells were compared with differentiating cells at 24 hrs to assess the effect of differentiation on gene expression. Differentiation was induced by historical differentiation cocktail, ctrl (-DHA) differentiation cocktail, or DHA cocktail.

overall_design: RNAseq of differentiating 3T3L1 cells at 2 time points and four conditions (submitted to SRA: SRP156744, PRJNA484984)

first: Keren

last: Hilgendorf

first: Janos

last: Demeter


title: Single cell RNA-seq of mouse embryoid bodies and yolk sac

city: St. Louis

first: Kyunghee

last: Choi

state: MO

address: 660 S Euclid Ave

institute: Washington University in St. Louis, School of Medicine

summary: Blood and endothelial cells arise from hemangiogenic progenitors that are specified from FLK1-expressing mesoderm by the transcription factor ETV2. FLK1 mesoderm also contributes to other tissues, including vascular smooth muscle (VSM) and cardiomyocytes. However, the developmental process of FLK1 mesoderm generation and its derivatives and the lineage relationship among FLK1 mesoderm derivatives these tissues remain obscure. Recent single cell RNA-sequencing (scRNA-seq) studies of early stages of embryogenesis embryos, or in vitro differentiated human embryonic stem (ES) cells have differentiation provided unprecedented information on the spatiotemporal resolution of cells in embryogenesis. Nonetheless, these snapshots still nonetheless offer insufficient information on dynamic developmental processes due to inadvertently missing intermediate states and unavoidable batch effects. Here we performed scRNA-seq of mouse ES cells in asynchronous embryoid bodies (EBs), in vitro differentiated embryonic stem (ES) cells containing undifferentiated ES cells and its differentiated hemangiogenic progeny, as well as  yolk sacs, the first hematopoietic extraembryonic tissue in developing embryo that contains  hemangiogenic and VSM lineages. We captured a continuous developmental process from undifferentiated pluripotent cells to FLK1 mesoderm-derived tissues involved in hemangiogenesis. This continuous transcriptome map will benefit both basic and applied studies of mesoderm and its derivatives.

overall_design: Examination of single cell level RNA-seq of two samples

first: Haiyong

last: Zhao


title: ERG controls B-cell development by promoting Igh V-to-DJ recombination

status: Public on Nov 24 2019

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

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

overall_design: Refer to individual Series


title: ERG controls B-cell development by promoting Igh V-to-DJ recombination [microarray]

summary: B-cell development is dependent on the coordinated expression and cooperation of several transcription factors. Here, we show that the transcription factor ETS Related Gene (ERG) is crucial for normal B-cell development, and that its deletion results in a substantial loss of bone marrow B-cell progenitors and peripheral B-cells as well as a skewing of splenic B-cell populations. We found that ERG-deficient B-lineage cells exhibited an early developmental block, at the pre-B cell stage, and proliferated less. The cells failed to express the immunoglobulin heavy chain due to inefficient V-to-DJ recombination and cells that managed to undergo recombination displayed a strong bias against incorporation of distal V gene segments. Furthermore, antisense transcription at PAX5-activated intergenic repeat (PAIR) elements located in the distal region of the Igh locus was completely dependent on ERG. These findings identify ERG as a novel critical regulator of B-cell development by ensuring efficient and balanced V-to-DJ recombination.

overall_design: Microarray-based gene expression of FACS-sorted progenitor B-cells (Lin-, B220+, CD19+, CD93+ CD43+/lo) derived from Erg fl/fl (WT) and Erg fl/fl;CD2iCre (KO) mice. Three biological replicates were made for each genotype.

middle: T

first: Elisabeth

last: Søndergaard

first: Alexander

last: Rauch

first: Magali

last: Michaut

first: Nicolas

last: Rapin

first: Matilda

last: Rehn

first: Wilhelmson

last: Anna

first: Alessandro

last: Camponeschi

first: Marie

last: Hasemann

first: Frederik

middle: O

last: Bagger

first: Johan

last: Jendholm

first: Kasper

last: Knudsen

first: Susanne

last: Mandrup

first: Inga-Lill

last: Mårtensson


title: ERG controls B-cell development by promoting Igh V-to-DJ recombination [ATAC-seq]

overall_design: ATAC-seq of FACS-sorted progenitor B-cells (Lin-, B220+, CD19+, CD93+ CD43+/lo) derived from Erg fl/fl (WT) and Erg fl/fl;CD2iCre (KO) mice. Four biological replicates of each genotype were sequenced.


title: TLR2 dimerization blockade allows generation of homeostatic intestinal macrophages under acute colitis challenge

city: Rehovot

first: Steffen

last: Jung

address: 234 Herzl Street

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Recruited blood monocytes contribute to the establishment, perpetuation and resolution of tissue inflammation. Specifically, in the inflamed intestine, monocyte ablation was shown to ameliorate colitis scores in preclinical animal models. However, the majority of intestinal macrophages that seed the healthy gut are also monocyte-derived. Monocyte ablation aimed to curb inflammation would therefore likely interfere with intestinal homeostasis. Here, we used a TLR2 trans-membrane peptide which blocks TLR2 dimerization that is critical for TLR2 /1 and TLR2 / 6 heterodimer signaling to blunt inflammation in a murine colitis model. We show that while the TLR2 peptide treatment ameliorated colitis, it allowed recruited monocytes to give rise to macrophages that lack the detrimental pro-inflammatory gene signature and reduced potentially damaging neutrophils infiltrates. Finally, we demonstrate TLR blocking activity of the peptide on in vitro cultured human monocyte-derived macrophages. Collectively, we provide a significantly improved anti-inflammatory TLR2 peptide and critical insights in its mechanism of action towards future potential use in the clinic.

overall_design: 65 samples from mice, total of 3 experiments. 15 samples from human

first: Mor

last: Gross-Vered

first: Liraz

last: Shmuel-Galia

first: Batya

last: Zarmi

first: Fiachra

last: Humphries

first: Christoph

last: Thaiss

first: Tomer-Meir

last: Salame

first: Eyal

last: David

first: Louise

last: Chappell-Maor

first: Katherine

last: Fitzgerald

first: Yechiel

last: Shai


title: ERG controls B-cell development by promoting Igh V-to-DJ recombination [RNA-seq]

first: Bo

last: Porse

overall_design: Transcriptomes from P1 (B220+, CD19+, CD93+, CD43+, CD25-), P2 (B220+, CD19+, CD93+, CD43+, CD25+) and P3 (B220+, CD19+, CD93+, CD43-, CD25+) progenitor B-cells derived from Erg fl/fl (WT) and Erg fl/fl;CD2iCre (KO) mice. Four biological replicates of each genotype were sequenced.

first: Elisabeth

last: Søndergaard

first: Alexander

last: Rauch

first: Magali

last: Michaut

first: Nicolas

last: Rapin

first: Matilda

last: Rehn

first: Wilhelmson

last: Anna

first: Alessandro

last: Camponeschi

first: Marie

last: Hasemann


title: Hepatic PPARα function and lipid metabolic pathways are dysregulated in polymicrobial sepsis

status: Public on Nov 23 2019

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Despite intensive research and constant medical progress, sepsis remains one of the most urgent unmet medical needs of today. Most studies have been focused on the inflammatory component of the disease, however, recent advances support the notion that sepsis is accompanied by extensive metabolic perturbations. During times of limited caloric intake and high energy needs, the liver acts as the central metabolic hub in which PPARa is crucial to coordinate the breakdown of fatty acids. The role of hepatic PPARa in liver dysfunction during sepsis has hardly been explored. We demonstrate that sepsis leads to a starvation response that is hindered by the rapid decline of hepatic PPARa levels, causing excess free fatty acids, leading to lipotoxicity, and glycerol. In addition, treatment of mice with the PPARa agonist pemafibrate protects against bacterial sepsis by improving hepatic PPARa function, reducing lipotoxicity and tissue damage. Since lipolysis is also increased in sepsis patients and pemafibrate protects after the onset of sepsis, these findings may point towards new therapeutic leads in sepsis.

overall_design: Liver RNA from mice subjected to CLP or SHAM operation followed by administration of GW7647 or DMSO (control).

first: Lise

last: Van Wynege

first: Tineke

last: Vanderhaeghen

first: Jolien

last: Vandewalle

first: Kelly

last: Van Looveren

last: Souffriau

first: Charlotte

last: Wallaeys

first: Melanie

last: Eggermont

first: Sam

last: Ernst

first: Evelien

last: Van Hamme

first: Amanda

last: Gonçalves

first: Guy

last: Eelen

last: Scott

first: Caroline

last: Rombouts

first: Lynn

last: Vanhaecke

first: Liesbet

last: De Bus

first: Johan

last: Decruyenaere

first: Peter

last: Carmeliet

first: Claude

last: Libert


title: Targeting chronic NFAT activation with calcineurin inhibitors in diffuse large B-cell lymphoma

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary: Diffuse large B-cell lymphoma (DLBCL) represents the most common form of lymphoma. We could show that in DLBCL cell lines the transcription factor NFAT is constitutively activated and drives the survival of a DLBCL subset. Aim of the analysis was to identify NFAT target genes in a NFAT-dependent (HBL-1) or  -independent (HT) DLBCL cell line. To block NFAT activity, the DLBCL cells were treated with the calcineurin inhibitor cyclosporin A (CsA) up to 48 h.  With this approach, we identified several survival-related NFAT target genes in HBL-1 cells that might explain the toxic effects of calcineurin inhibitors.

overall_design: Gene expression in HBL-1 and HT cells after treatment with cyclosporin A (CsA) for several durations as indicated was compared to that of untreated cells (DMSO).

first: Lenz

last: Georg

first: Stephan

last: Hailfinger


title: Direct detection of circulating microRNA-122 using dynamic chemical labelling with single molecule detection overcomes stability and isomiR challenges for biomarker qualification

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

type: Non-coding RNA profiling by high throughput sequencing

summary: Circulating microRNAs are biomarkers reported to be stable and translational acrossspecies. miR-122 (miR-122-5p) is a hepatocyte-specific microRNA biomarker for drug-induced liver injury (DILI). Our objective was to develop an extraction-free andamplification-free detection method for measuring miR-122 that has translationalutility in context of DILI. We developed a single molecule dynamic chemical labelling(DCL) assay based on miR-122 hybridization to an abasic peptide nucleic acid probethat contained a reactive amine instead of a nucleotide at a specific position in thesequence. The single molecule DCL assay specifically measured miR-122 directly from10 μL of serum or plasma without any extraction steps, with a fit-for-purpose limit ofdetection of 1.32 pM. In 192 human serum samples, DCL accurately identified patientsat risk of DILI (area under ROC curve 0.98 (95%CI 0.96-1), P<0.0001). The miR-122assay also quantified liver injury in rats and dogs. When DCL beads were added toserum, the miR-122 signal was stabilised (no loss of signal after 14 days at roomtemperature). By contrast, there was substantial degradation of miR-122 in the absenceof beads (≈60% lost in 1 day). RNA sequencing demonstrated the presence of multiplemiR-122 isomiRs with DILI that were at low concentration or not present in healthypatient serum. Sample degradation over time produced more isomiRs, particularlyrapidly with DILI. PCR was inaccurate when analysing miR-122 isomiRs, whereas theDCL assay demonstrated accurate quantification. In summary, the DCL assay canaccurately measure miR-122 directly from serum and plasma to diagnose liver injury inhumans and other species, and can overcome important microRNA biomarker analyticaland biological challenges.

overall_design: small RNAs for RNA-seq were isolated from 100 uL of serum of (i) a DILI patient and (ii) a healthy volunteer at three different time points. Time 0 = just after being defrozen from -80 ºC. Time 24 h = after the samples were left at room temperature for 24 hours and T = 7days after samples were left at room temperature for 7 days. There were three technical replicates of each condition

first: Barbara

last: López-Longarela

first: Emma

middle: E

last: Morrison

first: John

last: Tranter

first: Lianne

last: Chahman-Vos

first: Jean-François

last: Léonard

first: Jean-Charles

last: Gautier

first: Sébastien

last: Laurent

first: Aude

last: Lartigau

first: Eric

last: Boitier

first: Lucile

last: Sautier

first: Pedro

last: Carmona-Sáez

last: Martorell-Marugán

first: Richard

last: Mellanby

first: Salvatore

last: Pernagallo

first: Hugh

last: Ilyine

first: David

last: Risin

last: Duffy

first: James

middle: W

last: Dear

first: Juan

last: Díaz-Mochón


title: CPF is required for heterochromatin assembly and gene silencing

status: Public on Nov 29 2019

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

first: Tommy

middle: V

last: Vo

first: Jothy

last: Dhakshnamoorthy

first: Madeline

last: Larkin

first: Martin

last: Zofall

first: Gobi

last: Thillainadesan

first: Vanivilasini

last: Balachandran

first: Sahana

last: Holla

last: Wheeler

middle: I


title: Transcriptomic analysis of human coronary artery endothelial cells stimulated with TNF-alpha in the presence and absence of ACSL3 siRNA

city: SEATTLE

first: KARIN E

last: BORNFELDT

state: WA

address: 750 Republican St

institute: UNIV WASHINGTON

summary: TNF-alpha has a number of pro-atherogenic effects in macrovascular endothelial cells, including induction of leukocyte adhesion molecules and chemokines. We investigated the role of acyl-CoA synthetase 3 (ACSL3) in the response of cultured human macrovascular endothelial cells to TNF-alpha. TNF-alpha induced ACSL3 both in human umbilical vein endothelial cells (HUVECs) and in human coronary artery endothelial cells (HCAECs). RNA sequencing demonstrated that knockdown of ACSL3 had no marked effects on the TNF-alpha transcriptome in HCAECs. Instead, ACSL3 was required for TNF-alpha-induced lipid droplet formation from fatty acids.

overall_design: Samples analyzed in triplicates from one donor, 4 different conditions (basal+control siRNA, TNF-alpha+control siRNA, basal+ACSL3 siRNA, TNF-alpha+ACSL3 siRNA)

first: Karin

last: Bornfeldt


title: Protect-seq: Genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin

city: Worcester

first: George

last: Spracklin

state: Massachusetts

address: 368 Plantation Street

department: Systems Biology

institute: University of Massachusetts Medical School

summary: We compare  histone modifications, chromatin accessibility, and replication timing domain  genome-wide in HCT116 colon cancer cells with its genetic derivative DKO cells which lack DNMT3B and DNMT1 activity and the fibrosarcoma cell line HT1080.

overall_design: This submission contains the following experiments on HCT116, DKO (DNMT1-/-;DNMT3b-/-), and HT1080 cells: 3 biological replicates of Protect-seq for each cell lines using Illumina and 1 Oxford Nanopore run on HCT116, 1 replicate of WGS on DKO and  HT1080 for Protect-seq input, 2 biological replicates of H3K9me2, H3K9me3, H3K27me3, HP1alpha, CTCF, and input ChIP-seq and Early and Late fractions of Repli-seq  for HT1080 cells. 1 biological replicate of H3K9me2, H3K9me3, HP1beta, HP1alpha, H3, and input ChIP-seq for HCT116 and DKO cells.

first: Sriharsa

last: Pradhan


title: Imprinted maternally-expressed microRNAs in induced neurons

first: Amanda

last: Whipple

state: MA

address: 16 Divinity Ave

department: Molecular & Cellular Biology

institute: Harvard University

summary: Imprinted genes with parental-biased allelic expression are enriched in pathways regulating energy homeostasis. Here, we functionally characterize a large cluster of maternally-expressed microRNAs (miRNAs) to explore the molecular and cellular consequences of imprinted miRNA activity in neurons. Using an induced neuron (iN) culture system, we show maternally-expressed miRNAs from the miR-379/410 cluster direct the RNA induced silencing complex (RISC) to transcriptional and developmental regulators, including paternally-expressed transcripts. Maternal deletion of this imprinted miRNA cluster results in increased protein levels of several targets and up-regulation of a broader gene program regulating synaptic transmission and neuronal function. A subset of these transcriptional changes can be attributed to de-repression of Plagl1, a paternally-expressed transcriptional activator that regulates Igf2, a major factor in energy homeostasis. These data suggest non-coding RNAs actively engage as maternally-expressed miRNAs antagonize paternally-driven gene programs in neurons.

overall_design: We examined gene expression in hybrid mouse embryonic stem cells (mESCs, Day 0) and induced neurons (iNs, Day 10) upon deletion of maternal miR-379/410 using rRNA-depleted RNA-seq and small RNA-seq. We also performed Ago2 seCLIP-seq in iNs expressing exogenous untagged-Ago2 or HA-Ago2 with HA antibody.


title: Microarray Analyses of the Dorsal Root Ganglia Support a Role for Innate Neuro-Immune Pathways in Persistent Pain in Experimental Osteoarthritis

status: Public on Nov 22 2019

city: Chicago

first: Rachel

last: Miller

address: 1735 W Harrison St

institute: Rush University Medical Center

summary:
Objective – Following destabilization of the medial meniscus (DMM), mice develop experimental osteoarthritis (OA) and associated pain behaviors that are dependent on the stage of disease. We aimed to describe changes in gene expression in knee-innervating dorsal root ganglia (DRG) after surgery, in order to identify molecular pathways associated with three pre-defined pain phenotypes: “post-surgical pain”, “early-stage OA pain”, and “persistent OA pain”.   Design – We performed DMM or sham surgery in 10-week old male C57BL/6 mice and harvested L3-L5 DRG 4, 8, and 16 weeks after surgery or from age-matched naïve mice (n=3/group). RNA was extracted and an Affymetrix Mouse Transcriptome Array 1.0 was performed. Three pain phenotypes were defined: “post-surgical pain” (sham and DMM 4-week vs. 14-week old naïve), “early OA pain” (DMM 4-week vs. sham 4-week), and “persistent OA pain” (DMM 8- and 16-week vs. naïve and sham 8- and 16-week). ‘Top hit’ genes were defined as p<0.001. Pathway analysis (Ingenuity Pathway Analysis) was conducted using differentially expressed genes defined as p<0.05. In addition, we performed qPCR for Ngf and immunohistochemistry for F4/80+ macrophages in the DRG.  Results – For each phenotype, top hit genes identified a small number of differentially expressed genes, some of which have been previously associated with pain (7/67 for “post-surgical pain”; 2/14 for “early OA pain”; 8/37 for “persistent OA pain”). Overlap between groups was limited, with 8 genes differentially regulated (p<0.05) in all three phenotypes. Pathway analysis showed that in the persistent OA pain phase many of the functions of differentially regulated genes are related to immune cell recruitment and activation. Genes previously linked to OA pain (CX3CL1, CCL2, TLR1, and NGF) were upregulated in this phenotype and contributed to activation of the neuroinflammation canonical pathway. In separate sets of mice, we confirmed that Ngf was elevated in the DRG 8 weeks after DMM (p=0.03), and numbers of F4/80+ macrophages were increased 16 weeks after DMM (p=0.002 vs. Sham).  Conclusion- These transcriptomics findings support the idea that distinct molecular pathways discriminate early from persistent OA pain. Pathway analysis suggests neuroimmune interactions in the DRG contribute to initiation and maintenance of pain in OA.
We grouped samples based on pain phenotype in the DMM mouse model of osteoarthritis. Group 1: post-surgical pain (DMM and sham +4 week samples); Group 2: post-surgical control (Naïve +4 week samples); Group 3: Early osteoarthritis pain (DMM +4 week samples); Group 4: Early controls (sham+4 and naive+4 week samples); Group 5: Persistent pain (DMM+8 and DMM+16 week samples); Group 6: Persistent controls (sham+8, naive+8, sham+16, and naive +16 samples). We compared Group 1 vs Group 2; Group 3 vs Group 4; and Group 5 vs Group 6 to draw the conclusions presented in our manuscript.

overall_design: We collected n=3 samples for each treatment, at each time point. Two of the three Sham+8wk samples did not meet QC and were not included in further analyses. Treatments: naïve, sham, DMM; Time points: +4wk, +8wk, +16wk

first: Anne-Marie

last: Malfait

first: Ana

last: Valdes


title: RNA-Seq analysis of the Neisseria gonorrhoeae GntR-type transcriptional regulator GdhR

city: Atlanta

first: Julio

middle: C.

last: Ayala

state: Georgia

address: 1600 Clifton Rd NE Rm 3-642

department: Division of STD Prevention

institute: Centers for Disease Control and Prevention

summary: In this work we have determined by RNA-Seq the whole set of genes regulated by the N. gonorrhoeae GdhR transcriptional regulator (NGO1360 gene in reference strain FA1090). The results showed that GdhR regulates the expression of 2.3% of all the genes in the gonococcal (strain FA19) genome, of which 39 were activated and 11 were repressed. Most of the GdhR-regulated genes lie in the category of fimbrial proteins and membrane antigens or transporters. GdhR was found not be a cryptic regulator since there is an overlap in the set of GdhR-regulated genes between the wild type and a strain expressing gdhR ectopically from the lac promoter. Among the GdhR-regulated genes linked to gonococcal pathogenesis we found that lctP, encoding a unique L-lactate transporter, was the highest of GdhR-repressed genes.

overall_design: Total RNA samples were isolated from N. gonorrhoeae cultures grown to late exponential phase (OD600 1.0), depleted from ribosomal RNA and subjected to paired-end high throughput sequencing on the Illumina NextSeq 500 platform (Illumina Inc., San Diego, CA). Each strain (condition) was sequenced in duplicates. Transcript differential expression analyses were conducted between the transcriptomes of a wild type FA19 strain and its isogenic gdhR mutant, and between the gdhR mutant and its complemented strain expressing gdhR ectopically from the lac promoter.

first: William

last: Shafer


title: RNA sequence analysis between ECM1- sufficient and -deficient peritoneal macrophage

city: shanghai

first: Yaguang

last: Zhang

address: Yueyang road 320, Shanghai, China

country: China

institute: CAS, SIBCB

summary: We report the differential gene expression between ECM1- sufficient and -deficient peritoneal macrophage. Inflammatory bowel disease (IBD) comprises chronic relapsing disorders of the gastrointestinal tract characterized pathologically by intestinal inflammation and epithelial injury. Here, we uncover a new function of extracellular matrix protein 1 (ECM1) in promoting the pathogenesis of human and mouse IBD. ECM1 was highly expressed in macrophages, particularly tissue-infiltrated macrophages under inflammatory conditions, and ECM1 expression was significantly induced during IBD progression. The macrophage-specific knockout of ECM1 resulted in increased arginase 1 (ARG1) expression and impaired polarization into the M1 macrophage phenotype following LPS treatment.RNA-sequencing data indicated an alternative metabolic process and a higher arginine metabolic level in ECM1-deficient macrophages compared with ECM1-sufficient macrophages. A mechanistic study showed that ECM1 can negatively regulate M1 macrophage polarization through the GM-CSF/STAT5 signalling pathway. Pathological changes in mice with dextran sodium sulphate-induced IBD were alleviated by the specific knockout of the ECM1 gene in macrophages. Taken together, our findings show that ECM1 has an important function in promoting M1 macrophage polarization, which is critical for controlling inflammation and tissue repair in the intestine.

overall_design: ThG induced macrophages for 3 days from ECM1- sufficient and -deficient mice peritoneal cavity

first: Bing

last: Sun


title: The Toxoplasma gondii virulence factor ROP16 acts in cis and trans and suppresses T cell responses

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania


title: Ligand dependent gene regulation by transient ERa clustered enhancers

city: Bangalore

first: Bharath

last: Saravanan

state: Karnataka

address: Bellary Road

department: Genetics and Development

country: India

institute: National centre for Biological Sciences

summary: Unliganded Estrogen receptor alpha (ERa) has been implicated in ligand-dependent gene regulation. Upon ligand exposure, ERa binds to several EREs relatively proximal to the pre-marked, or persistent, ERa-bound sites and affects transient but robust gene expression. However, the underlying mechanisms are not fully understood. Here we demonstrate that upon ligand stimulation, persistent sites interact extensively, via chromatin looping, with the proximal transiently ERa-bound sites, forming Ligand Dependent ERa Enhancer Cluster in 3D (LDEC). The E2-target genes are regulated by these clustered enhancers but not by the H3K27Ac super-enhancers. Further, CRISPR-based deletion of TFF1 persistent site disrupts the formation of its LDEC resulting in the loss of E2-dependent expression of TFF1 and its neighboring genes within the same TAD. The LDEC overlap with nuclear ERa condensates that coalesce in a ligand and persistent site dependent manner. Furthermore, formation of clustered enhancers, as well as condensates, coincide with the active phase of signaling and their later disappearance results in the loss of gene expression even though persistent sites remain bound by ERa. Our results establish a direct link between ERa condensates, ERa enhancer clusters, and transient, but robust, gene expression in a ligand-dependent fashion.

overall_design: Using ChIP-seq, 5C and microscopy, we establish that ERa-occupied regions around unliganded sites form clusters that regulate target gene expression.

first: Dimple

last: Notani

first: Sridhar

last: Hannenhalli

first: Deepanshu

last: Soota

first: Sweety

last: Meel

first: Zubairul

last: Islam

first: Umer

last: Farooq

first: Rajat

last: Mann

first: Kaivalya

last: Walavalkar

first: Anurag

last: Singh

first: Srimonta

last: Gayen

first: Sudeshna

last: Majumdar


title: The Toxoplasma gondii virulence factor ROP16 acts in cis and trans and suppresses T cell responses [CEP_invivo_Ai6_1dpi]

summary: The ability of Toxoplasma gondii to inject the rhoptry kinase ROP16 into host cells results in the activation of the transcription factors STAT3 and STAT6, but it is unclear how these events impact infection. Here, parasites that inject Cre-recombinase with rhoptry proteins were used to distinguish infected macrophages from those only injected with parasite proteins. Transcriptional profiling revealed that injection of rhoptry proteins alone was sufficient to induce an M2 phenotype that is dependent on STAT3 and STAT6, but only infected cells displayed reduced expression of anti-microbial genes and antigen presentation pathways. In vivo, the absence of STAT3 or STAT6 improved parasite control while the loss of ROP16 resulted in a marked reduction in parasite numbers and heightened parasite-specific T cell responses. Thus, ROP16 is a virulence factor that can act in cis and trans to promote M2 programs and which limits the magnitude of parasite-specific T cell responses.

overall_design: Four biological replicates were analyzed for each of 3 conditions

first: Daniel

last: Beiting

first: David

last: Christian

first: Longfei

last: Chen

first: Christopher

last: Hunter


title: Transcriptomic, epigenetic and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS


title: ATACseq of 3T3L1 cells undergoing differentiation

city: Stanford

first: Peter

last: Jackson

address: 279 Campus Dr., CCSR 3230

institute: Stanford University

summary: Confluency-arrested, undifferentiated 3T3-L1 cells were compared with DHA and Dexamethasone treated cells at 4 hrs to assess the effect of early differentiation on chromatin architecture.

overall_design: ATAC-seq of differentiating 3T3L1 cells at 0 and 4hrs of treatment with differentiating agents (submitted to SRA: PRJNA484811, SRP156565)

first: Keren

last: Hilgendorf

first: Janos

last: Demeter


title: Helios enhances the preferential differentiation of human fetal CD4+ naïve T cells into regulatory T cells [RNA-Seq - induced Treg cells].

city: San Francisco

first: Melissa

last: Ng

state: California

address: 35 Medical Centre Way, Regeneration Medicine Building 903B

institute: University of California, San Francisco

summary: RNA sequencing was used to compare the transcriptome of in vitro differentiated adult and fetal induced Treg (iTreg) cells that were culture with IL-2 alone or supplemented with additional TGFb. Additionally, fetal iTreg cells also had Helios knocked out by CRISPR-Cas9 editing, with paired samples treated with the Helios guide RNA1 (HeliosKO) or with the non-targeting control (HeliosWT). Differential gene expression was assessed using generalised linear model designs. This revealed that fetal iTreg cells retain a expression of Treg-specific signature previously identified to be unregulated in primary ex vivo fetal naive T cells, and this signature was not expressed by adult iTreg cells. Helios expression then regulates the Treg-specific transcriptome within fetal iTreg cells by enhancing upregulation of genes associated with Treg differentiation and function, and repressing genes associated with effector specification and pro-inflammatory function.

overall_design: RNA sequencing for 4 biological replicates of ex vivo sorted CD4+CD25-CD45RA+CD27+ adult peripheral blood and fetal splenic naïve T cells differentiated in vitro for 6 days with IL-2 alone or in the presence of added TGFb. 6 biological replicates across two sequencing runs (3 biological replicates each) of ex vivo sorted CD4+CD25-CD45RA+CD27+ fetal naive T cells subjected to CRISPR-Cas9 mediated editing with the Helios gRNA1 (HeliosKO) or non-targeting control (HeliosWT). Cells were differentiated after resting for 6 days in the presence of IL-2 alone or with added TGFb.

first: Trevor

last: Burt


title: Interleukin-6 modifies the expression profile of microRNA in rat primary skeletal muscle cells

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

summary:
In the present study we examined the expression profile of microRNA in rat primary skeletal muscle cells (RSkMC) treated with IL-6, a known adipo-myokine and an inflammation-associated factor. The miRNA microarray analysis revealed increased expression of 2 miRNA species, which were not yet described in skeletal muscle, in RSkMC exposed to IL-6 (1 ng/ml) for 11 days of differentiation.
In order to verify the microarray data, qRT-PCR analysis was performed to quantify miRNA expression. We confirmed the increased expression of miR-154-3p (fold change =3.25) and miR-338-3p (fold change =3.37). Using Target Scan database we found potential targets for these miRNAs with expression modified by IL-6 and focused our further interest on genes involved in cytoskeleton organization and cell migration, that is: ephrinA4, pacsin3, actin, alpha-actinin, dyneins and desmin.

overall_design: We compared the miRNA expression profiles of RSkMC exposed to IL-6 (1 ng/ml) for 11 days of differentiation to control group (untreated samples). Three or four microarrays were done for each experimental condition.

first: Marta

last: Milewska

first: Tomasz

last: Domoradzki

first: Maciej

last: Błaszczyk

first: Małgorzata

last: Gajewska

first: Magdalena

last: Hulanicka

first: Katarzyna

last: Grzelkowska-Kowalczyk


title: Transcriptome analysis on TDP-43 downstream genes in Tardbp KO mice by Next Generation Sequencing

city: Kunming

first: Baowei

last: Jiao

state: Yunnan

address: 32 Jiaochang Donglu Kunming

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

summary: TDP-43 has been reported to be RNA-binding proteins; however their roles in mammary gland development has not been  examined previously. Here, we performed RNA-seq on mammary gland of WT and Tardbp KO mice at lactation day 1.

overall_design: The mammary gland of of WT and Tardbp KO mice at lactation day 1 were achieved.Then, RNA-seq was performed to study the effect of Tardbp KO.

first: Limin

last: Zhao

first: Hao

last: Ke


title: GM-CSF drives dysregulated hematopoietic stem cell activity and pathogenic extramedullary myelopoiesis in experimental spondyloarthritis

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

summary: We report the application of next generation sequencing (RNA-seq) to characterize the transcriptome of different types of hematopoeitic stem cells and progenitor cells in bone marrow of healthy and spondyloarthritic mice.

overall_design: Characterization of  FACS sorted long term hematopoietic stem cells (LT-HSC) , short term hematopoietic stem cells (ST-HSC) and multipotent progenitor cells (MPP) from bone marrow of healthy and spondyloarthritic mice. Three separate experiments were performed. LT-HSC were characterized as Lineage-ve, c-Kit+ve, Sca-1+ve, CD34-ve, CD150+ve, CD48-ve. ST-HSC were characterized as Lineage-ve, c-Kit+ve, Sca-1+ve, CD34+ve, CD150+ve. MPP were characterized as Lineage-ve, c-Kit+ve, Sca-1+ve, CD34+ve, CD150-ve, CD48+ve

first: Daniel

last: Regan-Komito

first: Thibault

last: Griseri


title: Automated High Frequency Sampling of Stem Cell Differentiation Reveals Early Stage Divergence of Human and Mouse Gene Expression Kinetics

city: Gainesville

first: Rhonda

last: Bacher

state: FL

address: 2004 Mowry Rd.

institute: University of Florida

summary: We performed whole transcriptome RNA sequencing experiments of neural differentiation time courses starting from human ES cells (EGFP-H1) and mouse EGFP-EpiS cells. Cells were sampled at high temporal frequency using an automated Tecan Tissue Culture robotics system to sample mouse cells every 4 mins and human cells every 10 mins for the first 10 hours of neural differentiation.

overall_design: Cells were sampled at high temporal frequency using an automated Tecan Tissue Culture robotics system to sample mouse cells every 4 mins and human cells every 10 mins for the first 10 hours of neural differentiation. Cells were pre-seeded in pluripotent conditions (E8 on matrigel for H1 cells and TSS on matrigel for mEpiS cells), then were switched to neural differentiation media and immediately sampled every 4 or 10 mins for mouse and human cells, respectively, for 10 hours.

first: Christopher

last: Barry

first: Matthew

last: Schmitz

first: Cara

last: Argus

first: Jennifer

last: Bolin

first: Mitchell

last: Probasco

first: Ning

last: Leng

first: Bret

last: Duffin

first: John

last: Steill

first: Scott

last: Swanson

first: Brian

last: McIntosh

first: Ron

last: Stewart

first: Christina

last: Kendziorski

first: James

last: Thomson


title: Stationary phase gene regulation by the group A Streptococcus protein RocA

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

summary: We used RNA-Seq to assess how RocA regulates gene expression in stationary phase GAS cultures

overall_design: Parental M3 isolate MGAS10870 (which is naturally a rocA mutant) and a fixed rocA derivative strain (10870rocAFIXED) were compared following growth to stationary phase in THY broth

first: Eric

last: Miller


title: Translational regulation contributes to the elevated CO2 response in two Solanum species

city: Davis

first: Siobhan

last: Brady

address: 451 Health Sciences Drive, 4303 GBSF

department: GBSF

institute: UC Davis

summary: A systems-level study identifies inter-specific translational regulation as important in the elevated CO2 response in two Solanum species

sample_organism:
Solanum lycopersicum
Solanum pennellii

platform_organism:
Solanum lycopersicum
Solanum pennellii

overall_design: RNA-Seq and TRAP-Seq data from S. lycopersicum and S. pennellii from roots or shoots, at 3 developmental stages (6,9 and 12 days after planting), under elevated (700ppm) or ambient (400ppm) CO2 conditions.

first: Sharon

middle: B

last: Gray

first: Joel

last: Rodriguez-Medina

first: Samuel

last: Rusoff

first: Ted

last: Toal

first: Kaisa

last: Kajala

first: Daniel

last: Runcie


title: Helios enhances the preferential differentiation of human fetal CD4+ naïve T cells into regulatory T cells. [RNA-Seq - ex vivo]

first: Melissa

last: Ng

summary: RNA sequencing was used to compare the transcriptome of ex vivo isolated adult and fetal naïve and regulatory T (Treg) cells. A Treg-specific transcriptome was defined by genes upregulated and downregulated preferentially in adult and fetal Treg cells relative to adult naive T cells. Fetal naive T cells show an intermediate expression of genes in the Treg-specific transcriptome.

overall_design: RNA sequencing for 4 biological replicates of ex vivo sorted CD4+CD25-CD45RA+CD27+ naïve and CD4+CD25hiCD127lo Treg cells from fetal spleen and adult peripheral blood mononuclear cells.

first: Trevor

last: Burt


title: Helios enhances the preferential differentiation of human fetal CD4+ naïve T cells into regulatory T cells. [Epigenetics]

summary: Human fetal naïve T cells preferentially differentiate into CD25hiFOXP3hi regulatory T (Treg) cells upon T cell receptor (TCR) stimulation, which contribute to the generation of immunotolerance in the developing human fetus. We utilized ATACseq and H3K27ac ChIPseq to characterize the human fetal naive T cell epigenome relative to that of adult naive T cells and Treg cells. Fetal naive T cells share a partial Treg epigenome with increased chromatin accessibility and H3K27ac enrichment at a subset of Treg-specific enhancers.

overall_design: ATACseq and H3K27ac ChIPseq for ex vivo sorted adult CD4+CD25-CD45RA+CD27+ naïve T, adult CD4+CD25hiCD127lo regulatory T and fetal naïve T cells from fetal spleen and adult peripheral blood mononuclear cells


title: Altered chromatin remodeling by FOXA1 mutations promotes androgen independence and  prostate cancer aggressiveness [ChIP-seq]

status: Public on Nov 21 2019

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: FKHD-mutant (FKHDm) FOXA1 has impaired ability to bind chromatin and thus failed to rescue wildtype FOXA1-mediated transcriptional program.   FKHDm FOXA1 formed much stronger interaction with the AR protein, thereby preventing AR from binding to the chromatin.

overall_design: ChIP-seq examination of AR and FOXA1 (HA-tag) binding sites in LNCaP shCtr and shFOXA1 cells with overexpressed FOXA1 wildtype or various FOXA1 mutants in the presence or absence of androgen.

first: Bohan

last: Xu

first: Bing

last: Song

first: Xiaodong

last: Lu


title: Random mono-allelic expression in MECP2-mutated cells

city: Paris

first: Thierry

last: Bienvenu

address: 24 rue du faubourg St jacques

country: France

institute: INSERM

summary: To improve our knowledge on this largely unknown phenomenon, and to study the role of MeCP2 in RMAE, we compared RMA gene expression profiles in clonal cell cultures expressing wild-type MeCP2 versus mutant MeCP2 from a RTT patient carrying a pathogenic non-sense variant.

overall_design: RNA sequencing

first: Juliette

last: Nectoux

first: Brigitte

last: Izac

first: Franck

last: Letourneur

first: Benjamin

last: Saintpierre

first: Nicolas

last: Cagnard


title: Altered chromatin remodeling by FOXA1 mutations promotes androgen independence and  prostate cancer aggressiveness [gene expression]

overall_design: Microarray analysis on LNCaP shCtr and shFOXA1 cells with overexpressed FOXA1 wildtype or various FOXA1 mutants in the presence or absence of androgen (R1881).


title: Altered chromatin remodeling by FOXA1 mutations promotes androgen independence and  prostate cancer aggressiveness

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

overall_design: Refer to individual Series


title: TIMP-GLIA (gliadin nanoparticle) treatment in transgenic mice expressing celiac disease associated HLA-DQ8

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

summary: This submission contains raw data obtained from RNA sequencing of mouse spleen cells. Spleen cells were derived from adult female HLA-DQ8, huCD4 transgenic Ab0 NOD mice, treated intravenously either with tolerogenic, immune-modifying nanoparticles containing gliadin (TIMP-GLIA), particles containing irrelevant control ovalbumin (TIMP-OVA), or not receiving treatment. Mice were then immunized with gliadin (except for negative controls), and spleens were collected after 28-30 days. Spleen cells were stimulated with gliadin (or controls) in culture for 72h, and RNA was obtained from cells for transcriptomic studies.

overall_design:
2 groups of female HLA-DQ8, huCD4 transgenic Ab0 NOD mice (Jackson Laboratories) were treated i.v. on days -11 and -3 with TIMP-GLIA, or TIMP-OVA, while other groups remained without treatment (2.5mg/dose; n=11-19, 10-12 weeks of age, raised on gluten-free diet AIN-76A). On day 0, mice from the TIMP-GLIA group, the TIMP-OVA group and a control group of mice (IMMU ONLY) were injected at the base of the tail with 100 μg gliadin in complete Freund’s adjuvant, followed by 50 μg gliadin in incomplete Freund's adjuvant on day 14. Another control group (NO TREATMENT) remained untreated/non-immunized. On days 28-30, mice were anesthetized with ketamine/xylazine. Spleens were harvested for analyses.

The raw data files for each sample in this submission are not de-multiplexed.  All sample metadata are included in the file sample_information.xls linked to to the foot of this record.

first: Katarzyna

last: Leskinen

first: Tobias

last: Freitag


title: Transcriptome of day 6 EBs [WT, hWDR5iRescue,Wdr5 KO clone #3  with or without early (T12h) and late rescue (T48h)]

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

summary: This study describes the transcriptome profiling of day 6 SFEBq embryonic bodies (EBs): 1) WT; 2) Wdr5 KO ; 3) Wdr5 KO with T12h hWDR5 rescue; 4) Wdr5 KO with T48h hWDR5 rescue

overall_design: RNA-Seq profiling on mouse Rx:GFP KI embryonic stem cell during differeniatiation via SFEBq method. Biological duplicates of each sample are labled as rep1/2. Technical repeats of each sample are labeled as Run1/2

first: Rajesh

last: Rao


title: Differential roles of human PUS10 in miRNA processing and tRNA pseudouridylation

city: Beijing

first: Jinghui

address: 5 Yiheyuan Road, Haidian District

institute: Peking university

summary: Pseudouridine synthases (PUSs) are responsible for the installation of pseudouridine (Ψ) modification in RNA. However, the activity and function of the PUS enzymes remain largely unexplored. Here we focus on human PUS10 and find that it co-expresses with the microprocessor (DROSHA–DGCR8 complex). Depletion of PUS10 results in a marked reduction of the expression level of a large number of mature miRNAs and concomitant accumulation of unprocessed primary microRNAs (pri-miRNAs) in multiple human cells. Mechanistically, PUS10 directly binds to pri-miRNAs and interacts with the microprocessor to promote miRNA biogenesis. Unexpectedly, this process is independent of the catalytic activity of PUS10. Additionally, we develop a sequencing method to profile Ψ in the tRNAome and report PUS10-dependent Ψ sites in tRNA. Collectively, our findings reveal differential functions of PUS10 in nuclear miRNA processing and in cytoplasmic tRNA pseudouridylation.

overall_design: DM-Ψ-seq,  PolyA RNA-seq,  rRNA(-) nuclear RNA-seq, Ribo-seq of PUS10 knockout and wild-type HEK293T cells and PAR-CLIP-seq against PUS10 in HEK293T cells.

first: Chengqi

last: Yi


title: Chromatin accessibility profiling of mouse embryonic bodies using SFEBq differetiation methods upon transient mWdr5 deletion with or without hWDR5 rescue

summary: This study describes time-course chromatin accessibility profiling of mouse embryonic bodies upon transient mWdr5 deletion with or without hWDR5 rescue

overall_design: ATAC-seq profile of day 2, day 4 embryoid bodies in WT and transient Wdr5 deletion (with T12h or T48h resuce) groups, WT, transient Wdr5 deletion (with T12h or T48h resuce), P53 and Wdr5 double knockout (DKO) embryoid bodies (with T12h or T48h resuce) at embryoid bodies day 6 were preprared in 2 replicates (rep-1 ad rep-2).


title: Stationary phase gene regulation in M1 GAS by the group A Streptococcus protein RocA

first: Paul

last: Sumby

summary: We used RNA-Seq to assess how RocA regulates gene expression in stationary phase cultures of serotype M1 GAS

overall_design: A parental M1 isolate (MGAS2221) and mutant rocA derivative (M1ΔrocA) were compared following growth to stationary phase in THY broth

first: Ira

last: Jain


title: Genome-wide study of the role of the histone demethylase dLsd1 in oogenesis

city: Toulouse

first: Luisa

last: Di Stefano

address: 118 Route de Narbonne

institute: Centre de Biologie Intégrative (CBI)

summary: To study the effect of dLsd1 knockdown on gene expression in oogenesis, we performed transcripts profiling by microarray in wild type ovaries and ovaries depleted for dLsd1.

overall_design: Changes in gene expression upon dLsd1 depletion were measured in Drosophila ovaries. To deplete dLsd1, we drove the expression of an RNAi against dLsd1 using the Act5C-GAL4 driver, which drives the expression of the RNAi ubiquitously. Experiments were performed in biological triplicates.


title: Age-Related Changes in the Transcriptome of Antibody-Secreting Cells

first: Louise

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

summary: We analyzed age-related defects in B cell populations from young and aged mice. Microarray analysis of bone marrow resident antibody secreting cells (ASCs) showed significant changes upon aging, affecting multiple genes, pathways and functions including those that play a role in immune regulation, humoral immune responses, chromatin structure and assembly, cell metabolism and the endoplasmic reticulum (ER) stress response. Aged ASCs expressed higher levels of immunoregulators including PD-1. Increased PD-1 expression was also seen on mature aged B cells indicating early defects in the lineage. High PD-1 expression on the aged ASCs correlated with high cellular reactive oxygen species levels. Mitochondrial defects in aged B cells were further confirmed by the absence of an increases in basal respiration observed upon in vitro stimulation of young B cells

overall_design: B cells from young and old mice were isolated and assayed using Illumina Mouse 6v2 arrays to find transcriptional changes upone aging

first: Ertl

last: Hildegund

first: Kannan

last: Senthil

first: Dawany

last: Noor


title: High Cervical IFNε in Female Sex Workers

summary: Highly Exposed-Seronegatives (HESN) individuals do not contract HIV-1 infection despite long-term exposure; few comprehensive studies examining behavior, mucosal tissue, and peripheral immune parameters in sexually-exposed HESN have been completed. To this end, we assessed rate of condomless vaginal sex, the immune activation status (peripheral blood) and gene expression (ectocervical biopsies) in female cohort of high-risk female sex workers [FSW] (n=50) and non-sex worker women [CG] (n=32) in San Juan, Puerto Rico, USA.    Of the 50 FSWs examined only 5 had detectable anti-HIV responses by either HIV gag-specific CD8+ T-Cell responses or mucosal anti-HIV envelope IgG/IgA. FSW had a uniform lower CD38 expression on circulating CD4+ or CD8+ T-Cells (both: p<0.0001:Wilcoxon Rank Sum).  Cervical tissue from FSWs had greater levels of CD4+ T-Cell (p=0.040), CD123+ plasmacytoid Dendritic Cells (p=0.013) and CD68+ macrophage infiltrates (p=0.038). Cervical gene expression by RNA microarray indicated that FSW had a gene signature characterized by lower expression of genes associated with leukocyte homing and chemotaxis; partial interferon regulated gene signature; and lower gene expression of genes required for HIV infection such as CD4 and NUP153 indicating a lower mucosal immune activation state and reduced susceptibility to HIV-1 infection within mucosal tissue.     Notably, Interferon (IFN)-ε expression was higher in FSW than CG women, as detected by RNA (microarray) and protein (IHC) expression in cervical epithelium.  The observed levels of IFNε were associated with the reported frequency of unprotected intercourse. Finally, IFNε was induced by treatment of the ECT1 cell line with seminal fluid, suggesting that semen exposure may contribute to long-term protection.      Decreased levels of immune activation and gene expression required for HIV infection along with semen-induced epithelial Interferon ε production within the reproductive tract of FSWs highlight distinct host intrinsic resistance mechanisms that may contribute to long-term HIV seronegative status in spite of high-risk condomless sex.

overall_design: In total 23 ectocervical biopsy samples were analyzed. Fourteen (14) biopsy samples were from a population of HIV-1 High-Risk Female Sex Workers (FSW) operating in San Juan, PR, USA. As a control, nine (9) biopsy samples were taken from women attending a maternal health clinic at the University of Puerto Medical Campus.

first: Louis

last: Montaner


title: Efficacy and safety of ustekinumab treatment in adults with moderate-to-severe atopic dermatitis

status: Public on Nov 20 2019

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: This was a phase II, randomized, placebo-controlled, double-blinded single center study (clinicaltrials.gov: NCT01806662) to investigate safety and efficacy of ustekinumab treatment in moderate-to-severe AD patients. Patients underwent 1:1 randomization using a computer generated subject randomization table by an unblinded pharmacist. to Subjects received subcutaneous ustekinumab or placebo at weeks 0, 4, and 16 with a crossover to the other agent (either ustekinumab or placebo) at weeks 16, 20, and 32 (Figure 1A) to ensure patient retention.

overall_design: Comparisson Ustekinumab vs. Placebo, Lesional vs. Non-lesional tissue,Timepoint vs. Baseline

first: Emma

last: Guttman

first: Saakshi

last: Khattri

first: Patrick

last: Brunner

first: Sandra

last: Garcet


title: Qualitative changes in cortical thymic epithelial cells drive postpartum thymic regeneration.

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

summary: During gestation, sex hormones cause a significant thymic involution which enhances fertility. This thymic involution is rapidly corrected following parturition. As thymic epithelial cells (TECs) are responsible for the regulation of thymopoiesis, we analyzed the sequential phenotypic and transcriptomic changes in TECs during the postpartum period in order to identify mechanisms triggering postpartum thymic regeneration. In particular, we performed flow cytometry analyses and deep RNA-sequencing on purified TEC subsets at several time points before and after parturition. We report that pregnancy-induced involution is not caused by loss of TECs since their number does not change during or after pregnancy. However, during pregnancy, we observed a significant depletion of all thymocyte subsets downstream of the double-negative 1 (DN1) differentiation stage. Variations in thymocyte numbers correlated with conspicuous changes in the transcriptome of cortical TECs (cTECs). The transcriptomic changes affected predominantly cTEC expression of Foxn1, its targets and several genes that are essential for thymopoiesis. By contrast, medullary TECs (mTECs) showed very little transcriptomic changes in the early postpartum regenerative phase, but seemed to respond to the expansion of single-positive (SP) thymocytes in the late phase of regeneration. Together, these results show that postpartum thymic regeneration is orchestrated by variations in expression of a well-defined subset of cTEC genes, that occur very early after parturition.

overall_design: As the swift postpartum thymic regrowth does not require thymic epithelial cell (TEC) expansion, we hypothesized that it might rather depend on qualitative changes in TECs. We therefore performed RNA-sequencing of cortical and medullary TECs (cTECs and mTECs) extracted from controls, and at 15 time points spanning between D-2 (i.e. 2 days before parturition) to D28 postpartum. Thymi were expracted and TEC were isolated through enzymatic digestion of the stroma. Poly-A enriched mRNA sequencing was performed on two populations of TECs (EpCAM+CD45-): cTECs (UEA1-) and mTECs (UEA1+). Purified cell populations from non-pregnant females (NP), pregnant females at 18 days of gestation (D-2) and following parturition (D0 to D28) were extracted using fluorescence activated cell sorter (FACS) after enzymatic digestion of the stroma. Each replicate was extracted from one mouse (each sample containing between 13,800 and 96,700 cells). RNA extraction was performed using TrizolTM as recommended by the manufacturer (Invitrogen), and purified using RNeasy Micro columns (Qiagen). Samples quality was confirmed using Bioanalyzer RNA Pico (Agilent). Transcriptome librairies were synthesized with KAPA RNA HyperPrep PolyA (Roche), and validated with Bioanalyzer (Agilent). Sequencing was performed with the Nextseq500 (NextSeq High Output, 75 cycles) at the genomic core facility of the Institute for Research in Immunology and Cancer (Université de Montréal).

first: Maude

last: Dumont-Lagacé

first: Tariq

last: Daouda

first: Lucyle

last: Depoërs

first: Jérémie

last: Zumer

first: Yahya

last: Benslimane

first: Sylvie

last: Brochu

first: Lea

last: Harrington

first: Sébastien

last: Lemieux


title: Overcoming Resistance to Anabolic SARM therapy in Experimental Cancer Cachexia with an HDAC Inhibitor

city: Columbus

first: Christopher

last: Coss

state: Ohio

address: 496 W. 12th Avenue

department: College of Pharmacy

institute: The Ohio State University

summary: No approved therapy exists for cancer-associated cachexia.  The colon-26 mouse model of cancer cachexia mimics recent late stage clinical failures of anabolic anti-cachexia therapy, and was unresponsive to anabolic doses of diverse androgens, including the selective androgen receptor modulator (SARM) GTx-024.  The histone deacetylase inhibitor (HDACi) AR-42 exhibited anti-cachectic activity in this model.  We explored combined SARM/AR-42 therapy as an improved anti-cachectic treatment paradigm.  A reduced dose of AR-42 provided limited anti-cachectic benefits, but, in combination with GTx-024, significantly improved body weight, hind limb muscle mass, and grip strength versus controls.  AR-42 suppressed the IL-6/GP130/STAT3 signaling axis in muscle without impacting circulating cytokines.  GTx-024-mediated β-catenin target gene regulation was apparent in cachectic mice only when combined with AR-42.  Our data suggest cachectic signaling in this model involves catabolic signaling insensitive to anabolic GTx-024 therapy and a blockade of GTx-024-mediated anabolic signaling.  AR-42 mitigates catabolic gene activation and restores anabolic responsiveness to GTx-024. Combining GTx-024, a clinically established anabolic therapy, with AR-42, a clinically evaluated HDACi, represents a promising approach to improve anabolic response in cachectic patients.

overall_design: 31 Samples

first: Moray

last: Campbell

first: Michael

last: Sovic

first: Samuel

last: Kulp

first: Sophia

middle: G

last: Liva


title: Genome profiling of HA-hWDR5 binding in mouse embryonic bodies using SFEBq differetiation methods

first: Fengbiao

last: Mao

summary: This study describes the binding profile of  HA-hWDR5 in mouse embryonic bodies with early (T12h) and late (T48h) rescue of HA-hWDR5

overall_design: ChIP-Seq profile of HA-hWDR5 in day 6 embryonic embryoid bodies with T12h and T48h rescue of HA-hWDR5.  Corresponding sequence profiles of genomic DNA (Input) for each data set are also included.

first: Rajesh

last: Rao


title: The Toxoplasma gondii virulence factor ROP16 acts in cis and trans and suppresses T cell responses [BMMC_invitro_stim_24hr]

city: Philadelphia

first: daniel

last: beiting

address: 380 S. University Ave

institute: University of Pennsylvania

summary: The ability of Toxoplasma gondii to inject the rhoptry kinase ROP16 into host cells results in the activation of the transcription factors STAT3 and STAT6, but it is unclear how these events impact infection. Here, parasites that inject Cre-recombinase with rhoptry proteins were used to distinguish infected macrophages from those only injected with parasite proteins. Transcriptional profiling revealed that injection of rhoptry proteins alone was sufficient to induce an M2 phenotype that is dependent on STAT3 and STAT6, but only infected cells displayed reduced expression of anti-microbial genes and antigen presentation pathways. In vivo, the absence of STAT3 or STAT6 improved parasite control while the loss of ROP16 resulted in a marked reduction in parasite numbers and heightened parasite-specific T cell responses. Thus, ROP16 is a virulence factor that can act in cis and trans to promote M2 programs and which limits the magnitude of parasite-specific T cell responses.

overall_design: Two biological replicates were analyzed for each of 6 conditions.

first: Daniel

last: Beiting

first: David

last: Christian

first: Longfei

last: Chen

last: Hunter


title: Defining lncRNAs Associated with  CHO Cell Growth and IgG Productivity by RNA-Seq II

city: Canterbury

first: Davide

last: Vito

state: Kent

address: Ingram Building, University of Kent

institute: University of Kent

summary:
Small-scale bioreactors used in Chinese hamster ovary (CHO) cell line development allow transcriptomic studies on multiple cell lines. Here we define the CHO cell long non-coding RNA (lncRNA) transcriptome from cells grown in controlled miniature bioreactors under fed-batch conditions using RNA-Seq to identify lncRNAs and how the expression of these changes throughout growth and between IgG producers.
We identify lncRNAs associated with productivity and growth characteristics, finding that Adapt15, linked to ER stress, GAS5, linked to mTOR signalling/growth arrest, and PVT1, linked to Myc expression, are differentially regulated during fed-batch culture and whose expression relates to productivity and growth.
Changes in (non)-coding RNA expression between the seed train and the equivalent day of fed-batch culture are also reported, showing large differences in gene expression between these, and compared with existing datasets. Collectively, we present a comprehensive lncRNA CHO cell profiling and identify targets for engineering growth and productivity characteristics of CHO cells.

overall_design: Coding and lncRNAs by RNA-Seq in CHO cells at differente time points obtained through Illumina ribosomal RNA-depleted RNA-Seq

first: Jens

last: Eriksen


title: Defining lncRNAs Associated with  CHO Cell Growth and IgG Productivity by RNA-Seq I


title: Drug repurposing of bromodomain inhibitors as potential novel therapeutic leads for lymphatic filariasis guided by multi-species transcriptomics

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Brugia malayi, Wolbachia (wBm), and Aedes aegypti transcriptome reads from across the B. malayi FR3 life cycle

sample_organism:
Brugia malayi
Aedes aegypti
Wolbachia endosymbiont of Brugia malayi

overall_design: A total of 16 distinct Brugia malayi life cycle stages were sampled and sequenced to assess the B. malayi, Wolbachia (wBm), and Aedes aegypti transcriptomes

first: Matthew

last: Chung

first: Laura

last: Teigen

first: Silvia

last: Libro

first: Robin

last: Bromley

first: Dustin

last: Olley

first: Nikhil

last: Kumar

first: Lisa

last: Sadzewicz

first: Luke

middle: J

last: Tallon

first: Anup

last: Mahurkar

first: Jeremy

last: Foster

first: Michelle

middle: L

last: Michalski

first: Julie

last: Hotopp


title: Defining lncRNAs Associated with  CHO Cell Growth and IgG Productivity by RNA-Seq


title: Real-time quantitative PCR analysis of human low-density (LDNs) and normal-density neutrophils (NDNs)

city: Pieve Emanuele

first: Elvezia

middle: Maria

last: Paraboschi

address: via Rita Levi Montalcini 4

department: Department of Biomedical Sciences

country: Italy

institute: Humanitas University

summary: NDNs and LDNs were isolated by density gradient centrifugation of PBMCs from 8 patients affected by tubercolosis (TB). In detail, RNA was extracted from NDNs and LDNs by Maxwell® RSC miRNA Tissue kit (Promega, Madison, USA), following manufacturer’s instructions. RNA concentration and quality was measured using NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific).  Total RNA (600 ng) was reverse transcribed using the RT2 First Strand Kit (SABiosciences, Qiagen, UK). 84 human cytokines and chemokines were tested using the RT2 Profiler PCR Array Human Innate & Adaptive Immune Responses array (Qiagen). A semiquantitative real-time RT-PCR was performed using a real-time PCR detection system (QuantStudio 7 Flex Real-Time PCR System, Thermo Fisher Scientific) with a two-step thermal cycling: 95 °C for 10 min, followed by 40 cycles (95 °C for 15 sec, 60 °C for 1 min). Data were analysed using the RT² Profiler PCR Array Qiagen data analysis software, and ACTB and B2M as housekeeping genes.

overall_design: qPCR gene expression profiling.  Neutrophil populations from 8 TB patients were used as indicated in the summary. Equal amount total RNA from each individual was used for gene expression analysis.

first: Marco

middle: P

last: La Manna

first: Valentina

last: Orlando

first: Bartolo

last: Tamburini

first: Paola

last: Di Carlo

first: Antonio

last: Cascio

first: Rosanna

last: Asselta

first: Francesco

last: Dieli

first: Nadia

last: Caccamo


title: LGP2 virus sensor enhances apoptosis by upregulating apoptosis-regulatory genes through TRBP-bound miRNAs during viral infection

city: Bunkyo-ku

first: Kumiko

last: Ui-Tei

state: Tokyo

country: Japan

institute: The University of Tokyo

summary: To reveal the fuction of cytoplasmic virus sensor protein, LGP2, on RNA silencing, we analyzed gene expression profiles on HeLa WT and LGP2 knockout cells during SeV infection, which were generated with CRISPR/Cas system.

overall_design: Total RNAs were extracted form SeV-infected HeLa WT and LGP2 knockout cells and performed microarray analysis.

first: Tomoko

last: Takahashi


status: Public on Nov 19 2019

city: Nanjing

first: JUN

last: HE

state: Jiangsu

address: Weigang 1

institute: Nanjing Agricultural University

summary: Transcriptome analysis of BPH-resistant and BPH-susceptible rice seedlings in response to BPH infestation. RH vs. 02428: a microarray analysis of genes that were differentially expressed in a BPH-resistant cultivar, Rathu Heenati (RH) and a susceptible cultivar 02428 after infestation with BPH for 24h. RB vs. SB: a microarray analysis of genes that were differentially expressed in resistant seedling pool and susceptible seedling pool both infested with BPH for 24h. RB vs. RN: a microarray analysis of genes that were differentially expressed in resistant seedling pool infested with BPH for 24h and resistant seedling pool without BPH infestation. Goal was to explore the molecular basis underlying BPH-resistance in rice.

overall_design: RH vs. 02428: 2 Biological replicates; RB vs. SB: 3 Biological replicates; RB vs. RN: 3 Biological replicates.

first: Yuqiang

last: Liu

first: Jun

last: He


title: Long term effects on performance physiology and fillet quality of Atlantic salmon (Salmo salar L.) fed low fish meal and n-3 LC-PUFA diets where fish oil was substituted by whole Schyzochytrium limacinum biomass

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Atlantic salmon individuals were grown, from fresh water to salt water in tanks on diets with low fish meal (10%) and 1-1.25% total n-3 LC-PUFA levels. Dietary n-3 LC-PUFAs were supplemented by 1) fish oil (FO), 2) Schyzochytrium limacinum biomass (AA). Further, the fish from all treatments were mixed and redistributed in sea cages reared to slaughter (ca. 3kg body weight) on either FO or AA. Transcriptomics analyses in liver and intestinal tissues revealed significant dietary effects on the expression of immune modulating, as well as ion, lipid, protein and xenobiotic metabolism genes.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Salmon were grown in tanks from 18 g to 800 g on two diets with different sources of essential fatty acids: fish oil algae

first: Katerina

last: Kousoulaki


title: Transcriptomics of zebrafish cardiac valve regeneration

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

summary: We performed a transcriptome analysis to identify molecular signatures associated with the regenerative process.

overall_design: The atrioventricular tissue of uninjured, 48 hours post ablation and 21 days post ablation valves were isolated from heart cryosections by Laser capture microdissection.

first: Anabela

last: Bensimon-Brito

first: Stefan

last: Günther


title: Transcriptome of Hymenophyllum caudiculatum during a desiccation-rehydration cycle

city: Temuco

first: Giovanni

middle: A

last: Larama

address: Francisco Salazar 01145

department: Ingenieria Matematica

country: Chile

institute: Universidad de La Frontera

summary: A study to explore the transcriptome response of hymenophyllum caudiculatum in a desiccation-rehydration cycle using high-throughput sequencing (Illumina).

first: Leon

last: Bravo

first: Enrique

last: Ostria


title: Transcriptome of Hymenophyllum dentatum during a desiccation-rehydration cycle

summary: A study to explore the transcriptome response of hymenophyllum dentatum in a desiccation-rehydration cycle using high-throughput sequencing (Illumina).

overall_design: Transcriptome of Hymenophyllum dentatum through a desiccation-rehydration cycle


title: Dexamethasone inhibits respiratory syncytial virus-driven mucus production while increasing viral replication without altering antiviral interferon signaling

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

country: USA

institute: Genomics Institute of the Novartis Research Foundation

summary:
Purpose: To understand how dexamethasone has beneficial effects on reducing mucus production but inhibits viral defense mechanisms
Methods: RSV-infected mouse lungs and various cell lines, plus and minus dexamethason, were examined by RNAseq, and pathway analysis of differentially-expressed genes were compared
Results:  Using RNA-seq we identified a subset of cytokines that were induced by RSV and repressed by dexamethasone.  Interestingly, while RSV induced interferons (IFNs) and IFN stimulated genes (ISGs), dexamethasone treatment did not affect the expression of these genes or antiviral IFN signaling pathways as has been observed with glucocorticoid treatment of other respiratory viruses [13].  Using an unbiased approach, we found that certain RSV-driven gene expression networks and genes were specifically modulated by dexamethasone treatment.  Importantly, dexamethasone also reduced RSV clearance in vivo, which correlated with a reduction in specific immune response markers.
Conclusion:  Our results support the possibility that the beneficial anti-inflammatory effects of dexamethasone treatment are counterbalanced by the increased viral load in patients, accounting for the lack of clinical benefit derived from treatment during RSV infection.

overall_design: Lungs from RSV-infected and dexamethasone treated or non-treated mice, or various cell lines infected and/or dexamethasone-treated were compared

first: Christopher

middle: S

last: McAllister

first: Dan

last: Ansaldi

first: Ellena

last: Growcott

first: Yang

last: Zhong

first: Doug

last: Quackenbush

first: Karen

last: Wolff

first: Olga

last: Tanaseichuk

first: Gerald

last: Lelais

first: S

last: Barnes

first: Glenn

last: Federe

first: Fabio

last: Luna

first: Yingyao

last: Zhou

first: Kelli

last: Kuhen


title: Early transcriptional landscapes of Chlamydia trachomatis-infected epithelial cells at single cell resolution

city: Wurzburg

first: Regan

last: Hayward

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

summary: Here we examined host cell gene expression in response to Chlamydia trachomatis infection by applying scRNA-Seq to in vitro C. trachomatis-infected HEp-2 epithelial cells and time-matched uninfected cells over the early chlamydial developmental cycle (3, 6 and 12 hours). We collected 264 single cells across both conditions all time points. The aims of the experiment were examining host cell responses to infection at single cell resolution, and identifying early host cell signatures of infection.

overall_design: Examination of chlamydial infection (Chlamydia trachomatis) on human epithelial cells (HEp2) from three early time points using both infected and uninfected samples applying single cell RNA-Sequencing

first: James

last: Marsh

first: Mike

last: Humphrys

first: Willa

last: Huston

first: Garry

last: Myers


title: Microarray analysis of developmentally programmed hepatic steatosis in Undernourishment in utero mouse model

city: Hamamatsu

first: Hiroaki

last: Itoh

address: #1-20-1 Handayama, Higashi-ku

department: Obstetrics and Gynecology

institute: Hamamatsu University School of Medicine

summary:
Nutritional imbalances in the early developmental period have an impact on the long-term risk of developing non-alcoholic fatty liver disease (NAFLD). In the present study, we demonstrated that tauroursodeoxycholic acid (TUDCA), a secondary bile acid,  and markedly ameliorated hepatic steatosis in a mouse model of undernourishment in utero.
Herein, we studied the effect of maternal caloric restriction on genetic expression by microarray analysis among 3 different time points of independent cohorts. Cohort 1 (at 9 weeks; without HFD), cohort 2 (at 17 weeks; with HFD), and cohort 3 (at 22 weeks; HFD with or without the TUDCA treatment) (Muramatsu-Kato et al., 2015).  We compared the alteration in gene expression between NN pups and UN pups before and after postnatal high-fat diet (HFD) at 9 weeks and 17 weeks. Later we studied the TUDCA treatment responce on NN pups and UN pups.

overall_design: Hepatic tissues were obtained from mice with Normal nutrtition in utero (NN) and Undernourishment in utero (UN, 40% caloric restriction) at 9, 17 and 22 weeks. A high-fat diet (HFD) was provided to pups (9-22 weeks) treated with TUDCA or vehicle (17-22 weeks).

first: Jeenat

middle: F

last: Urmi

first: Keiko

middle: M

last: Kato

first: Yukiko

middle: K

last: Kobayashi

first: Kazuki

last: Mochizuki

first: Takeo

last: Kubota

first: Naohiro

last: Kanayama


title: Transcriptomes analysis for the regulation of Z36 induced autophagy in HeLa cell death

city: Beijing

first: Bin

last: Xia

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: Z36 is a small molecule that induces Beclin1-dependent autophagy and autophagic cell death in HeLa cells. This is different from the typical autophagy induced by Rapamycin, which plays a protective role for cells. To gain insights into the regulation of autophagy in cell death by Z36, high-throughput RNA-sequencing were performed on HeLa cells treated with DMSO (as control), Z36 and Rapamycin. Two biological replaces were collected for each of the three conditions. The sequencing generated more than 30 million reads for each sample. RNA-seq data showed that there were about 3000 DEGs with over 2 folds changes (|log2 (fold change)| > 1 & P value < 0.05) in Z36 treated cells versus those of DMSO. On the contrary, there were only 200 DEGs for cells treated with Rapamycin. Noteworthily, expression levels of autophagic genes were significantly changed in Z36 treated cells, and the change pattern was different from Rapamycin treated ones. 8 of the ATG genes were up-regulated for more than 2 folds (log2 > 1) after Z36 treatment, while Rapa only caused small changes for the ATG genes, with the highest log2 change of 0.7. These study indicate that Z36 leads to significant modulation of a large number of genes at transcriptional level.

overall_design: mRNA profiles of HeLa cells treated with DMSO (as control), Rapamycin (Rapa) and Z36 were generated by deep sequencing, in two biological replaces(1 and 3), using Illumina Hiseq 2000 Sequencing System

first: Yangjie

last: Liao

first: Bo

last: Duan


title: NELFA is a novel regulator of the 2C-like state

status: Public on Nov 18 2019

city: Singapore

first: Zhenhua

last: hu

state: singapore

address: 31 Biopolis drive

country: Singapore

institute: IMCB, A*STAR

summary: Mouse embryonic stem cells (mESCs) are not homogenous; a rare subpopulation of cells can sporadically transit into a early-embryonic-like state and exhibits a gene expression program resembling that of the 2-cell (2C) embryo. We identified the maternal factor NELFA as a novel driver of the 2C-like gene expression through multiple mechanisms. We further demonstrate that the entry of mESCs into the 2C-like state is accompanied by epigenetic and metabolic reprogramming, and that perturbation of the metabolic state via a small molecule can promote this cell fate reversion in a NELFA-dependent manner, obviating the need for any genetic manipulation. Our findings thus place NELFA as one of the earliest regulators of 2C gene expression, extending contemporary knowledge of how totipotency may be regulated.

overall_design: To compare the gene expression differences between NELFAhigh and NELFAlow mESCs, we generated both a NELFA-StrepHA-P2A-EGFP reporter and a Dox-inducible NELFA- StrepHA-P2A-EGFP mESC stable line. The NELFA-reporter mESCs was treated with 4mM 2-DG for 4 days before harvesting total RNA for unbiased transcriptomic analysis with RNA-Seq, while Dox-inducible NELFA was induced with 0.4 µg/ml of Dox for 16 hours before FACS enrichment for both GFP positive and negative populations for RNA-seq, with an additional ERCC spike-in included in library preparation for normalization purposes in the downstream analysis for those two experiments. Both NELFA reporter and Dox-inducible mESCs were cultured in standard ESC media containing serum, LIF and 2i; briefly, knockout DMEM was supplemented with 15% FCS, L-Glutamine, non-essential amino acids, penicillin/streptomycin, 2-mercaptoethanol and supplemented with LIF, 1 µM PD0325901 and 3 µM CHIR99021.

last: Hu

first: Tan

middle: E

last: Kiat

first: Chia

last: Bin

first: Chen

last: Jieming

first: Hweifen

last: Leong

first: Wee-Wei

last: Tee

first: Mei Sheng

last: Lau

first: Haihan

last: Tan


title: Transcriptome data from ascorbic acid 2-glucose (AA2G) treated murine embryonic stem cell vs. non treated murine embryonic stem cell

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

country: South Korea

institute: University of Ulsan College of Medicine

summary: Naive or primitive states of stem cells (SCs) resided in specific niches are unstable and difficult to stabilized in vitro. Vitamin-C (VitC), more than suppressing oxygen radicals, exerts the pleiotropic effects on primitive SC functions through various mechanisms. However, instability and unfavorable cellular toxicity by liable oxidation present crucial pitfalls in its reliable application. Here, we show that a VitC derivate, ascorbic acid 2-glucoside (AA2G), without cellular toxicity, stably induces naïve or primitive status of embryonic (ESCs), inducible pluripotent (iPSCs), and mesenchymal SCs (MSCs). AA2G supplement recapitulated the well-known mechanisms of VitC including promoting TET dependent DNA demethylation in murine ESCs or suppressing p53 in iPSCs generation. Particularly, activation of cAMP responsive element binding protein-1 (CREB1) pathway was commonly involved in AA2G potency of ESCs, iPSCs, and MSCs. Importantly, MSCs maintained with AA2G supplement increased the therapeutic outcomes in an asthma mouse model by enhancing their self-renewal, anti-inflammatory, and engraftment capacity. Thus, this study demonstrates that AA2G supplement should be of broad utility to provide an environment supporting naïve pluripotent or primitive state of several types of SCs which critically influences their developmental potency and also efficacy of therapeutic applications.

overall_design: Murine embryonic stem cell line (R1-mESC) was maintained in the absence (NT) or presence of 250 ug/ml (0.74 mM; 250ug) for 3 days. Total RNA from three independent replicates was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA), including treatment with DNase I (QIAGEN). One ug of total RNA was used for the Affymetrix GeneChip Mouse Gene 2.0 ST Array (Affymetrix, Santa Clara, CA), in accordance with the manufacturer’s instructions.

first: Dong-Myung

last: Shin

first: Seungun

last: Lee

first: Hyein

last: Ju


title: Transcriptome data from ascorbic acid 2-glucose (AA2G) treated human embryonic stem cell vs. non treated human embryonic stem cell

overall_design: Multipotent mesenchymal stem cells (M-MSCs) derived from human embryonic stem cells (H9) were maintained in the absence (AG_0) or presence of 250 ug/ml (0.74 mM; AA250) for 3 days. Total RNA from three independent replicates was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA), including treatment with DNase I (QIAGEN). One ug of total RNA was used for the Affymetrix GeneChip Human 2.0 ST Array (Affymetrix, Santa Clara, CA), in accordance with the manufacturer’s instructions.

first: Jisun

last: Lim


title: RNA-seq to profile the transcriptome changes induced by the EZH2 degrader MS1943

status: Public on Nov 17 2019

city: New York

first: Anqi

last: Ma

address: 1425 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: To gain mechanistic insights into how MS1943 induces cell death, MDA-MB-468 cells were treated with 5 µM of MS1943 or DMSO control and changes of gene expression were assessed after 3 days of treatment. Interestingly, MS1943-treated cells were characterized by a unique set of deregulated genes that could readily separate them from control cells. We identified 8,730 significant differentially expressed genes with a false discovery rate (FDR) at 5%, in which 2,120 genes have an absolute log fold change above 1. We next performed gene set enrichment analyses (GSEA) that capture pathways perturbed towards both directions simultaneously using the 24,448 ranked genes identified in our dataset and annotated in ENSEMBL (version 94) against the KEGG pathways and the hallmarks gene set collection (MSigDB V6.2). Induction of the unfolded protein response (UPR) / endoplasmic reticulum (ER)-stress pathway was commonly identified using both types of analyses and we therefore decided to pursue this further.

overall_design: Examination of difference in gene expression in one breast cancer cell line, MDA-MB-468, between treated with 5 µM of MS1943 (n=2) and treated with DMSO as control (n=2).

first: Alessandro

last: Lagana

first: Tiphaine

middle: C

last: Martin

first: Violetta

last: Leshchenko


title: Banana transcriptome in response to blood disease infection

city: Bandung

first: Popi

last: Septiani

state: West Java

address: jl. Ganeca 10

department: School of Life Science and Technology

country: Indonesia

institute: Institut Teknologi Bandung

summary: We report the first data of RNA sequencing from two different banana cultivars from Musa acuminata cv. Mas Kirana (AA group) genome and Musa balbisiana cv. Klutuk (BB group) genome in response to blood disease infection caused by Ralstonia syzygii subsp. celebesensis (Rsc)

sample_organism:
Musa acuminata
Musa balbisiana

platform_organism:
Musa acuminata
Musa balbisiana

overall_design: mRNA from two different Banana genomes from pseudo-stem tissue in un-inoculated (triplicates) and inoculated (duplicates) condition following Ralstonia syzygii subsp. celebesensis infection

first: F

last: Dwivany

first: H

last: Nugrahapraja

first: A

last: Rahmawati

first: D

last: Meitasari

first: N

last: Farah

first: P

first: S

last: Subandiyah


title: Chronic allergen exposure drives accumulation of long-lived IgE plasma cells in the bone marrow, giving rise to serological memory

status: Public on Nov 16 2019

city: Tarrytown

first: Wei Keat

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

summary:
Summary: Long-lived IgE plasma cells reside in the bone marrow of allergic mice and atopic humans, confer IgE serological memory and produce allergen-specific IgE that can drive anaphylaxis.
Abstract: Immunoglobulin E (IgE) plays an important role in allergic diseases. Nevertheless, the source of IgE serological memory remains controversial. We re-examined the mechanism of serological memory in allergy using a dual-reporter system to track IgE plasma cells (PCs) in mice. Short-term allergen exposure resulted in the generation of IgE plasma cells that resided mainly in secondarylymphoid organs and produced IgE that was unable to degranulate mast cells. In contrast, chronic allergen exposure led to the generation of long-lived IgE plasma cells that were primarily derived from sequential class switching of IgG1, accumulated in the bone marrow (BM) and produced IgE capable of inducing anaphylaxis. Most importantly, IgE plasma cells were found in the BM of human allergic, but not non-allergic donors, and allergen-specific IgE produced by these cells was able to induce mast cell degranulation when transferred to mice. These data demonstrate that longlived IgE BMPCs arise during chronic allergen exposure and establish serological memory in both mice and humans.

overall_design: To study the IgE response in vivo, a house dust mite (HDM) driven lung inflammation model was conducted in WT, membrane-IgEvenus/Blimp-1mCherry single or dual reporter mice. Cellular responses were tracked by harvesting lymphoid tissues from the mice at the end of each experiment and analyzing them by flow cytometry. Molecular readouts were assessed using prepared RNA from harvested cells. Serum readouts, such as IgE or IgG1 levels, were assessed using ELISA. Pathogenicity of serum IgE derived from short-term and chronic HDM exposed mice was determined by passive cutaneous and passive systemic anaphylaxis assays (PCA and PSA). The human IgE response was also examined ex-vivo using BM samples from allergic and non-allergic donors. Human IgE-producing BMPCs were quantified using intracellular IgE staining, secretion of IgE was determined by ELISA from cultured BM supernatant and the capacity of the IgE to induce anaphylaxis was determined by PCA.

first: Seblewongel

last: Asrat

first: Navneet

last: Kaur

first: Xia

last: Liu

first: Li-Hong

last: Ben

first: Daisuke

last: Kajimura

first: Andrew

last: Murphy

first: Matthew

last: Sleeman

first: Andre

last: Limnander

first: Jamie

last: Orengo