title: Next Generation Sequencing Facilitates Quantitative Analysis of  Spleenic Macrophage Transcriptomes in mouse acute myeloid leukemia

city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

institute: Chinese Academy of Medical Science& Peking Union  Medical College

summary: The goals of this study aim to reveal functional and phenotypic diversity of macrophages in response to the different microenvironmental in acute myeloid leukemia

overall_design: Comparion the Transcriptomes of macrophages from acute myeloid leukemia with overexpression of M-CSF or not

first: GuoGuang

first: Rong


title: Knockout of HDAC1 and HDAC2 in Microglia

status: Public on Mar 14 2018

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Cancer-associated IDH1 promotes growth and resistance to targeted therapies in the absence of mutation

status: Public on Mar 13 2018

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

country: USA

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

summary: Oncogenic mutations in two isocitrate dehydrogenase (IDH)-encoding genes (IDH1 and IDH2) have been identified in acute myelogenous leukemia, low-grade glioma, and secondary glioblastoma (GBM). Our in silico and wet-bench analyses indicate that non-mutated IDH1 mRNA and protein are commonly overexpressed in primary GBM. We show that genetic and pharmacologic inactivation of IDH1 decreases GBM cell growth, promotes a more differentiated tumor cell state, increases apoptosis in response to targeted therapies, and prolongs survival of animal subjects bearing patient-derived xenografts (PDXs). On a molecular level, diminished IDH1 activity results in reduced a-ketoglutarate (aKG) and NADPH production, paralleled by deficient carbon flux from glucose or acetate into lipids, exhaustion of reduced glutathione, increased levels of reactive oxygen species (ROS), and enhanced histone methylation and differentiation marker expression. These findings suggest that IDH1 upregulation represents a common metabolic adaptation by GBM to support macromolecular synthesis, aggressive growth, and therapy resistance.

overall_design: H3K4me3 histone modification in 2 patient-derived glioma cell lines with shScramble, or 2 independent shRNAs targeted to IDH1.

first: Alexander

middle: H

last: Stegh

first: Andrea

middle: E

last: Calvert

middle: T


title: Development, phenotype and function of a distinct macrophage subpopulation induced by IL-23

status: Public on Mar 12 2018

city: Beijing

first: Yong

last: Zhao

address: 1 Beichen West Road, Chaoyang District

department: State Key Laboratory of Biomembrane and Membrane Biotechnology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Macrophages acquire distinct phenotypes during tissue stress and inflammatory responses. Classically, macrophages are categorized into two different subsets named inflammatory M1 and anti-inflammatory M2 macrophages. We herein identified a unique pathogenic macrophage subpopulation, named M17, driven by IL-23 with a distinct gene expression profile including cytokines and membrane molecules. In contrast to M1 and M2-polarized macrophages, M17 macrophages express high levels of CXCR5 on the cell surface and produce large amounts of IL-17A, IL-22 and IFN-γ. IL-23 induces IL-17A expression in macrophages through the signal transducer and activator of transcription 3 (STAT3)-retinoid related orphan receptor-γ T (RORγT) pathway, while induces IFN-γ through T-bet. Importantly, IL-23-induced M17 macrophage polarization promotes the pathogenesis of psoriasis in vivo. The characteristics and significances of M17 macrophage subpopulation in the physiological status and pathogenesis caused by infections, tumors and graft rejection needs to be explored.

overall_design: To further demonstrate whether M17 macrophage polarization represents a distinct polarization of macrophages, we detected gene expression profiles of M1, M2 and M17 polarized macrophages by microarray methods.

first: Yuzhu

last: Hou

first: Linnan

last: Zhu

first: Hongling

last: Tian

first: Hai-Xi

last: Sun

first: Chenming

first: Hui

last: Chen

first: Tingting

last: Wu

first: Xuelian

last: Hu

first: Biyi

last: Li

first: Jun

last: Lu

first: Lianfeng

last: Zhang

first: Ruoyu

last: Wang


title: Transcriptomic sequencing after HOXA9 knockdown in A431 cells

city: Guangzhou

first: yinghui

last: wang

state: Guangdong

address: No.1023 Shatai South Road，Baiyun District,

department: radiation medicine

institute: southern medical university

summary: Cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. In this study, Homeobox A9 (HOXA9), a direct target of onco-miR-365, was identified to be significantly down-regulated in CSCC tumors and cell lines. We conducted RNA sequencing to characterize gene expression changes in HOXA9-silenced cutaneous squamous cell carcinoma cells（A431）.

overall_design: RNA-Seq analysis of cSCC cells followed by siRNA-induced gene knockdown of HOXA9. Total RNAs from negative control (siNC) and HOXA9 siRNA-treated cSCC cells (siHOXA9_02) were extracted. The samples were sequenced using Illumina sequencing.

first: Zhenhua

last: Ding

first: Liang

last: Zhou

first: Yinghui


title: Mammalian low cell number and in vivo DamID-seq for transcription factor binding analyses

city: Edinburgh

first: Keisuke

last: Kaji

state: Midlothian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

country: United Kingdom

institute: University of Edinburgh

overall_design:
DamID-seq peaks were called for Oct4 from mouse embryonic stem cells (mESC), late streak, early bud mouse embryos (LSEB) and DamID-seq peaks were called for Sox2 from ES-derived neural stem cells (NSC)

DNase-seq hyper-sensitivity data was downloaded from GEO with the BioSample accession number GSM1014154 and compared with DamID-seq signal for E14 mouse embryonic stem cells. This data is linked below as DNase-seq_GSM1014154.tar.

ChIP-Seq raw data was downloaded from GEO (GSE11724, GSE44286, GSE56098) and ERA (ERR216111, ERR414096, ERR414097). Peaks called from Oct4 ChIP-seq were compared to Oct4 DamID-seq peaks for E14 mouse embryonic stem cells. This data is linked below as ChIP-Seq_reanalysis.tar.

first: Luca

last: Tosti

first: James

last: Ashmore

first: Nicholas

middle: B

last: Tan

first: Benedetta

last: Carbone

first: Tapan

middle: K

last: Mistri

first: Valerie

last: Wilson

first: Simon

middle: R

last: Tomlinson


title: Global delay in nascent strand DNA methylation

city: Cambridge

first: Jocelyn

last: Charlton

state: MA

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

type: Methylation profiling by high throughput sequencing

summary: BrdU labeling combined with genome-wide bisulfite sequencing (Repli-BS-Seq) reveals a global lag in the inheritance of CpG methylation following DNA replication, giving rise to cell-cycle-dependent epigenetic variation.

overall_design: In this study, we pulsed cells with BrdU to label nascent DNA and then performed whole genome bisulfite sequencing on either the immunoprecipitated nascent DNA or bulk DNA.

first: Timothy

middle: L

last: Downing

first: Zachary

middle: D

last: Smith

first: Honcang

last: Gu

first: Kendell

last: Clement

first: Ramona

last: Pop

first: Veronika

last: Akopian

first: Sven

last: Klages

first: Alexander

middle: M

last: Tasnkov

first: David

last: Santos

first: Bernd

last: Timmermann

first: Michael

middle: J

last: Ziller

first: Evangelos

last: Kiskinis

first: Andreas

last: Gnirke

last: Meissner


title: Expression data from adult mouse adrenal tissue

status: Public on Mar 11 2018

city: Riyadh

first: Katharine

middle: Sara

last: Collison

state: Riyadh

address: Takhasussi Street

department: Department of Cell Biology

country: Saudi Arabia

institute: King Faisal Specialist Hospital and Research Centre

summary:
Chronic dietary aspartame may impair rodent insulin tolerance and may affect behavior. Previous studies have shown the aspartame effects may be modulated by developmental NMDA receptor antagonism. Present study was designed to assess effects of aspartame and NMDAR antagonism on components of the HPA axis.
We used microarray analysis to examine changes in adult rodent adrenal gene expression following chronic aspartame exposure and/or developmental NMDA receptor antagonism.

overall_design: Aspartame exposure in C57Bl/6J mice commenced in utero via the mother's diet. NMDAR antagonism with the competitive drug CGP 39551 was limited to the developmental period (E0 to P28). Control mice received neither dietary aspartame nor developmental NMDAR antagonism.  At 21 weeks of life animals were euthanized and RNA was extracted from snap-frozen mouse adrenal tissue for microarray analysis.

first: Kate

middle: S

first: Angela

last: Inglis

first: Sherin

last: Shibin


title: Expression data from adult mouse hypothalamus

summary:
Chronic dietary aspartame may impair rodent insulin tolerance and may affect behavior. Previous studies have shown the aspartame effects may be modulated by developmental NMDA receptor antagonism. Present study was designed to assess effects of aspartame and NMDAR antagonism on components of the HPA axis.
We used microarray analysis to examine changes in adult rodent hypothalamic gene expression following chronic aspartame exposure and/or developmental NMDA receptor antagonism.

overall_design: Aspartame exposure in C57Bl/6J mice commenced in utero via the mother's diet. NMDAR antagonism with the competitive drug CGP 39551 was limited to the developmental period (E0 to P28). Control mice received neither dietary aspartame nor developmental NMDAR antagonism.  At 21 weeks of life animals were euthanized and RNA was extracted from snap-frozen mouse hypothalamic tissue for microarray analysis.


title: Overexpression nub-RB and Pdm2-RB

status: Public on Mar 10 2018

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

country: Sweden

institute: SciLifeLab. Stockholm University

summary: The intricate regulation of gut homeostasis is dependent on a fine-tuned regulation of the host defense to avoid detrimental immune activation. We have previously applied Drosophila to show that mutants of the short isoform of the POU transcription factor Pdm1/nubbin (nub) have a constitutively active immune response, altered gut microbiota and shortened lifespan. Here, we studied the role of Nub-PB, the larger isoform derived from the nub gene. Both Nub protein isoforms contain the C-terminal POU and Homeo domains whereas Nub-PB encompasses a longer N-terminal end. Microarray analysis revealed that targeted misexpression of Nub-PB in immunocompetent organs triggers a strong and broad expression of immune genes in a comparable manner to Nub-PD mutants. The seemingly antagonistic functions of the two isoforms were confirmed by co-overexpression of both forms, which resulted in normal expression levels of antimicrobial peptide (AMP) genes. Cell line experiments demonstrated a synergistic activation of AMPs by the combined transfection with Nub-PB and NF-kB/Relish. In agreement with this finding, Relish was indispensable for Nub-PB-driven diptericin expression, suggesting that Nub-PB acts as a Relish co-activator. Moreover, Nub-PB triggered strong expression of gut-specific drosomycin-like genes in a JAK/STAT pathway-dependent manner. Using RNA interference, we found that Nub-PB influences antimicrobial peptide expression in gut but not fat body tissues. Moreover, Nub-PB expression levels in gut enterocytes correlated with the gut bacterial load as well as host lifespan, suggesting a profound role in host immunity. Surprisingly, Nub-PB-overexpression caused a hypersensitive infection phenotype as flies succumbed within 24 h to orally administered Erwinia carotovora carotovora 15. Nub-PB thus appears to be a central activator of gut immunity that requires tight control, executed at least in part, by isoform antagonism to maintain immune homeostasis.

overall_design: Overexpression of nub-RB and Pdm2-RB, was carried out in flies of the genotype w1118;UAS-nub-RB/c564-Gal4 and w1118;UAS-Pdm2-RB/c564-Gal4 respectively, and compared with flies carrying the c564-Gal4 driver but no UAS target gene (w1118;c564-Gal4/+), called w1118 in the data. Flies were reared in mixed gender populations and kept at 25°C for moderate overexpression. Female flies were used at 10 days of age, dissected to separate guts (“gut”) and the rest (flies without guts and heads). Total RNA was extracted followed by DNAse treatment, RNA purification, labeling and hybridization.

first: Ylva

last: Engstrom


title: Genome-wide analysis of KAP1 recruitment in mouse regulatory T cells

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

summary: We aim to determine the role of KAP1 in regulatory T cells. KAP1 is originally defined as a chromatin remodeler but there are some evidence suggesting KAP1 also works as a transcription activator. Because Treg specific KAP1 deficient mice spontaneously develop autoimmune disease, KAP1 seems to be an important transcription factor for Tregs. To address the genes which are regulated by KAP1, we performed ChIP-seq of KAP1 using mouse Tregs. We found large part of KAP1 was rectuited to transcription start sites of T cell associated genes.

overall_design: Regulatory T cells were sorted and cultured for two weeks. Expanded Tregs were subjected and nuclear lysate was immunoprecipitated with anti-KAP1 antibody. Precipitated chromatin was sequenced by Hiseq2500.

first: Steven

middle: F

last: Ziegler


title: Integration of metabolomics and transcriptomic expression profiling discloses pivotal role of arachidonic acid metabolism pathway in response to acute hypoxia exposure

status: Public on Mar 09 2018

city: Chongqing

first: Chang

last: Liu

address: 30 Gaotanyan street

institute: 3rd Military Medical University

summary:
Background: Arachidonic acid (AA) metabolism pathway is dominant in metabolic programming after hypoxia exposure, but its biological function is disputed and require in-depth studies. In this research, we aimed at integrating plasma metabolomics and transcriptomics approaches to systematically explore its roles in response to acute hypoxia based on model of acute high-altitude exposure.
Methods: Blood samples were taken from 53 enrolled subjects before and after their exposure to high altitude. Ultra-performance liquid chromatography- quadrupole time-of-flight mass spectrometry and RNA sequencing were performed to acquire corresponding metabolomic and transcriptomic profiling along with hypoxia exposure, separately. Influential modules comprising essential metabolites and genes were identified by weighted gene co-expression network analysis (WGCNA) after integrating metabolic information with phenotypic and transcriptomic datasets, respectively.
Results: Enrolled individuals showed significant alterations in heart rate, SpO2, hemoglobin and Lake Louise Score (LLS) in response to hypoxia. Metabolomics profiling demonstrated that AA metabolism pathway was remarkable in these metabolic alterations. Integrated analysis of metabolomic and transcriptomic data revealed that increasing AA metabolism pathway might count for gas transport incapacitation and disorders in hemoglobin metabolism under hypoxia stimuli. Moreover, identified in further analysis and another cohort, excessively elevated AA metabolism pathway was involved in poor response to hypoxia.
Conclusion: Our study, for the first time, constructed the maps of AA metabolism pathway in response to hypoxia; and revealed the crosstalk between phenotypic variation to hypoxia and AA metabolism pathway. These findings will not only advanced pathophysiological mechanisms for acute hypoxic diseases, but provided new insights into critical roles of AA metabolism pathway in development and prevention of these diseases.

overall_design: Transcriptome from blood samples of  individuals were measured and analyzed before their departure and upon their arrival at high altitude (5300m).

first: Bao

first: Binda

last: Sun

first: Er-long

last: Zhang

first: Jian

last: Chen

first: Yuqi

last: Gao


title: Effect of developmental NMDAR antagonism on aspartame-induced hypothalamic and adrenal gene expression


title: Tracking of dCas9-methyltransferase footprints

first: Jocelyn

last: Charlton

summary: In normal mammalian development cytosine methylation is essential, and is directed to specific regions of the genome. Despite notable advances in mapping the genome-wide distribution, studying the direct contribution of DNA methylation to gene regulation has been limited by the lack of tools for its precise manipulation. Thus, combining the targeting capability of CRISPR/Cas9 systems with an epigenetic modifier has attracted interest in the scientific community. In contrast to profiling the genome-wide cleavage of a nuclease competent Cas9, tracing the global activity of a dead Cas9-methyltransferase is challenging within a highly modified genome. To overcome this, we utilized an engineered, methylation depleted but maintenance competent mouse ES cell line and find a surprisingly ubiquitous nuclear activity of dCas9-methyltransferases. Our results provide new insights into the targeted regulation of DNA methylation and point to an important difference between genetic and epigenetic editing tools that require unique experimental considerations.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Here, we took advantage of an engineered cell line with little background DNA methylation (DKOzero) and performed transient transfections with dCas9-cat3a constructs in the presence of an sgRNA. We also created three doxycycline inducible constructs that when co-introduced with the reverse trans-activator (M2rtTA) enabled controlled expression of dCas9-cat3a (dCas9 fused to the catalytic domain of Dnmt3a), cat3a (the catalytic domain alone) or Dnmt3a (the full-length enzyme, including its N-terminal regulatory domain). We tested the dCas9-cat3a construct in the absence and presence of one or many sgRNAs. Finally, we perform transient transfection experiments of dCas9-cat3a with a guide RNA in the MCF7 and 293T cancer cell lines.

first: Christina

last: Galonska

first: Alexandra

last: Mattei

first: Julie

last: Donaghey

first: Kendell

last: Clement

first: Hongcang

last: Gu

first: Arman

last: Mohammad

first: Elena

last: Stamenova

first: Davide

last: Cacciarelli

first: Sven

last: Klages

first: Bernd

last: Timmermann

first: Tobias

last: Cantz

first: Hans

last: Scholer

first: Michael

first: Alexander


status: Public on Mar 08 2018

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

institute: Graduate School of Medical Sciences, Kumamoto University

summary: Macrophages are differentiated from human circulating monocytes using M-CSF and GM-CSF. Oligodendrocytes are differentiated from human oligodendrocyte precursopr cells (#1610, ScienCell) using oligodendrocyte precursor cell differentiation medium.

overall_design: Gene expressions of human macrophages and oligodendrocytes were compared.

first: Takuichiro

last: Hide


title: Regulatory integration of Hox factor action with Tbox factors in limb development

city: Montreal

first: Amandine

last: Bemmo

state: QC

address: 110 Avenue des Pins

country: Canada

institute: IRCM

summary: Hindlimb and Forelimb-specific Tbox factors integrates their mode of action with distinct Hox factors resulting in different transcriptional outcomes. In addition, hindlimb-specific Tbx4, Hoxc10 and Pitx1 act on the same platform to target common putative downstream genes for hindlimb development

overall_design: ChIPseq of hindlimb-specific transcription factors Tbx4 and Hoxc10 using e11.5 HL-buds

first: Deepak

last: Jain

first: Stephen

last: Nemec

first: Maëva

last: Luxey

first: Yves

last: Gauthier

first: Aurélio

last: Balsalobre

first: Jacques

last: Drouin


title: NOTCH Signaling Specifies a Transient Arterial-Type Hemogenic Endothelium that Gives Rise to Definitive-Type Hematopoiesis from Human Pluripotent Stem Cells

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

summary: Recently, we identified and characterized specific endothelial progenitors with varying hemogenic potential during human pluripotent stem cell differentiation. Based on these studies we established a platform on which we can manipulate NOTCH signaling on these subsets to elucidate the specific role of this signaling pathway during hemogenic endothelial specification, endothelial-to-hematopoietic transition, and definitive hematopoietic specification.

overall_design: Manipulate NOTCH signaling during hemogenic endothelial specification, endothelial-to-hematopoietic transition, and definitive hematopoietic specification and expansion.

first: Igor

last: Slukvin

first: Gene

last: Uenishi

first: Scott

last: Swanson


title: BRCA1/RNApII regulation in Ewing's sarcoma (ChIP-seq)

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Ewing sarcoma (EwS) is an aggressive pediatric bone and soft tissue cancer. It is driven by a fusion oncogene involving the EWSR1 gene, predominantly EWS-FLI1. EwS is exquisitely sensitive to genotoxic agents, but the molecular basis for this sensitivity is relatively underexplored. We have discovered that EwS displays alterations in damage-induced transcription regulation and an accumulation of R-loops. Consequently, we observe an increase in replication stress but impaired homologous recombination. We demonstrate an enriched interaction between BRCA1 and the elongating transcription machinery and suggest that this interaction may be the underlying cause for impaired recombination. Investigation into the unique transcription profile of EwS also revealed upregulated mechanisms (including RNASEH2, FEN1 and Fanconi Anemia pathway) to compensate for the increased EWS-FLI1 induced toxicity. Finally, we have uncovered a novel role for EWSR1 transcriptional response to damage, suppressing R-loops and promoting homologous recombination. Taken together, our findings improve the current understanding of wild-type EWSR1 function, elucidate the mechanistic basis for EwS chemosensitivity (including PARP1 inhibitors) and suggest potential targets for novel second-line therapy.

overall_design: Four different cell lines, IMR90, U2OS, TC32 and EWS502 were profiled for RNAPII and BRCA1 via ChIP protocol. Samples treated with etoposide for 6 hours were profiled as well.

first: Aparna

last: Gorthi

first: Chen

last: Yidong

last: Bishop


title: ATAC-seq of HFF exposed to salt and heat stress

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Primary human foreskin fibroblasts (HFF) were exposed to either salt stress (80mM KCl) or heat stress (44ºC). ATAC-seq libraries were prepared starting with 50,000 cells per condition following the protocol described by Buenrostro et al., Nature Methods 2013

overall_design: HFF were exposed either salt stress (80mM KCl) or heat stress (44ºC) for 1 or 2h. ATAC-seq samples were prepared at the indicated times of infection. Two independent biological replicates were analysed for salt and heat stress and four replicates for untreated cells.

first: Thomas

last: Hennig

first: Marco

last: Michalski

first: Andrzej

last: Rutkowski

first: Lara

last: Djakovic

first: Adam

last: Whisnant

first: Marie-Sophie

last: Friedl

first: Bhaskar

last: Jha

first: Marisa

last: Baptista

first: Anne

last: L'Hernault

first: Florian

last: Erhard

first: Lars

last: Dölken

middle: C


title: Identification of ZEB2 binding sites in Hepatocellular Carcinoma Cell Line SNU398

city: Kocaeli

first: Tamer

last: Yagci

address: Istanbul Street

department: Molecular Biology and Genetics

country: Turkey

institute: Gebze Technical University

summary: ZEB2, a member of the ZEB family of EMT inducers, is involved in cellular proliferation, senescence, and invasion in most of the human cancers. However, genes regulated by ZEB2 in hepatocellular carcinoma (HCC) are not identified so far. Hence, we conducted a ChIP-Seq study in high ZEB2 expressing HCC cell line SNU398 by using a homemade anti-ZEB2 antibody (clone 6E5).

overall_design: Chromatin fragments bound by ZEB2 were subject to ChIP using ZEB2 antibody and followed by high-throughput sequencing

first: Yagci

last: Tamer

first: Ercin

last: Pelin

first: Cetin

last: Metin

first: Yalim-Camci

last: Irem


title: Gene expression response to simulated gravity and hypergravity in human T cells

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

summary: We investigated differentially regulated and stably expressed genes in human Jurkat T lymphocytic cells in 5min simulated microgravity and hypergravity and compared expression profiles to identify  gravity-regulated and unaffected genes as well as adaptation processes.

overall_design: Human Jurkat T cells were exposed to altered gravity conditions during  ground based facility experiments

first: Andreas

last: Huge

first: Swantje

last: Hauschild

first: Svantje

last: Tauber

first: Beatrice

middle: A

last: Lauber

first: Jennifer

last: Polzer

first: Katrin

last: Paulsen

first: Hartwin

last: Lier

first: Frank

last: Engelmann

first: Burkhard

last: Schmitz

last: Schütte

first: Liliana

last: Layer

first: Oliver

last: Ullrich


title: Adenylosuccinate lyase (ADSL) enhances endometrial cancer aggressiveness via increasing killer cell lectin like receptor C3 expression by fumarate

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Although ADSL is an enzyme that is involved in de novo purine synthesis, it was reported that ADSL knockdown did not result in decreases in adenine nucleotides (AMP, ADP, and ATP) or GTP. Then, we hypothesized that decreased cell proliferation, migration and invasion capability by ADSL knockdown in endometrial cancer cells were caused through a mechanism independent of purine synthesis. To elucidate a mechanism, we performed DNA microarray-based gene expression profiling using ADSL knockdown and control HEC1B cells. In the analysis, 940 out of 34,127 probes showed greater than two-fold changes in expression with a significant difference, p value < 0.05.

overall_design: The labeled cRNAs were hybridized on a Whole Human Genome Oligo Microarray ver. 2 (G4845A) in two dye swap experiments, resulting in four individual microarrays.

first: Haengki

last: Park

first: Kenji

last: Ohshima

first: Eiichi

last: Morii


title: Modulation of gene expression after inducing expression of 14q32 miRNAs by CRISPR activation technology in lung adenocarcinoma

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Most lung adenocarcinoma deaths are related to metastases, indicating the necessity of detecting and inhibiting tumor cell dissemination. We have identified that overexpression of miRNAs located on 14q32 was associated with metastasis in lung adenocarcinoma patients. For functional analysis, we utilized CRISPR activation technology to increase levels of miRNAs clustered on 14q32 in a coordinated manner, and the results showed that 14q32 miRNA overexpression promoted tumor cell migratory and invasive properties. Whole transcriptome microarray analysis of the miRNA-overexpressing cells was performed to define the underlying molecular mechanisms.
Microarray analysis was used to investigate the gene expression changes underlying the tumor cell migratory and invasive properties induced by 14q32 miRNAs in lung adenocarcinoma.

overall_design: CRISPR-Cas9-based gene activation technology (CRISPRa) using a mutant Cas9 lacking endonuclease activity (dCas9) fused with the activating domains VP64, p65, and Rta (VPR) was used to generate cell lines overexpressing the miRNAs located on 14q32. Two different miRNA-overexpressing cell clones were generated from H2009 lung adenocarcinoma cells by using two distinct single guide RNAs (sgRNA-A and sgRNA-B). Cells transfected with the empty sgRNA vector were used as control. Increased expression of 14q32 miRNA levels in CRISPRa-sgRNA-A and CRISPRa-sgRNA-B cells in comparison with CRISPRa-control cells was confirmed by RT-qPCR before microarray expression analysis. Three biological replicates from each cell clone were used for hybridization on Affymetrix microarrays.

first: Margarita

last: González-Vallinas

first: Carolina

last: De La Torre

first: Norbert

last: Gretz

first: Kai

last: Breuhahn


title: H2AX controls motor learning and response to oxidative stress

city: Bethesda

first: Urbain

last: Weyemi

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

summary: ATM drives DNA repair through rapid phosphorylation of the histone variant H2AX. Similarities between ATM and H2AX are evident in the phenotypes of their knockout mouse models, but the role of H2AX in the brain remains obscure. Here, we provide the first evidence that H2AX loss leads to neurobehavioral deficits. H2AX regulates proper response to oxidative stress through Nrf2-transcriptional targets and treatment with antioxidant ameliorates the neurobehavioral deficits.

overall_design: 6 samples in total including 3 replicates of parental mouse embryonic fibroblasts (MEF) and 3 replicates of H2AX knockout MEF.

first: Bindu

last: Paul

first: Adele

last: Snowman

first: Parthav

last: Jailwala

first: Andre

last: Nussenzweig

first: William

last: Bonner

first: Solomon

last: Snyder


title: BRCA1, R-loops and Recombination defects in Ewing's sarcoma

first: Yidong

last: Chen

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

overall_design: Refer to individual Series


title: Activity-dependent neuronal Klotho enhances astrocytic aerobic glycolysis

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Mutations of the β-glucuronidase protein α-Klotho have been associated with premature aging, and altered cognitive function. Although highly expressed in specific areas of the brain, Klotho functions in the central nervous system remain unknow.  Here, we show that cultured hippocampal neurons respond to insulin and glutamate stimulation by elevating Klotho protein levels. Conversely, AMPA and NMDA antagonism suppress neuronal Klotho expression. We also provide evidence that soluble Klotho enhances astrocytic aerobic glycolysis by hindering pyruvate metabolism through the mitochondria, and stimulating its processing by lactate dehydrogenase. Pharmacological inhibition of FGFR1, Erk phosphorylation, and monocarboxylic acid transporters prevents Klotho-induced lactate release from astrocytes. Taken together these data suggest Klotho is a potential new player in the metabolic coupling between neurons and astrocytes. Neuronal glutamatergic activity and insulin modulation elicit Klotho release, which in turn stimulates astrocytic lactate formation and release. Lactate can then be used by neurons as a metabolic substrate contributing to fulfill their elevated energy requirements.

overall_design: For both the mouse primary cortical neuron and cortical astrocyte cultures, control (1xPBS, N=4 per cell type) and Klotho-treated samples (1nM, N=4 per cell type) were incubated for 24 hours prior to RNA extraction.

first: Caio

middle: H

last: Mazucanti

first: Elisa

last: Kawamoto

first: Mark

middle: P

last: Mattson

first: Cristoforo

last: Scavone

first: Simonetta

last: Camandola


title: TREM2 Gene Dosage Increase Reprograms Microglia Responsivity and Ameliorates Pathological Phenotypes in Alzheimer’s Disease Models

status: Public on Mar 07 2018

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: TREM2 BAC transgenic mice with elevated expression of human TREM2 in microglia under its endogenous regulation without overexpression of other TREM-like genes on the BAC were generated and crossed with 5xFAD mice, an mouse model of AD. Transcriptome and gene coexpression analyses were performed to obtain chronical view of TREM gene dosage dependent changes in the context of amyloid pathology. The results confer strong evidence that increased TREM2 alters brain transcriptome network response only in the context of a disease state and with an overall rescuing effect in 5xFAD mice.

overall_design: Brain cortical tissues were dissected from WT, BAC-TREM2, 5xFAD and 5xFAD/BAC-TREM2 at 2, 4 and 7 months of age. RNA was extracted using Qiagen RNeasy kit. Libraries prepared using the Illumina TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq4000 sequencer using strand-specific, paired-end, 69-mer sequencing protocols to a minimum read depth of 30 million reads per sample. Reads were aligned to mouse genome mm10 using the STAR aligner with default settings. Read counts for individual genes were obtained using HTSeq.

first: C

middle: Y

last: Lee

first: Anthony

last: Daggett

first: Xiaofeng

last: Gu

first: Lu-Lin

last: Jiang

first: Peter

last: Langfelder

first: Yingjun

last: Zhao

first: Xiaoguang

last: Li

last: Wang

first: Chang

last: Park

first: Yonatan

last: Cooper

first: Isabella

last: Ferando

first: Istvan

last: Mody

first: Huaxi

last: Xu

first: X

middle: W

last: Yang


title: Lung gene expression after long-term styrene inhalation in three strains of C57BL/6 mice, and CD-1 mice

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

summary:
Lung gene expression after long-term (26 weeks, 52 weeks, 78 weeks & 104 weeks) styrene inhalation exposure at a single concentration (120ppm) in three strains of C57BL/6 mice -- wild-type (WT), CYP2F2 knockout (KO), and CYP2F1 humanized (TG) mice, and CD-1 mice.
These data examine transcriptomic changes in lung tissue after long-term styrene inhalation in male C57Bl/6 and CD-1 mice. Styrene causes increased lung tumors in mice, but not in rats. Mouse lung tumors were found mostly at the conclusion of a life-time (104 weeks for males) exposure study and most were benign. Styrene is largely negative in genotoxicity assays. Styrene metabolism by CYP2F2 produced a different metabolite pattern in mouse lung than in liver or in rats or humans. The purpose of this study was to use genomic analyses to further investigate potential modes of action (MoA) of styrene in mice after long-term exposure to styrene. Mice strains exposed were C57BL/6 wild-type (WT), CYP2F2 knockout (-/-; KO) and CYP2F21 humanized transgenic (2F2-KO + 2F1,2A13,2B6-transgenic, TG), and CD-1 male mice using 120 ppm styrene at 6 hr/day 5 days/wk for 26, 52, 78 and 104 weeks. Lungs were analyzed by Affymetrix whole genome microarrays for each strain relative to sample time-specific vehicle controls for each strain.

overall_design: A total of 154 male C57BL/6 and CD-1 mice were exposed to a single inhalation dose of styrene (120ppm) for 26, 52, 78 & 104 weeks. For each treatment, a total of from 2 to 10 biological replicates (both treated animals and corresponding strain- & time-specific vehicle controls) were used, from 3 strains of C57Bl/6 mice: wild type (WT), CYP2F2(-/-) knock-out (KO) and CYP2F2(-/-),2F1,SA13,2B6 transgenic (TG), and CD-1 mice. A _Tu in a CEL file name indicates the presence of tumors or tumorous lesions observed in the animal, but tumor-specific lung tissue was not separately assayed.

middle: B

first: Melvin

middle: E

last: Andersen


title: SPOP mutation confers intrinsic BET inhibitor resistance in prostate cancer (BRDs_OE_RNA-seq)

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: Bromodomain and extraterminal domain (BET) protein inhibitors are emerging as promising therapeutics of cancers including prostate cancer.  The E3 ubiquitin ligase adaptor protein speckle-type POZ protein (SPOP) is implicated in human prostate cancers due to its frequent mutation.  Here we demonstrate that SPOP binds to the BET proteins BRD2, BRD3 and BRD4.  Wild-type SPOP, but not prostate cancer-associated mutants, promotes polyubiquitination and proteasome degradation of BET proteins by recognizing a common degron motif.  BET protein levels are highly elevated in SPOP-mutated prostate cancers in patients.  Expression of cancer-derived SPOP mutants upregulates cholesterol biosynthesis genes and confers resistance to the BET inhibitor in cultured prostate cancer cells and tumors in mice, and this effect can be overcome by the AKT inhibitor.  Our findings reveal BET proteins as proteolytic targets of SPOP and identify deregulated cholesterol biosynthesis as a downstream event of SPOP mutation-mediated tumorigenesis and therapy resistance in prostate cancer.

overall_design: Examination of updated genes in the BRD2/3/4 overexpressed cells compared to empty vector (EV) cells.

first: Yu

first: Zhenqing

last: Ye

first: Wang

last: Liguo

first: Haojie

last: Huang


title: Gene expression profiles from islets of a β-cell-specific CB1-knockout mice

first: Supriyo

last: De

summary: The cannabinoid 1 receptor (CB1) regulates insulin sensitivity and glucose metabolism in peripheral tissues. CB1 is expressed on pancreatic beta (β)-cells where its functions have not been fully described. We generated a β-cell-specific CB1-knockout (β-CB1-/-) mouse to study the long-term consequences of CB1 ablation on β-cell function in adult mice. β-CB1-/- mice had increased basal- and stimulated-insulin secretion and intra-islet cAMP levels, resulting in primary hyperinsulinemia, as well as increased β-cell viability, proliferation, and islet area. Hyperinsulinemia led to insulin resistance, which was aggravated by a high fat/high glucose diet and weight gain, although β-cells maintained their insulin secretory capacity in response to glucose. Strikingly, islets from β-CB1-/- mice were protected from diet-induced inflammation. Mechanistically we show that this is a consequence of curtailment of oxidative stress and reduced activation of Nlrp3 inflammasome in β-cells. Our data demonstrate CB1 to be a negative regulator of β-cells and a mediator of islet inflammation under conditions of metabolic stress.

overall_design: Gene expression profiles from islets from wildtype (β-CB1+/+) (N=4) and a β-cell-specific CB1-knockout (β-CB1-/-) mice (N=3) were examined using gene expression microarray analysis.

first: Isabel

last: González-Mariscal

first: Rodrigo

last: Montoro

first: Qing-Rong

last: Liu

first: Maire

last: Doyle

last: Rouse

first: Jennifer

last: O’Connell

first: Susan

last: Krzysik-Walker

first: Sara

last: Santa-Cruz Calvo

first: Soumita

last: Ghosh

first: Olga

middle: D

last: Carlson

first: Elin

last: Lehrmann

first: Yongqing

last: Zhang

first: Kevin

middle: G

last: Becker

first: Chee

last: Chia

first: Paritosh

first: Josephine

last: Egan


title: Genome-wide expression profiling of the LRRK2-G2019S mutation in hNES cells

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

summary:
Parkinson’s disease (PD) has a neuro-developmental component with multiple genetic predispositions. The most prevalent mutation, LRRK2-G2019S is linked to familial and sporadic PD. Based on the multiple origins of PD and the incomplete penetrance of LRRK2-G2019S, we hypothesize that modifiers in the patient genetic background act as susceptibility factors for developing PD. To assess the developmental component of LRRK2-G2019S pathogenesis, we used 19 human iPSC-derived neuroepithelial stem cell lines (NESCs). Isogenic controls distinguish between LRRK2-G2019S dependent and independent cellular phenotypes. LRRK2-G2019S patient and healthy mutagenized lines showed altered NESC self-renewal. Within patients, phenotypes were only partly LRRK2-G2019S dependent, suggesting Parkinson’s disease (PD) has a neuro-developmental component with multiple genetic predispositions. The most prevalent mutation, LRRK2-G2019S is linked to familial and sporadic PD. Based on the multiple origins of PD and the incomplete penetrance of LRRK2-G2019S, we hypothesize that modifiers in the patient genetic background act as susceptibility factors for developing PD. To assess the developmental component of LRRK2-G2019S pathogenesis, we used 19 human iPSC-derived neuroepithelial stem cell lines (NESCs).
Isogenic controls distinguish between LRRK2-G2019S dependent and independent cellular phenotypes. LRRK2-G2019S patient and healthy mutagenized lines showed altered NESC self-renewal. Within patients, phenotypes were only partly LRRK2-G2019S dependent, suggesting a significant contribution of the genetic background. We identified Serine racemase (SRR) as a novel patient-specific, developmental, genetic modifier contributing to the abberant phenotypes. Its enzymatic product, D-Serine, rescued altered NESC renewal. Susceptibility factors in the genetic background, such as SRR, could be new targets for early PD diagnosis and treatment.

overall_design: 51 samples analyzed, 4 outliers excluded based on QC, 17 coditions, 3 biological replicates, 6 LRRK2G2019S patients, 6 healthy indiviuals, 3 gene corrected lines, 2 inserted mutated lines

first: Sarah

last: Nickels

first: Jens

last: Schwamborn

first: Ginholac

last: Aurélien


title: Staphylococcus aureus bona fide sRNAs in the model strain HG003

city: Jouy-en-Josas

first: Tatiana

last: Rochat

address: Domaine de Vilvert

country: France

institute: INRA

type: Non-coding RNA profiling by high throughput sequencing

summary: Accurate annotation of regulatory RNAs is a complex task but nevertheless essential as sRNA molecular and functional studies ensue from it. Several formerly considered small RNAs (sRNA) are now known to be parts of UTR transcripts. In light of experimental data, we review hundreds of Staphylococcus aureus putative regulatory RNAs. We pinpoint those that are likely acting in trans and are not expressed from the opposite strand of a coding gene. We conclude that HG003, a NCTC8325 derivative strain, has about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated.

overall_design: Total RNA samples were extracted from HG003 grown in various biological conditions. All 16 RNA samples were pooled together for RNA sequencing. Pooled RNAs were processed using the MICROBExpress kit (Ambion, AM1905) as recommended by the suppliers, for rRNAs removal and before high-throughput sequencing using Illumina Genome Analyzer IIx generating single-end 40-nt reads.

first: Philippe

last: Bouloc


title: Post-transcriptional remodelling is temporally deregulated during motor neurogenesis in human ALS models

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

institute: Idiap Research Institute

summary: Mutations causing amyotrophic lateral sclerosis (ALS) strongly implicate regulators of RNA-processing that are ubiquitously expressed throughout development. To understand the molecular impact of ALS-causing mutations on early neuronal development and disease, we performed transcriptomic analysis of differentiated human control and VCP-mutant induced pluripotent stem cells (iPSCs) during motor neurogenesis. We identify intron retention (IR) as the predominant splicing change affecting early stages of wild-type neural differentiation, targeting key genes involved in the splicing machinery. Importantly, IR occurs prematurely in VCP-mutant cultures compared with control counterparts; these events are also observed in independent RNAseq datasets from SOD1- and FUS-mutant motor neurons (MNs). Together with related effects on 3’UTR length variation, these findings implicate alternative RNA-processing in regulating distinct stages of lineage restriction from iPSCs to MNs, and reveal a temporal deregulation of such processing by ALS mutations.  Thus, ALS-causing mutations perturb the same post-transcriptional mechanisms that underlie human motor neurogenesis.

overall_design: Bulk RNA-seq at different timepoints throughout a 35-day differentiation protocol that converted iPSC cells to highly enriched motor neurons.

first: Giulia

last: Tyzack

first: Claire

last: Hall

first: Jernej

last: Ule

first: Nicholas

middle: M

last: Luscombe

first: Rickie

last: Patani


title: Global changes of H3K27me3 domains and PcG protein distribution in the absence of the PcG recruiters Spps or Pho

first: Mingan

last: Sun

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

summary: Polycomb group (PcG) proteins maintain the silenced state of key developmental genes in animals, but how these proteins are recruited to specific regions of the genome is still poorly understood. In Drosophila, PcG proteins are recruited to Polycomb response elements (PREs) that include combinations of sites for sequence specific DNA binding “PcG recruiters,” including Pho, Cg, and Spps. To understand their roles in PcG recruitment, we compared Pho-, Cg-, and Spps-binding sites against H3K27me3 and key PcG proteins by ChIP-seq in wild-type and mutant third instar larvae. H3K27me3 in canonical Polycomb domains is decreased after the reduction of any recruiter. Reduction of Spps and Pho, but not Cg, causes the redistribution of H3K27me3 to heterochromatin. Regions with dramatically depleted H3K27me3 after Spps knockout are usually accompanied by decreased Pho binding, suggesting their cooperative binding. PcG recruiters, the PRC2 component E(z), and the PRC1 components Psc and Ph cobind thousands of active genes outside of H3K27me3 domains. This study demonstrates the importance of distinct PcG recruiters for the establishment of unique Polycomb domains. Different PcG recruiters can act both cooperatively and independently at specific PcG target genes, highlighting the complexity and diversity of PcG recruitment mechanisms.

overall_design: Using ChIP-Seq, we proviled the genome-wide binding of different PcG recruiters (Spps, Pho, Cg), H3K27me3 and several PcG proteins (Ez, Ph, Psc, Pc) in wild type and mutant larval tissue to Spps maternal-zygotic mutants, and zygotic pho and cg mutants. We also examined differential expression in wild-type and mutants with RNA-Seq.

first: Lesley

last: Brown

first: Ming-an

first: Judith

last: Kassis


title: Whole blood gene expression after stimulation with TLR2 ligands (chitin oligomers, Pam2, Pam3) and the TLR4-ligand LPS

city: Tuebingen

first: Alexander

middle: NR

last: Weber

address: Auf der Morgenstelle 15

department: Department of Immunology

institute: University of Tuebingen

summary: Chitin is the second most abundant polysaccharide in nature and a biomolecule intimately linked to fungal infection and allergic asthma, conditions that affect millions of patients worldwide. Chitin is known to stimulate multiple mammalian immune cells, but the precise molecular sensing mechanism has not been elucidated, hampering strategies to specifically target chitin-mediated pathologies. The study associated with this microarray dataset uses defined chitin oligomers to identify six chitin subunits as the smallest immunologically active chitin motif and the innate immune receptor TLR2 as the molecular chitin sensor on human and murine immune cells, in vitro and in vivo. The goal of this microarray dataset was to elucidate transcriptional differences of human whole blood cells when responding to chitin, to other TLR2 ligands (Pam2, Pam3), and furthermore to the TLR4 ligand LPS. All four stimulants are compared to each other and to the unstimulated whole blood samples as a reference. We conclude that chitin oligomers elicitd overlapping yet distinct signaling outcomes compared to canonical TLR2 ligands.

overall_design: Whole blood was incubated for three hours with different stimulants (chitin oligomers, Pam2CSK4, Pam3CSK4, lipopolysaccharide) or without (unstimulated control) to characterize the transcriptional response of chitin compared to other TLR ligands. Each of the five conditions was repeated in the same five patients, except LPS which was repeated in only three of these patients, adding up to a total of 23 samples. The unstimulated whole blood served as a reference sample.

first: Katharina

last: Fuchs

first: Yamel

last: Gloria

first: Olaf-Oliver

last: Wolz

first: Franziska

last: Herster

first: Lokesh

last: Sharma

first: Carly

last: Dillen

first: Christoph

last: Taeumer

first: Sabine

last: Dickhoefer

first: Zsofia

last: Bittner

first: Truong-Minh

last: Dang

first: Anurag

last: Singh

first: Maria

last: Schloeffel

first: Kirsten

middle: J

last: Koymans

first: P

last: Chandran

first: Tharmila

last: Sanmuganantham

first: Milena

last: Krach

first: Nadine

last: Schilling

first: Felix

last: Frauhammer

first: Louris

last: Feitsma

first: Lloyd

last: Miller

first: Eric

last: Huizinga

first: Torsten

last: Nürnberger

first: Salomé

last: LeibundGut-Landmann

first: Andrea

last: Gust

first: Boris

last: Macek

first: Martin

last: Frank

first: Cécile

last: Gouttefangeas

first: Charles

last: Dela Cruz

first: Dominik

last: Hartl

middle: R


title: Atherosclerotic and control peripheral artery gene expression

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

institute: L'institut du thorax

summary: Transcriptome analysis of human peripheral arteries from carotid, femoral and infra-popliteal territories in atherosclerotic and control tissue

overall_design: Atherosclerotic lesions and control arteries without atherosclerotic lesions (from deceased organ donors) were obtained from carotid, femoral and infra-popliteal arteries. RNA was extracted and hybridized to microarrays.


title: Identification and characterization of microRNAs in the intestinal tissues of sheep (Ovis aries)

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

summary: Here, we analyzed and identified the miRNA expression profile of three different intestinal tissues (i.e., duodenum, cecum, and colon) of sheep (Ovis aries) using high-throughput sequencing and bioinformatic methods. In total, 128 known miRNAs were identified, 526 novel miRNAs were predicted, and 202 differentially expressed miRNAs were found between the different tissues. Additionally, 4,422 candidate target genes were predicted, and 185 non-redundant GO annotation terms were identified using enrichment analysis. A total of 529 target genes were found to participate in 37 KEGG biological pathways, and 270 of these genes were significantly enriched in the metabolism category.

overall_design: Examination of miRNA expression in 3 sheep intestinal regions.

first: Lei

last: Hou

first: Jianmin

last: Wang


title: Epitope mapping of human Fabs directed against 4CmenB protein components by protein microarray

city: Siena

first: Erika

last: Bartolini

state: Italy

address: Via Fiorentina 1

department: AIMB

country: Italy

institute: GSK Vaccines

summary: The aim of the study was to determine the epitope targeted by a panel of Human Fabs. Fabs were diluted at 1:50 and incubated on a non-commercial Protein Microarray platform printed with fHbp, NHBA and NadA specific recombinant protein fragments and full length fHbp, NHBA and NadA of different variants.

overall_design: A panel of recombinant fragments of different length spanning the entire sequence of  fHbp, NHBA and NadA plus different full length fHbp, NHBA and NadA variants were printed in 8 or 16 replicated on non-commercial Protein Microarray. All fragments were expressed in E. coli as either glutathione S-transferase-, His-tagged or TRX-fusions, purified from the cytoplasmic fraction as soluble forms. Human IgG (at 8 different concentration points) was distributed in each array copy as control. Fabs were profiled for anti-Human IgG specific analysis of reactivity to the spotted proteins.

first: Marco

last: Bruttini


title: Epitope mapping of 4 monoclonal antibodies directed against Neisserial Heparin Binding Antigen by peptide microarray

summary: The aim of the study was to determine the epitope targeted by four different HumAbs and the cross-reactivity to linear peptide epitopes of 10 different Neisserial Heparin Binding Antigen (NHBA) variants. the HumAbs were diluted at 1:60 and incubated on a custom PepStar Peptide Microarray platform printed with 561 different peptides.

overall_design: A panel of 561 peptides (15-mer overlapping peptides with an offset of 4 amino acids) covering the entire sequence of ten different NHBA variants (p1, p2, p3, p5, p10, p17, p18, p20, p21 and p29) were printed in triplicate on a custom PepStar Peptide Microarray. Process-control peptide (GGSGGGSDYKDDDDK) and human IgG were distributed in each array copy as controls. the HumAbs were profiled for anti-human IgG specific analysis of reactivity to the peptide epitopes


title: Epitope mapping of 5 monoclonal antibodies directed against meningococcal factor H binding protein by peptide microarray

summary: The aim of the study was to determine the epitope targeted by 5 different HumAbs and the cross-reactivity to linear peptide epitopes of 12 different factor H binding protein (fHbp) variants. The HumAbs were diluted at 1:200 and incubated on a custom PepStar Peptide Microarray platform printed with 363 different peptides.

overall_design: A panel of 363 peptides (15-mer overlapping peptides with an offset of 4 amino acids) covering the entire sequence of 12 different fHbp variants (1.1, 1.4, 1.13, 1.14, 1.15, 2.16, 2.19, 2.25, 2.77, 3.28, 3.45, NL10A) were printed in triplicate on a custom PepStar Peptide Microarray. Process-control peptide (GGSGGGSDYKDDDDK) and human IgG were distributed in each array copy as controls. HumAbs were profiled for anti-human IgG specific analysis of reactivity to the peptide epitopes


title: Placental methylation arrays for the assessment of epigenetic regulation in transcriptional subtypes of human preeclampsia

city: Toronto

first: Brian

last: Cox

state: Ontario

address: 1 King's College Circle

department: Physiology

institute: University of Toronto

type: Methylation profiling by genome tiling array

summary: Preeclampsia (PE) is a complex, heterogeneous disorder of pregnancy, demonstrating considerable variability in observed maternal symptoms and fetal outcomes. We recently identified five clusters of placentas within a large gene expression microarray dataset (N=330, GSE75010), of which four contained a substantial number of PE samples. However, while transcriptional analysis of placentas can subtype patients, we hypothesized that the addition of epigenetic information should reveal gene regulatory mechanisms behind the distinct PE pathologies. We, therefore, subjected 48 of our samples to Infinium Human Methylation 450K arrays and investigated relationships between the gene expression and DNA methylation data.

overall_design:
Bisulfite-converted DNA from 48 placentas belonging to transcriptional clusters 1, 2, 3, and 5 were hybridized to Illumina Infinium HumanMethylation450 BeadChips. Methylation data was analyzed separately, as well as integrated with matched gene expression information.
Both the gene expression (from GSE75010) and methylation array data for these 48 placentas are available below.

first: Katherine

last: Leavey

first: Samantha

last: Wilson

first: Shannon

last: Bainbridge

first: Wendy

last: Robinson


title: mRNA-seq of Arabidopsis mutants of UPR modulators responding to UPR inducers

city: Yokohama

first: June-Sik

last: Kim

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN CSRS

summary: The NGS-associated mRNA-seq analysis was conducted to survey transcriptome changes responding to three UPR inducers (tunicamycin, DTT, & Azetidine-2-cytosine) by four double mutant of three UPR-associated transcription factors (bZIP17, bZIP28, & bZIP60) and two activators (S1P & S2P).

overall_design: Four double mutant lines (bz17/28, bz28/60, bz17/60, and s1p/s2p) were subjected to the analysis.

first: Kazuko

last: Yamaguchi-Shinozaki

first: Kazuo

last: Shinozaki


title: Epitope mapping of human antibodies directed against 4CmenB protein components

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

platform_organism:
Neisseria meningitidis
Neisseria meningitidis serogroup B

overall_design: Refer to individual Series


title: Identification and characterization of androgen receptor splice variants preferred bindings that drive prostate cancer progression

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio


title: Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs

status: Public on Mar 06 2018

city: Riverside

first: Junchao

last: Shi

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

institute: University of California, Riverside

summary: The discovery of RNAs (e.g. mRNAs, non-coding RNAs) in sperm has opened the possibility that sperm may function in delivering additional paternal information aside from solely providing the DNA1. Increasing evidence now suggests that sperm small non-coding RNAs (sncRNAs) can mediate intergenerational transmission of paternally acquired phenotypes, including mental stress2, 3 and metabolic disorders4-6. How sperm sncRNAs encode paternal information remains unclear, but the mechanism may involve RNA modifications. Here we show that deletion of a mouse tRNA methyltransferase, DNMT2, abolished sperm sncRNA-mediated transmission of high-fat diet (HFD)-induced metabolic disorders to offspring. Dnmt2 deletion prevented the elevation of RNA modifications (m5C, m2G) in sperm 30-40nt RNA fractions that are induced by HFD. Also, Dnmt2 deletion altered the sperm small RNA expression profile, including levels of tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNA-28S), which might be essential in composing a sperm RNA ‘coding signature’ that is needed for paternal epigenetic memory. Finally, we show that Dnmt2-mediated m5C contributes to the secondary structure and biological properties of sncRNAs, implicating sperm RNA modifications as an additional layer of paternal hereditary information.

overall_design: Mature sperm small RNA profiles among Dnmt2 (Trdmt1)+/+ High-fat-diet (HFD), Dnmt2+/+ Normal-diet (ND), Dnmt2-/- HFD and Dnmt2-/- ND mouse; Transfection of synthesized tsRNAs (with site-specific m5C modifications) into 3T3 cell line.

first: Qi

last: Chen


title: RNA-seq analysis of glucose fermentation by the natural Isopropanol producer Clostridium beijerinckii DSM6423

status: Public on Mar 05 2018

city: Rueil Malmaison

first: Frederique

last: Bidard

address: 1-4 avenue de Bois Préau

department: Biotechnology

institute: IFPEN

summary:
Purpose:C. beijerinckii DSM 6423 is the most cited natural IpOH producer. Improving the natural production of this strain through a targeted approach required a full sequencing and characterization of its genome, together with transcriptomic analyses of its own regulations.The goals of this study are then to evaluate the transcriptional profile (RNA-Seq) of  C. beijerinckii DSM6423, a natural isopropanol producer, during a fermentation of glucose in controlled bioreactors.
Methods : A RNA-Seq approach was chosen in order to have a timelapse study of DSM 6423 throughout the fermentation process. Three independent duplicate fermentations of DSM 6423 were carried out in bioreactors on three different weeks, showing good reproducibility. On each cultivation, five biomass samples were collected for RNA-Seq analyses.and DNA was eliminated after DNAse I treatment (AM1906, Invitrogen). The 15 resulting RNA samples were sequenced and analyzed using the previously reconstructed genome of DSM 6423.
Results: Using a data analysis workflow (TAMARA) developed by the Genoscope platform of Evry, we were able to highlight the transcriptional regulation along the fermentation by calculating the transcription profiles of each gene, using  the 3h sample as reference. Clustering was performed using CAST algorithm revealed 8 clusters containing 953 genes and corresponding to genes up-regulated at 6, 8, 11 or 24 hours and gene down-regulated at 6, 8, 11 or 24 hours.
Conclusion : Such analyses were carried out in this study and provide useful data to better understand the genetic background and the physiological specificities of C. beijerinckii DSM6423 isopropanol producer.   Notably, this work is the first omic study of a natural IBE producer.  The data gathered needs time for proper exploitation, but a better understanding of the metabolic pathways and various genes involved opens the door for future targeted approaches.

overall_design: Comparative analysis of samples taken from a serie a fermentations performed in controled conditions

first: Hadrien

last: de Gérando

first: Frédérique

last: Bidard-Michelot

first: Etienne

last: Jourdier

first: Ana

last: López-Contreras

first: Nicolas

middle: L

last: Ferreira


title: Epitope mapping of 11 monoclonal antibodies directed against Neisserial adesin A by peptide microarray

first: Erika

last: Bartolini

summary: The aim of the study was to determine the epitope targeted by four different HumAbs and the cross-reactivity to linear peptide epitopes of 5 different Neisserial adesin A (NadA) variants. the HumAbs were diluted at 1:200 and incubated on a custom PepStar Peptide Microarray platform printed with 348 different peptides.

overall_design: A panel of 348 peptides (15-mer overlapping peptides with an offset of 4 amino acids) covering the entire sequence of five different NadA variants (var1, var2, var3, var4 and var5) were printed in triplicate on a custom PepStar Peptide Microarray. Process-control peptide (GGSGGGSDYKDDDDK) and human IgG were distributed in each array copy as controls. the HumAbs were profiled for anti-human IgG specific analysis of reactivity to the peptide epitopes

first: Marco

last: Bruttini


title: Transcriptional and epigenetic profiling of aged mouse SVZ-derived neural stem / progenitor cells

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Here we analyse histone modifications, DNA methylation and transcriptome profiles of SVZ-derived neural stem / progenitor cells from young adult and aged mice.

overall_design: Histone modifications (H3K27me3, H3K4me3), DNA methylation (BS-Seq and oxBS-Seq) and transcriptome (mRNA-Seq) from young adult and aged neural stem / progenitor cells.

first: Giuseppe

last: Lupo

first: Emanuele

last: Cacci

first: Peter

last: Rugg-Gunn


title: Viral fitness correlates with the magnitude and direction of the perturbation induced in the host's transcriptome: the tobacco etch potyvirus - tobacco case study.

city: Valencia

first: Héctor

last: Cervera Benet

state: Valencia

address: Ingeniero Fausto Elio s/n

department: IBMCP

country: Spain

institute: CSIC-UPV

summary: Determination of fitness for viral genotypes is a standard practice in virology an essential to evaluate their evolutionary potential.  Darwinian fitness, defined as the advantage of a given genotype respect to a reference one, is a macroscopic property that captures into a single figure differences in performance at every stage of viral infection.  To which extent the expression of certain host genes determines viral fitness?  Can we identify host’s genes whose expression have a significant effect on viral fitness?  To which functional classes and regulatory networks do belong these genes?  We compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus (TEV) that differ in fitness.  The larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are.  Some genes were significantly altered by all genotypes while others depend on viral fitness.  We identified genes whose expression showed a positive correlation with TEV fitness and genes with a negative one.  To validate these correlations, we analyzed the expression of four positively and five negatively correlated genes.  Over-expression of the first group activates hormone-mediated plant defense pathways.  Under-expression of the second group reduces metabolism, growth and development and/or plant viral resistance, resulting in higher susceptibility

overall_design: All six TEV mutant genotypes used in this study (HC-Pro:AS13, HC-Pro:CLA2, HC-Pro:CLA11, CI:PC48, CI:PC55 and NIb:PC95 genotypes) were constructed by successive rounds of site-directed mutagenesis starting from template plasmid pMTEV. N. tabacum L. cv. Xanthi NN plants were used for production of a large stock of virus particles for each of the genotypes (including WT). At given dpi virus-infected leafs and apexes for each plant were collected individually. Total RNA was isolated and hybridized onto a genotypic designed N. tabacum Gene Expression 4×44K Microarray (AMADID: 021113), which contained 43,803 probes (60-mer oligonucleotides) and was used in a one-color experimental design. Three biological replicas for each viral genotype infected plant, wild-type infected plants and mock-inoculated plants were analyzed.

last: Cervera

first: Silvia

last: Ambrós

first: Guillermo

last: Rodrigo

last: Bernet

first: Santiago

middle: F

last: Elena


title: Functional TRIM24 degraders via conjugation of ineffectual bromodomain and VHL ligands [ChIP-seq]

city: Boston

first: Nathanael

last: Gray

state: Massachusetts

address: 360 Longwood Ave

department: Cancer Biology

institute: DFCI

summary: The addressable pocket of a target protein is often not functionally relevant. This is particularly true for multidomain gene regulatory proteins, such as the bromodomain-containing transcriptional regulator TRIM24. TRIM24 has been posited as a dependency in numerous human cancers, yet potent and selective ligands for the TRIM24 bromodomain do not exert effective anti-proliferative responses. We therefore repositioned these probes as targeting features for heterobifunctional protein degraders.

overall_design: TRIM24 localization to chromatin with treatments IACS-9571 and dTRIM24

first: Lara

last: Gechijian


title: Identification and characterization of androgen receptor splice variants preferred bindings that drive prostate cancer progression [ChIP-seq]

first: Zhenqing

last: Ye

summary: Androgen receptor (AR) splice variants (ARVs) are implicated in developing castration-resistant (CR) prostate cancer (CRPC). Little is known about the ARV-mediated transcription program in CRPC. We identified ARV-preferred binding sites (ARV-PBS) and unique transcriptome in CRPC cells. ARVs preferentially bind to enhancers located in nucleosome-depleted regions with the full AR-response element (AREfull), while full-length AR (ARFL)-PBS are enhancers resided in closed chromatin regions with the composite FOXA1-nnnn-AREhalf motif. ARV-PBS exclusively overlapped with AR binding sites in CR patients. ARV-driven genes were up-regulated in abiraterone-resistant patient specimens and promote CRPC growth. We uncover distinct genomic and epigenomic characteristics of ARV-PBS and a unique ARV-dependent transcriptional program that not only drives CR progression but could also offer new targets for therapy. Increasing evidence suggests a pivotal role of ARVs in the acquisition of anti-AR therapy resistance in CRPC. It has been shown previously that ARVs possess unique structural and functional features such as completely lacking or only containing an impaired ligand-binding domain but constitutively active.  Our findings advance the understanding of ARVs by demonstrating that ARV-PBS exhibit distinctive DNA-binding motif, GC content, and nucleosome and epigenetic characteristics.  We further unravel that ARV-PBS exclusively overlap with AR bindings identified from castration-resistant patients and ARV activity is significantly increased in abiraterone-resistant patients.  Given that there is no drug available to target ARVs at present, identification of ARV-mediated unique downstream pathways opens new avenues for the development of effective therapeutics for CRPC.

overall_design: ARVs preferred binding sites (ARV-PBS) were identified from regular AR ChIP-seq experiments after knocking down AR full length (ARFL) in 22Rv1 (R1881-). ARFL preferred binding sites (ARFL-PBS) were identified from regular AR ChIP-seq experiments after knocking down AR-V1, AR-V3, AR-V4 and AR-V7 in 22Rv1 (R1881+).

first: Liguo

last: Wang

first: Ji

last: Lu


title: Clonally expanded CD4+ T cells with a unique gene signature contribute to persistence of the HIV-1 latent reservoir

status: Public on Mar 02 2018

city: Sao Paulo

first: Israel

middle: Tojal da

last: Silva

state: SP

address: Tagua, 440

country: Brazil

institute: HOSPITAL A C CAMARGO

summary: Surface expression of the viral Envelope protein (Env) was used to enrich reactivated latent T cells producing HIV-RNA, and single cell RNASeq was performed to study gene expression differences between latent cells and controls.

overall_design: Latent CD4+ T cells from virologically suppressed patients were reactivated in vitro and isolated using antibodies against HIV-1 Env. Single cell RNASeq was performed comparing reactivated latent cells with control, unpurified cells from the same donor and with cells actively infected in vitro using HIV-1(YU2).

middle: T

last: da Silva

first: Renan

last: Valieris


title: c-Jun/AP-1 overexpression reprograms ERα signaling related to tamoxifen response in ERα-positive breast cancer [expression profiling]

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

institute: Karolinska Institutet

summary: A critical mechanism that has been proposed for transcription regulation by estrogen receptor α (ER) is the tethering of ER to DNA via other transcription factors, such as AP-1. However, genome-wide assessment of the overlap in chromatin binding repertoires of these two transcription factors has not been reported. Here, we show that the AP-1 transcription factor c-Jun interacts with ER and that c-Jun chromatin binding shows extensive overlap with ER binding at the global level. Further, we show that c-Jun overexpression reprograms ER chromatin binding and modulates ER-mediated gene regulation. Our data are consistent with a mechanism where estrogen/ER-dependent crosstalk with AP-1 at the transcriptional level is mediated through the tethering of ER to DNA bound AP-1. Additionally, in our system c-Jun overexpression causes reduced sensitivity to tamoxifen in ER+ breast cancer cells. Integrated cistrome, transcriptome, and clinical data reveal TGFBI as a candidate gene which may confer tamoxifen resistance by ER and AP-1 crosstalk. Further, we show that TGFBI expression is elevated in breast cancer compared to normal breast. Together, our data provide a novel genome-wide footprint of ER and AP-1 crosstalk and suggest AP-1 and TGFBI signaling as potential therapeutic targets in AP-1-overexpressing ER-positive breast tumors.

overall_design: Examination of E2 and Tamoxifen induced gene expression changes in MCF-7/c-Jun tet-off cells

first: Huan

last: He

first: Indranil

last: Sinha

first: Rongrong

last: Fan

first: Lars-Arne

last: Haldosén

first: Feifei

last: Yan

first: Chunyan

last: Zao


title: ERα and AP-1 coordinate transcription and tamoxifen response in ERα-positive breast cancer


title: c-Jun/AP-1 overexpression reprograms ERα signaling related to tamoxifen response in ERα-positive breast cancer [ChIP-seq]

summary: A critical mechanism for transcription regulation by estrogen receptor α (ER) is the tethering of ER to DNA via other transcription factors, such as AP-1. However, genome-wide assessment of the overlap in chromatin binding repertoires of these two transcription factors has not been reported. Here, we show that the AP-1 transcription factor c-Jun interacts with ER and is recruited globally to ER binding regions. Interestingly, we identify differential motif enrichment between unique ER binding regions and unique c-Jun binding regions, with FoxA1 motif enriched in both sets of binding regions, whereas GATA3 motif only specifically enriched in the unique ER binding regions but not in the unique Jun binding regions. We demonstrate that the primary mechanism for estrogen/ER-dependent transcriptional responses is the tethering of ER to DNA under conditions where it cooperates with AP-1. We provide evidence that c-Jun overexpression causes reduced sensitivity to tamoxifen in ER+ breast cancer cells. Integrated omics data reveal TGFBI as one of the most perturbed genes regulated by c-Jun. TGFBI knockdown suppresses the growth of breast cancer cells and is critical for increasing the sensitivity of tamoxifen-resistant cells to tamoxifen. We show that TGFBI expression is elevated in breast cancer than in normal breast and the basal-like tumors express high levels of TGFBI. TGFBI expression is associated with poor patient survival in ER+ breast cancer receiving endocrine therapy, highlighting a role of AP-1 via TGFBI signaling as a major determinant of endocrine response in ER+ breast tumor.

overall_design: Examination of E2 and Tamoxifen induced gene expression changes in MCF-7/c-Jun -Tet cells


title: Integrative analysis of reprogramming human fibroblast cells to naïve pluripotency

status: Public on Mar 03 2018

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University


title: Expression data from SIVagm-infected African green monkeys (Chlorocebus sabaeus)

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary:
In contrast to SIVagm, which does not cause disease in its natural simian host, HIV-1 expresses the accessory protein Vpu and encodes a Nef protein that fails to suppress T cell activation via down-modulation of CD3. Although both, Vpu and Nef have been implicated as pathogenicity determinants, their relevance for viral replication and disease progression in vivo has remained unclear. Here, we analyzed gene expression in African green monkeys infected with SIVagm chimeras differing in their expression of nef and/or vpu.
We used microarrays to analyze global gene expression of African green monkeys in response to infection with SIVagm and found that the viral accessory nef and vpu genes co-determine the induction of distinct gene sets.

overall_design: Twelve juvenile female AGMs (Chlorocebus sabaeus) were randomly distributed to four groups with three monkeys each. The monkeys were infected with wild type SIVagm (WT; monkeys #14623, 14625, 14629), a chimera expressing SIVgsn Vpu (GU; #14624, 14627, 14632); a chimera expressing HIV-1 Nef (1N; #14626, 14630, 14631); or a double chimera expressing both SIVgsn Vpu and HIV-1 Nef (GU1N; #14628, 14633, 14634). RNA was isolated from whole blood 170 weeks post infection and whole genome microarray analysis was performed.

first: Frank

last: Kirchhoff

first: Daniel

last: Sauter

first: James

last: Billingsley

first: Steven

last: Bosinger

first: Nirav

last: Patel


title: The effect of ddl-1 on small RNA profile

status: Public on Mar 01 2018

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: DAWDLE (DDL) is a conserved forkhead-associated (FHA) domain-containing protein that plays essential roles in development and immunity. It was found to act in the biogenesis of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which regulate gene expression at transcriptional and/or post-transcriptional levels. However, its global effect on miRNA accumulation still is not known. To determine the global effect of DDL on the accumulation of miRNAs and siRNAs, we compared the small RNA profile in ddl-1 with that in WS (Wild-type, WT). Small RNA libraries prepared from inflorescences of ddl-1 and WS was subjected to Illumina deep sequencing analyses. The results show that many miRNAs  and siRNAs were reduced in abundance in ddl relative to WS in two biological replicates

overall_design:
We compared the small RNA profile in ddl-1 with that in WS (Wild-type, WT)
non coding RNA deep sequencing

first: Ren

last: Guodong

first: Yu

last: Bin

first: Zhang

last: Chi


title: The effect of cdc5-1 on small RNA accumulation

summary: CDC5 is a conserved DNA-binding protein that is required for development and immunity. It promotes the accumulation of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which repress gene expression. In this project, we aim to determine its global effect of on the accumulation of miRNAs and siRNAs.  We compared the small RNA profile in cdc5-1 with that in Col (Wild-type, WT). Small RNA libraries prepared from inflorescences of cdc5-1 and Col was subjected to Illumina deep sequencing analyses. The results show that many miRNAs  and siRNAs were reduced in abundance in cdc5 relative to Col in two biological replicates.

overall_design: Non-coding RNA deep sequencing

first: Guodong

last: Ren

first: Bin

last: Yu


title: Transcriptomic characterization of spl7 and Col-0 ecotypes of Arabidopsis reveals new aspects of Fe-Cu crosstalk

summary: Iron (Fe) and copper (Cu) are essential metal micronutrients that are necessary for many redox reactions. The uptake of these metals is tightly regulated in plants. Some redox processes can alternatively use Fe-containing proteins or Cu-containing proteins, depending on nutritional status. Copper deficiency can rescue a Cucumis melo Fe uptake deficient mutant, and Fe deficiency can result in increased accumulation of Cu. However, the system responsible for Fe-deficiency-regulated Cu-uptake is unknown. To understand the genes and gene networks associated with Fe-deficiency regulated Cu uptake and Fe-Cu cross-talk, we conducted transcriptomic profiling of roots and rosettes of spl7 (a Cu uptake deficient mutant in arabidopsis) and Col-0 (WT) grown under Fe, Cu and simultaneous Fe and Cu deficiency conditions.

overall_design:
We conducted transcriptomic profiling of roots and rosettes of spl7 (a Cu uptake deficient mutant in arabidopsis) and Col-0 (WT) grown under Fe, Cu and simultaneous Fe and Cu deficiency conditions
mRNA deep sequencing

first: Brian

last: Waters


title: Functional TRIM24 degraders via conjugation of ineffectual bromodomain and VHL ligands

first: Nathanael

last: Gray


title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition

city: London

first: Peter

last: Hill

address: Kensington

institute: Imperial College London

summary:
Gametes are highly specialised cells that can give rise to the next generation through their ability to generate a totipotent zygote. In mouse, germ cells are first specified in the developing embryo as primordial germ cells (PGCs) starting around embryonic day (E) 6.25. Following subsequent migration into the developing gonad, PGCs undergo a wave of extensive epigenetic reprogramming at E10.5/E11.5, including genome-wide loss of 5-methylcytosine (5mC). The underlying molecular mechanisms of this process have remained enigmatic leading to our inability to recapitulate this step of germline development in vitro. Using an integrative approach, we show that this complex reprogramming process involves the coordinated interplay between promoter sequence characteristics, DNA (de)methylation, Polycomb (PRC1) complex and both DNA demethylation-dependent and -independent functions of Tet1 to enable the activation of a critical set of germline reprogramming responsive (GRR) genes involved in gamete generation and meiosis. Our results also unexpectedly reveal a role for Tet1 in safeguarding but not driving DNA demethylation in gonadal PGCs. Collectively, our work uncovers a fundamental biological role for gonadal germline reprogramming and identifies the epigenetic principles of the PGC-to-gonocyte transition that will be instructive towards recapitulating complete gametogenesis in vitro.

This SuperSeries is composed of the SubSeries listed below.


title: A widespread decrease of chromatin accessibility in age-related macular degeneration

city: Baltimore

first: Jie

last: Wang

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University

summary: Age-related macular degeneration (AMD) is a leading cause of blindness in the elderly. The extent to which epigenetic changes regulate the progression of AMD is unclear. Here we profiled chromatin accessibility in the retina and retinal pigmented epithelium (RPE) from AMD patients and controls. Global decreases in chromatin accessibility occur in the RPE in early AMD and in the retina with advanced disease. Footprints of photoreceptor and RPE-specific transcription factors are enriched in differentially accessible regions (DARs) and reduced AMD. Genes associated with DARs show altered expression in AMD. Cigarette smoke, an established risk factor for AMD, applied to human iPSC-derived RPE cells recapitulates epigenomic changes seen in AMD. In addition to providing a comprehensive profile of chromatin accessibility in human RPE and retina, this study shows that global decreases in chromatin accessibility may play a critical role in AMD progression.

overall_design: In the study, we profiled chromatin accessibility using ATAC-Seq (Assay for Transposase-Accessible Chromatin with high throughput sequencing) in 26 retinas and 20 RPE samples including one replicate. These samples are from fresh postmortem eyes which are healthy, early-stage AMD or late-stage AMD. Meanwhile, we profiled gene expression using RNA-Seq in 4 samples from retina and RPE tissues of one AMD patient whose right and left eyes are at  early stage and late stage of AMD diease, respectively. In addition, we performed ATAC-seq in human RPE cell lines.

first: Cristina

last: Zibetti

first: Seth

last: Blackshaw

first: Jiang

last: Qian


title: The ARID1A tumor suppressor controls global transcription via pausing of RNA Polymerase II

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

summary: We investigated the genomic consequences of the depletion of the SWI/SNF subumit ARID1A, in an ovarian cancer derived model. We produced genome wide data for nascent RNA (GRO-seq) and steady state RNA (total RNA-seq). Further, we used ChIP-seq to examine genome-wide distribution of ARID1A, as well as the changes in occupancy of  RNAPII, H3K4me3 and H3K36me3. Finally we used ATAC-seq to investigate chromatin accessibility.

overall_design: Analysis of global transcriptional changes associated to the depletion of ARID1A.

first: Elisa

last: Barbieri

first: Ana

last: Petracovici

first: Shuai

last: Wu

first: Sarah

last: Welsh

first: Tori

last: Owens

first: Silvia

last: Licciulli

first: Rugang

first: Alessandro

last: Gardini


title: Expression data ex vivo CD4 T cells systemic lupus erythematosus patients

city: Gainesville

first: Laurence

last: Morel

state: FL

address: 1395 Center Drive, D6-6

department: Pathology and Immunology

institute: University of Florida

summary: Compare ex vivo unstimulated CD4 T cells from SLE and HC female patients in an ethnically mixed cohort for transcriptional differences.

overall_design: Collection of blood and negative isolation for CD4+ T cells from 8 patients of varying disease activity, all females, and matched healthy controls. 3 tubes of 10mL each were taken and isolated for CD4 T cells by Rosette Sep antibodies and density centrifugation. These antibodies deplete CD8, CD16, CD19, CD36, CD56, CD66b, gamma/delta TCRs, by crosslinking to glycophorin A on red blood cells. Isolated cells were immediately lysed in Qiagen's buffer RLT with 0.1% 2-mercaptoethanol and stored at -80C until further isolation with Qiagen RNeasy mini kit. RNA was quantified with a nanodrop machine and 200 ng for each sample was used for fragmenting and labeling targets according to affymetrix recommendations for the HTA 2.0 microarrays. Scanning was performed with GeneChip Scanner 3000 7G, and washed and stained with the GeneChip  Fluidics Station 450.

first: Cecilia

last: Lopez

first: Henry

middle: V

last: Baker

first: Anton

middle: A

last: Titov


title: Integrative analysis of reprogramming human fibroblast cells to naïve pluripotency [RNA-seq]

first: Shaorong

last: Gao

summary: Derivation of human naïve cells in the ground state of pluripotency provides promising avenues for developmental studies and therapeutic manipulations. However, the molecular mechanisms involved in establishment and maintenance of human naïve pluripotency remain poorly understood. Using the human inducible reprogramming system together with 5iLAF naïve induction strategy, we performed integrative analysis across the timeline from human fibroblasts to naïve iPSCs, which reveals ordered expression waves of gene networks sharing signatures with embryonic development process from post-implantation to pre-implantation stages. We also observed a significant transient re-activation of transcripts with 8-cell-stage-like characteristics in late naïve reprogramming stages. Moreover, combined quantitative proteomics analysis with transcriptional dynamics during naïve pluripotency induction, we identified ALPPL2 as the specific surface marker for human naïve pluripotency. Altogether, our study deepens the understanding of molecular mechanisms of human naïve pluripotency.

overall_design: mRNA  profiles of transitioning cells at different time points in the naïve reprogramming process were performed by deep sequencing.

first: Yuanyuan

last: Yang

first: Yixuan

first: Chengchen

last: Zhao

first: Yong

last: Zhang


title: Expression data of 10-day old ssrp1-2 and spt16-1 mutants in comparison to wild type plants

city: Regensburg

first: Alexander

last: Pfab

address: Universitätsstraße 31

department: Cell Biology & Plant Biochemistry

institute: University of Regensburg

summary: Genome-wide transcript profiling was performed to identify possible alterations in gene expression of ssrp1-2 and spt16-1 mutants.

overall_design: Aerial parts of 10-day old wild type Col-0 and ssrp1-2 as well as spt16-1 mutants were harvested for RNA extraction and hybridization on Affymetrix microarrays. Plants were grown under standard growth conditions (100 µmol m-1 s-2) on 0.5xMS plates in the growth chamber. Several plants (100mg) were pooled to obtain a homogeneous population for the RNA isolation.

first: Klaus

last: Grasser


title: Gene and miRNA expression profiles in Polycythemia Vera and Essential Thrombocythemia according to CALR and JAK2 mutations [GEP]

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

institute: Centre for Regenerative Medicine

summary: Polycythemia vera (PV) and essential thrombocythemia (ET) are Philadelphia-negative myeloproliferative neoplasms (MPNs) characterized by erythrocytosis and thrombocytosis, respectively. Approximately 95% of PV and 50–70% of ET patients harbour the V617F mutation in the exon 14 of JAK2 gene, while about 20-30% of ET patients carry CALRins5 or CALRdel52 mutations. These ET CARL-mutated subjects show higher platelet count and lower thrombotic risk compared to JAK2-mutated patients. Here we showed that CALR-mutated and JAK2V617F-positive CD34+ cells have different gene and miRNA expression profiles. Indeed, we highlighted several pathways differentially activated between JAK2V617F- and CALR-mutated progenitors, i.e. mTOR, MAPK/PI3K and MYC pathways. Furthermore, we unveiled that the expression of several genes involved in DNA repair, chromatin remodelling, splicing and chromatid cohesion are decreased in CALR-mutated cells. According to the low risk of thrombosis in CALR-mutated patients, we also found the down-regulation of several genes involved in thrombin signalling and platelet activation.   As a whole, these data support the model in which CALR-mutated ET could be considered as a distinct disease entity from JAK2V617F-positive MPNs and may provide the molecular basis supporting the different clinical features of these patients.

overall_design: Gene expression profile (GEP) and miRNA expression profile (miEP) were performed starting from the same total RNA of CD34+ cells from 50 MPN patients (1 replicate for each sample). In particular, GEP and miEP were performed on 26 PV and 24 ET (n=17 JAK2V617F-positive ET, n=7 CALR-mutated ET). In addition, 15 bone marrow (BM) samples collected from normal donors were included in the study (GSE53482).  These re-analyzed samples have been included in this series for completeness.  This series includes only the GEP samples.

first: Roberta

last: Zini

first: Paola

last: Guglielmelli

first: Daniela

last: Pietra

first: Elisa

last: Rumi

first: Chiara

last: Rossi

first: Sebastiano

last: Rontauroli

first: Elena

last: Genovese

first: Tiziana

last: Fanelli

first: Laura

last: Calabresi

last: Bianchi

first: Simona

last: Salati

first: Mario

last: Cazzola

first: Enrico

last: Tagliafico

last: Vannucchi


title: Gene and miRNA expression profiles in Polycythemia Vera and Essential Thrombocythemia according to CALR and JAK2 mutations [miEP]

overall_design: Gene expression profile (GEP) and miRNA expression profile (miEP) were performed starting from the same total RNA of CD34+ cells from 50 MPN patients (1 replicate for each sample). In particular, GEP and miEP were performed on 26 PV and 24 ET (n=17 JAK2V617F-positive ET, n=7 CALR-mutated ET). In addition, 15 bone marrow (BM) samples collected from normal donors were included in the study (GSE53482).  These re-analyzed samples have been included in this series for completeness.  This series includes only the miEP samples.

first: Alessandro


title: STOP1 overexpressor vs. Col-0 and stop1 knockout vs Col-0 under control and NaCl

city: GIFU

first: AYAN

last: SADHUKHAN

state: GIFU

address: 1-1 YANAGIDO

department: APPLIED BIOLOGICAL SCIENCES

institute: GIFU UNIVERSITY

summary: Transcriptional profiling of Arabidopsis thaliana seedlings comparing overexpressor with wild type, and knockout with wild type separately under control and NaCl stress.

overall_design: Two-condition experiment, STOP1 overexpressor vs. Wild type (Col-0) and  STOP1 knockout vs. Wild type (Col-0) seedlings under control and NaCl. Biological replicates: 3 overexpressor/knockout, 3 wild type (Col-0).

first: Ayan

last: Sadhukhan

first: Hiroyuki

last: Koyama


title: Gene and miRNA expression profiles in Polycythemia Vera and Essential Thrombocythemia according to CALR and JAK2 mutations

first: Rossella

last: Manfredini

type:
Expression profiling by array
Non-coding RNA profiling by array

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual series


city: Montpellier

first: Gina

last: DEVAU

address: Place Eugene Bataillon

department: Universite de Montpellier CC105

institute: Inserm U1198-UM-EPHE

summary:
Parkinson disease (PD) is a neurodegenerative disease primarily associated with impaired movement affecting elderly people. To improve the understanding of the pathogenesis and to develop new therapies, we have developed a non-human primate model of PD using the lemurian Microcebus murinus (Mim). In this study, we tested the potential of canine adenovirus type 2 (CAV-2) as vector for gene transfer in the Mim brain by analyzing the gene expression changes in three regions involved in motor control: striatum, frontal cortex and midbrain. The CAV-2 viruses were injected in the right striatum of young adult females, 2 years old.
CAV-2 vectors preferentially transduce neurons in the primate brain and were carried by axonal transport to afferent structures in both hemispheres. The gene expression changes were analyzed at 2 critical times after infection by CAV-2: an acute time effect at 24h and a delayed time effect at 28 days post infection. In addition, the gene expression was compared in the ipsilateral side versus the contralateral side, and with a non-infected brain samples using human Affymetrix microarrays. The transcriptomic data were analyzed by Significance Analysis of Microarrays (SAM) to identify genes differentially expressed when comparing brain samples in the 3 conditions. The data were also analyzed by ANOVA one way and by Principal Component Analysis (PCA). The results have shown that the transduction of CAV2 in neurons induced specific changes. These changes differed during the immediate and the long-term-point. Gene expression changes were detected in transcriptional regulation, in synaptic transmission, in cellular trafficking and in immune response. More precisely, in the short term, CAV2 activated genes involved in a non-specific innate immune response. In the long term, CAV2 induced an adaptive tolerant immune response.
Gene expression changes in the frontal cortex of Microcebus murinus induced by Canine adenovirus type 2 (CAV-2)

overall_design: Microcebus murinus brain samples were divided in 3 groups : 1- right side (ipsilateral ton the infection site); 2- left side (contralateral; 3- non-infected samples. All the brain samples were analyzed at 24h  post infection, to detect the acute effect of CAV-2 and at 28 days after infection to detect the long term effect in the brain.

first: Nadine

last: MESTRE-FRNACES

first: Jean-Michel

last: VERDIER

first: Eric

last: KREMER


summary:
Parkinson disease (PD) is a neurodegenerative disease primarily associated with impaired movement affecting elderly people. To improve the understanding of the pathogenesis and to develop new therapies, we have developed a non-human primate model of PD using the lemurian Microcebus murinus (Mim). In this study, we tested the potential of canine adenovirus type 2 (CAV-2) as vector for gene transfer in the Mim brain by analyzing the gene expression changes in three regions involved in motor control: striatum, frontal cortex and midbrain. The CAV-2 viruses were injected in the right striatum of young adult females, 2 years old.
CAV-2 vectors preferentially transduce neurons in the primate brain and were carried by axonal transport to afferent structures in both hemispheres. The gene expression changes were analyzed at 2 critical times after infection by CAV-2: an acute time effect at 24h and a delayed time effect at 28 days post infection. In addition, the gene expression was compared in the ipsilateral side versus the contralateral side, and with a non-infected brain samples using human Affymetrix microarrays. The transcriptomic data were analyzed by Significance Analysis of Microarrays (SAM) to identify genes differentially expressed when comparing brain samples in the 3 conditions. The data were also analyzed by ANOVA one way and by Principal Component Analysis (PCA). The results have shown that the transduction of CAV2 in neurons induced specific changes. These changes differed during the immediate and the long-term-point. Gene expression changes were detected in transcriptional regulation, in synaptic transmission, in cellular trafficking and in immune response. More precisely, in the short term, CAV2 activated genes involved in a non-specific innate immune response. In the long term, CAV2 induced an adaptive tolerant immune response.
Gene expression changes in the midbrain of Microcebus murinus induced by Canine adenovirus type 2 (CAV-2)


title: Helper-dependent CAV-2 vector-mediated LRRK2G2019S expression in the M. murinus brain induces Parkinson's disease-like histological lesions and motor symptoms

overall_design: Refer to individual Series