title: Western diet triggers NLRP3-dependent persistent functional reprogramming of myeloid cells II [RNA-Seq]

first: Joachim

last: Schultze

summary: Here we investigated whether sterile triggers of inflammation  induce trained immunity and thereby influence innate immune responses. Western diet (WD) feeding of Ldlr-/- mice induced systemic inflammation, which was undectable in serum soon after mice were shifted back to chow diet (CD). In contrast, myeloid cell responses towards innate stimuli remained broadly augmented. WD induced transcriptomic and epigenomic reprogramming of myeloid progenitor cells, leading to increased proliferation as well as enhanced innate immune and interferon responses towards in vivo LPS challenge. QTL analysis in human monocytes trained with oxidized low-density lipoprotein (oxLDL) and stimulated with LPS suggested inflammasome-mediated trained immunity. Consistently, Nlrp3-/-/Ldlr-/--deficient mice lacked WD-induced systemic inflammation or myeloid progenitor proliferation and reprogramming. Hence, NLRP3 mediates trained immunity following WD and could thereby arbitrate the potentially deleterious effects of trained immunity in inflammatory diseases.

overall_design: Examination of GMPs in six different conditions by RNA-seq

first: Anette

last: Christ

first: Patrick

last: Günther

first: Mario

last: Lauterbach

first: Claus

last: Scholz

first: Kristian

last: Händler

first: Kevin

last: Baßler

first: Kathrin

last: Klee

first: Eicke

last: Latz


title: Western diet triggers NLRP3-dependent persistent functional reprogramming of myeloid cells [RNA-Seq]

status: Public on Jan 17 2018

city: Bonn

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

type: Expression profiling by high throughput sequencing

middle: A

middle: L


title: Western diet triggers NLRP3-dependent persistent functional reprogramming of myeloid cells [ATAC-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Examination of GMPs in three different conditions by ATAC-seq


title: Transcriptomic analysis of bacterial strains in the cbr/crc regulatory system

status: Public on Jan 04 2018

city: Wuhan

first: Zhixiong

last: Xie

state: Hubei

address: Bayi Road 299#

department: College of Life Science

country: China

institute: Wuhan University

summary: We screened a number of virulence genes in Pseudomonas donghuensis HYS, and genes in cbr/crc regulatory system were included. To investigate the relationship between this regulatory system and other virulence genes screened in the study, we performed transcriptome sequencing of strains related to cbr/crc system. Through analyzing the expression quantity, we found that the screened virulence genes were under the regulation of the cbr/crc system.

overall_design: Analyses of six samples, and two control strains are included

first: Guanfang


title: Exploring the RNA landscape of endothelial exosomes

status: Public on Feb 01 2018

city: Liege

first: Ingrid

last: Struman

address: Avenue de l'Hôpital, 1

department: BMGG

country: Belgium

institute: GIGA-R

type: Non-coding RNA profiling by high throughput sequencing

summary: Exosomes are small extracellular vesicles of around 100nm of diameter produced by most cell types. These vesicles carry nucleic acids, proteins, lipids and other biomolecules and function as carriers of biological information in processes of extracellular communication. The content of exosomes is regulated by the external and internal microenvironment of the parent cell, but the intrinsic mechanisms of loading of molecules into exosomes is still not completely elucidated. In this study, by the use of next generation sequencing we have characterized in depth the RNA composition of healthy endothelial cells and exosomes and provided an accurate profile of the different coding and non-coding RNA species found per compartment. We have also discovered a set of unique genes preferentially included (or excluded) into vesicles. Moreover, after studying the enrichment of RNA motifs in the genes unequally distributed between cells and exosomes, we have detected a set of enriched sequences for several classes of RNA. In conclusion, our results provide the basis to study the involvement of RNA-binding proteins capable to recognize RNA sequences and their role in the export of RNAs into exosomes.

overall_design:
Basal cellular and exosomal samples were prepared for smallRNA enriched sequencing and for total RNA sequencing using Illumina sample preparation and sequencing. Two biological replicates were prepared in parallel per condition and RNA type

Please note that the processed data was generated from all 8 samples together and thus, is linked to the Series records.

first: Jennifer

last: Perez-Boza

first: Michelle

last: Lion


title: Stabilization of NIK suppresses MLL-AF9-induced acute myeloid leukemia

status: Public on Jan 03 2018

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

country: USA

institute: University of Iowa

summary: Comparison of transcriptome between control and NIK-stabilized leukemia stem cells

overall_design: murine MLL-AF9 acute myeloid leukemia was generated using bone marrow progenitor cells (lin-cKit+) from NIKERT2 mice (crossing Rosa-loxp-STOP-loxp-NIK mice with Rosa-CreERT2 mice). Leukemia stem cells were sorted by FACS from tamoxifen treated (LSPCT group) and untreated (LSPC group) fully developed leukemia mice and used for RNAseq analysis.

first: Chen

last: Zhao


title: The Immunome in Two Inherited Forms of Pulmonary Fibrosis

status: Public on Jan 10 2018

city: Bethesda

first: Foo

last: Cheung

address: Bethesda

institute: NIH

summary: We analyzed via microarray gene expression profiles from patients with familial pulmonary fibrosis and HPS-1 pulmonary fibrosis collected under IRB-approved protocols.

overall_design: Microarray gene expression profiles in de-identified, clinically annotated samples from ficoll purified peripheral blood samples from patients with familial pulmonary fibrosis and HPS-1 pulmonary fibrosis collected under IRB-approved protocols.

first: F

first: B

middle: R

last: Gochuico


title: Transcriptomes analysis of marmoset liver progenitor cell line compared with adult marmoset liver

status: Public on Jan 01 2018

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

summary: We report the liver progenitor cell related gene expression of established marmoset liver progenitor cell line and provide the whole gene expression transcriptomes of marmoset liver.

overall_design: mRNA profiles of marmoset fetal liver-derived hepatic progenitor cell line at passage 10-30 and adult marmoset liver tissue were generated by sequencing.

first: Zhenglong

last: Guo


title: Downregulation of eca-mir-128 in seminal exosomes and enhanced expression of CXCL16 in the stallion reproductive tract are associated with equine arteritis virus long-term persistent infection

status: Public on Feb 12 2018

city: Louisville

first: Theodore

middle: Samuel

last: Kalbfleisch

state: KY

address: 221F Baxter II, 580 S Preston St

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: We have characterized miRNAs associated with equine seminal exosomes, and identified seminal exosomes eca-mir-128 to be specifically downregulated during equine arteritis virus long-term persistent infection in the reproductive tract of the stallion

overall_design: We have perfomed small RNAseq on 8 equine seminal exosome samples, including samples from naïve stallions (n=3), and experimentally infected with equine arteritis virus at two different time points (86 days [n=3] and 726 [n=2] days post infection). Findings were further confirmed by RT-qPCR and other experiments were performed to characterize the associateion between eca-mir-128 and the chemokine CXCL16.

first: Mariano

last: Carossino

first: Pouya

last: Dini

middle: S

first: Alan

middle: T

last: Loynachan

first: Igor

middle: F

last: Canisso

first: Kathleen

middle: M

last: Shuck

first: Peter

middle: J

last: Timoney

first: R

last: Cook

first: Ernest

last: Bailey

first: Udeni

last: Balasuriya


title: Downregulation of DDX5/DDX17 and REST

status: Public on Dec 31 2017

city: Lyon

first: jean-baptiste

last: claude

address: 46, allée d’Italie

country: France

institute: [CNRS/ENS Lyon/UCBL/HCL] Laboratoire de Biologie Moléculaire de la Cellule UMR5239

summary: We aimed at analysing the effect of RNA helicases DDX5 and DDX17 and of the transcription factor REST on gene expression in the human SH-SY5Y neuroblastoma cell line (European Collection of Cell Cultures, ECACC), which was cultured as recommended by the supplier.

overall_design: siRNA control (2 replicates) + siRNA DDX5/DDX17 (2 replicates) + siRNA REST (2 replicates) + siRNA REST/DDX5/DDX17 (2 replicates)

first: Marie-Pierre

last: Lambert

first: Clara

last: Benoit-Pilven

first: Didier

last: Auboeuf

first: Cyril

last: Bourgeois


title: Variation in activity state, axonal projection, and position define the transcriptional identity of individual neocortical projection neurons.

city: Baltimore

first: Loyal

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

summary: Single-cell RNA sequencing has generated the first catalogs of transcriptionally defined neuronal subtypes of the brain. However, the cellular processes that contribute to neuronal subtype specification and transcriptional heterogeneity remain unclear. By comparing the gene expression profiles of a subset of single layer 6 corticothalamic neurons in somatosensory cortex, we show that transcriptional subtypes primarily reflect axonal projection pattern, laminar position within the cortex, and neuronal activity state. Pseudotemporal ordering of 1023 cellular responses to sensory manipulation demonstrates that changes in expression of activity-induced genes both reinforced cell-type identity and contributed to increased transcriptional heterogeneity within each cell type. This is due to cell-type biased choices of transcriptional states following manipulation of neuronal activity. These results reveal that axonal projection pattern, laminar position, and activity state define significant axes of variation that contribute both to the transcriptional identity of individual neurons and to the transcriptional heterogeneity within each neuronal subtype.

overall_design: 1023 single cell RNA-Seq and 6 bulk RNA-seq

first: Maxime

last: Chevée

first: Johanna

middle: D

last: Robertson

first: Gabrielle

middle: H

last: Cannon

first: Solange

middle: P

last: Brown


title: Integrated analysis of mRNA and viral miRNA expression profiles in the kidney of Carassius auratus gibelio response to cyprinid herpesvirus 2

city: Shanghai

first: jianfei

last: lu

address: No.999, Huchenghuan Rd

department: Freshwater Fishery Germplasm Resources

institute: Shanghai Ocean University

summary: MiRNAs are small non-coding single stranded RNAs that play crucial roles in numerous biological processes. Vertebrate herpesviruses encode multiple viral miRNAs that modulate host and viral genes. However, the roles of viral miRNAs in invertebrates have not been fully determined. Here, we used high-throughput sequencing to analyse miRNA and mRNA expression proﬁles of Carassius auratus gibelio in response to infection by cyprinid herpesvirus 2 (CyHV-2). RNA sequencing obtained 26,664 assembled transcripts, including 2,978 differentially expressed genes, among which 12 were validated by qRT-PCR. Based on small RNA (sRNA) sequencing and secondary structure predictions, we identified 17 CyHV-2 encoded miRNAs. Target prediction for the viral miRNAs identiﬁed >1,109 host and virus gene target pairs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of the viral miRNAs revealed diverse affected immune signalling pathways, including the RIG-I-like receptor, the Toll-like receptor and the JAK-STAT signalling pathways. Finally, we presented a functional analysis of CyHV-2-encoded ORF60 and host gene TLR5, both of which are targeted by CyHV-2 miRNA miR-C1.

overall_design: Collectively, The present study is the first to provide a comprehensive overview of viral miRNA-mRNA co-regulation, which might have a key role in controlling post-transcriptomic regulation during CyHV-2 infection.

first: Jianfei

last: Lu

first: Dan

last: Xu

first: Youshen

last: Jiang

first: Zhaoyuan

last: Shen

first: Siyao

last: Xia

first: Sanyun

last: Kong

first: Liqun


title: RNA sequencing of hPSC-derived cardiac progenitors and endocardium

status: Public on Dec 27 2017

city: New York

first: Daylon

last: James

state: NY

address: 515 East 71st Street

institute: Weill Cornell Medicine

summary: We utilized a dual reporting hPSC line that identified cells expressing NKX2.5 and endothelal cells to characterize discrete milestones during cardiac and vascular differentiaiton. Comparing populations that express either or both reporters to human umbilical vein endothelial cells, we document a unique molecular phenotype in hPSC-derived endocardium that points toward an important role for Wnt signaling during vascular specification of cardiac progenitors.

overall_design: Sequencing mRNA from biological triplicate samples of: 1) hPSC derivatives expressing NKX2.5 alone; 2) hPSC derivatives expressing NKX2.5 and endothelial markers; and 3) hPSC derivatives expressing only endothelial markers.


title: Multiple sclerosis and EAE

status: Public on Dec 23 2017

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Reprogrammed neurons from adult dermal fibroblasts of patients with Huntington's disease

status: Public on Dec 11 2017

city: Saint Louis

first: Bo

last: Zhang

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

overall_design: De-identified human adult dermal fibroblasts from patients with Huntington's disease or age- and gender-matched healthy controls were obtained from the Coriell Institute for Medical Research Biorepository. These fibroblast samples were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124 and striatal-enriched transcription factors BCL11B (Also known as CTIP2), DLX1, DLX2, and MYT1L to directly convert fibroblasts into striatal neurons as previously established (Victor et al., Neuron 2014; Richner et al., Nat. Prot. 2015). Total mRNA from reprogrammed neurons and non-converted fibroblasts was collected and prepared for RNA-seq analysis 32 days after viral transduction.

first: Matheus

last: Victor

first: Andrew

last: Yoo


title: RNA sequencing data of whole blood cells of normal glucose tolerant (NGT) and gestational diabetes (GDM) pregnant women

city: Neuherberg

first: Steffen

last: Sass

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

summary: Total RNA was isolated from WBCs. For the analysis of genome-wide expression differences in small non-coding RNAs (sncRNAs) and long-coding and non-coding RNAs (mRNAs and lncRNAs), NGT and GDM pregnant women were selected. Twenty-nine GDM-associated mature micro-RNAs (miRNAs) with increased expression and one hundred sixty-three mRNAs with reduced expression associated with GDM were found (P<0.05 and FDR<0.1).

overall_design: Eight NGT and eight GDM women were matched based on body-mass-index and age. Paired data was adjusted for mid-pregnancy weight gain and pregnancy week.

first: Laura

last: Stirm

first: Peter

last: Huypens


title: Astrocyte-specific and region-specific transcriptomes in control and EAE mice: optic nerve

summary: Changes in gene expression that occur across the entire central nervous system (CNS) during disease do not take into account variability from one CNS region to another and can be confounded by alterations in cellular composition during disease. Multiple sclerosis (MS) is characterized by cell proliferation, migration and damage in various cell types in different CNS regions and causes disabilities related to distinct neurological pathways, such as walking, vision and cognition. Here, a cell-specific and region-specific transcriptomic approach was used to determine changes in gene expression in astrocytes derived from spinal cord, cerebellum, cerebral cortex, and hippocampus in the preclinical MS model, chronic experimental autoimmune encephalomyelitis (EAE). RNA sequencing and bioinformatics analysis showed that changes in gene expression pathways in astrocytes differed between neuroanatomic regions. Further, while astrocytes from spinal cord showed increased expression of immune pathway genes during EAE, cholesterol biosynthesis pathway genes were decreased. Translating these findings from the preclinical model to humans, optic nerve from EAE and optic chiasm from MS each showed a significant decrease in cholesterol biosynthesis pathways. Finally, a treatment targeting cholesterol homeostasis in astrocytes was protective in EAE, suggesting a novel neuroprotective strategy for MS. Using a cell-specific and region-specific gene expression approach can provide therapeutically relevant insights into mechanisms underlying specific disabilities in complex multifocal neurological diseases.

overall_design: The mice expressing HA-tagged ribosomal protein RPL22 in astrocytes were generated by crossing RiboTag mice with GFAP-Cre mice, and EAE was induced at age 8-12 week mice were injected with myelin oligodendrocyte glycoprotein (MOG) amino acids 35–55. Astrocyte specific RNA was isolated as the co-immunoprecipitation with anti-HA antibody from EAE (n=5) and age/gender matched control (n=4) mice.

first: Noriko

first: Alessia

last: Tassoni

first: Emily

last: Ren

first: Max

last: Kaito

first: Ai

last: Ohno

first: Yan

last: Ao

first: Hadley

last: Johnsonbaugh

first: Josh

last: Burda

first: Michael

middle: V

last: Sofroniew

first: Rhonda

last: Voskuhl


title: RNA-seq analysis of Jak1 KO and wt LT-HSCs

first: Christopher

middle: E

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

summary: Previous studies have illustrated the importance of Jak1-mediated cytokine signaling in immunological and neoplastic diseases such that JAK1 inhibition is currently being investigated in clinical trials. However, the role of Jak1 in hematopoietic stem cell (HSC) function has not been delineated. Here we show that conditional Jak1 loss in hematopoietic cells reduces HSCs and markedly alters lymphoid/myeloid differentiation in vivo. Jak1-deficient stem cells exhibit decreased competitiveness in vivo, and are unable to rescue hematopoiesis in the setting of myelosuppression. Jak1-deficient HSCs show increased quiescence, an inability to enter the cell cycle in response to hematopoietic stress, and do not respond to type I interferons demonstrating Jak1 as a central node for interferon signaling in HSCs. Moreover, the HSC defect induced by Jak1 loss is not fully rescued by expression of a constitutively active Jak2 allele. Our data highlights an essential role for Jak1 in HSC homeostasis and stress response.

overall_design: 6 samples per group; group 1: wt, group 2: KO

first: Maria

last: Kleppe

first: Matthew

last: Spitzer

first: Sheng

last: Li

first: Lauren

last: Dong

first: Efthymia

last: Papalexi

first: Corinne

last: Hill

first: Sofie

last: De Groote

last: Keller

first: Priya

last: Koppikar

first: Franck

last: Rapaport

first: Jorge

last: Gandara

first: Garry

last: Nolan

first: Ross

last: Levine


title: HDAC inhibitor SAHA reverses inflammatory gene expression in diabetic endothelial cells

status: Public on Dec 06 2017

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

summary: While histone deacetylase (HDAC) inhibitors are thought to regulate gene expression by post-translational modification of histone as well as non-histone proteins. While histone hyperacetylation has long been considered the paradigmatic mechanism of action, recent genome-wide profiles indicate more complex interactions with the epigenome. In particular, HDAC inhibitors also induce histone deacetylation at the promoters of highly active genes, resulting in gene suppression. This was linked to the loss of histone acetyltransferase (HAT) binding. To illustrate pre-clinical utility of the HDAC inhibitor SAHA as a therapeutic, we show reversal of diabetes-associated EP300 target genes in diabetic HAECs of primary origin. These results were confirmed using SAHA, C646 (EP300/CREBBP inhibitor) or EP300 siRNA. These findings suggest the inhibition of gene expression by SAHA is mediated by EP300 function and provide a rationale for clinical trials of safety and efficacy in patients with diabetes.

overall_design: Human aortic endothelial cells from a diabetic and non-diabetic individual were stimulated with DMSO (control), SAHA (2 μM, HDAC inhibitor) or C646 (10 μM, EP300 inhibitor) for 12 hours, or EP300 siRNA or non-target siRNA (control) for 4 hours, followed by 48 hours in fresh media. Study performed in triplicate.

first: Haloom

last: Rafehi

first: Antony

last: Kaspi

first: Mark

last: Zeimann

first: Jun

last: Okabe

first: Tom

middle: C

last: Karagiannis


title: Single Cell RNA Sequencing Analysis of Mouse E14.5 Fetal Liver Runx1 P2-hCD4 plus and minus MEPs and CMPs

status: Public on Dec 05 2017

city: manchester

first: Muhammmad

middle: Zaki

last: Fadlullah Wilmot

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary: In recent years, highly detailed characterization of adult bone marrow (BM) myeloid progenitors has been achieved and, as a result, the impact of somatic defects on different hematopoietic lineage fate decisions can be precisely determined.  Fetal liver (FL) hematopoietic progenitor cells (HPCs) are poorly characterized in comparison, potentially hindering the study of the impact of genetic alterations on midgestation hematopoiesis.  Numerous disorders, for example infant acute leukaemias, have in utero origins and their study would therefore benefit from the ability to isolate highly purified progenitor subsets.  We previously demonstrated that a Runx1 distal promoter (P1)-GFP::proximal promoter (P2)-hCD4 dual-reporter mouse (Mus musculus) model can be used to identify adult BM progenitor subsets with distinct lineage preferences.  In this study, we undertook the characterization of the expression of Runx1-P1-GFP and P2-hCD4 in FL.  Expression of P2-hCD4 in the FL immunophenotypic Megakaryocyte-Erythroid Progenitor (MEP) and Common Myeloid Progenitor (CMP) compartments corresponded to increased granulocytic/monocytic/megakaryocytic and decreased erythroid specification.  Moreover, Runx1-P2-hCD4 expression correlated with several endogenous cell surface markers’ expression, including CD31 and CD45, providing a new strategy for prospective identification of highly purified fetal myeloid progenitors in transgenic mouse models.  We utilized this methodology to compare the impact of the deletion of either total RUNX1 or RUNX1C alone and to determine the fetal HPCs lineages most substantially affected.  This new prospective identification of FL progenitors therefore raises the prospect of identifying the underlying gene networks responsible with greater precision than previously possible.

overall_design: mRNA profiles of single sorted Runx1 P2-hCD4+ Megakaryocyte Erythroid Progenitors (MEPs), Runx1 P2-hCD4- MEPs, Runx1 P2-hCD4+ Common Myeloid Progenitors (CMPs) and Runx1 P2-hCD4- CMPs from Mouse E14.5 Runx1 P2-GFP::P2-hCD4/+ Fetal Liver Samples

first: Julia

last: Draper

first: Muhammad

middle: Z

last: Fadlullah

first: Gillian

last: Newton

first: Wolfgang

last: Breitwieser

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud


title: Comparison of  fibroblast with WT PPAR-gamma vs. S273 A knock inComparison of  fibroblast with WT PPAR-gamma vs. S273 A knock in

city: Boston

first: Melin

middle: J.

last: Khandekar

state: MA

address: 100 Blossom St. Cox 3

institute: Massachusetts General Hospital

summary: We prepared RNA and used microarrays to compare the differences in gene expression based on genetic lack of phosphorylated PPAR-gamma

overall_design: 3 samples of each genotype, treated with carboplatin or saline

first: Bruce

last: Spiegelman


title: The Gene Expression Study (GEP) was based on a cohort of 27 MCL cases enrolled in the Fondazione Italiana Linfomi (FIL)-MCL-0208 randomized Italian clinical trial.

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: D-RT

country: Italy

institute: CRO Aviano

summary: The aggressive clinical behavior of mantle cell lymphoma (MCL) is attributed to specific genetic and molecular mechanisms involved in its pathogenesis, mainly the t(11;14)(q13;q32) traslocation and cyclin D1 (CCND1) overexpression. Nevertheless, evidence of a certain degree of clinical/biological heterogeneity has been disclosed by gene expression profile (GEP) and (immuno)genetic/immunohistochemistry studies. AIM: To use a GEP approach to identify MCL subsets with peculiar clinical/biological features in the context of of MCL patients treated homogeneously with an autologous transplantation-based program.

overall_design: GEP experiments were performed in 27 cases, with Agilent platform. Bioinformatics analyses were performed by Gene Springs

first: Tiziana

last: D'Agaro

first: Valter

last: Gattei


title: Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice.

status: Public on Dec 01 2017

first: Thomas

middle: W

last: Battaglia

address: 423 E 23rd Street

department: Medicine

institute: NYU School of Medicine

summary: Antibiotics have long-lasting consequences on the gut microbiota with the potential to impact host physiology and health. However, little is known about the transgenerational impact of an antibiotic-perturbed microbiota. Here we demonstrated that adult pregnant female mice inoculated with a gut microbial community shaped by antibiotic exposure passed on their dysbiotic microbiota to their offspring. This dysbiotic microbiota remained distinct from controls for at least 5 months in the offspring without any continued exposure to antibiotics. By using IL-10 deficient mice, which are genetically susceptible to colitis, we showed mice that received an antibiotic-perturbed gut microbiota from their mothers had increased risk of colitis. Taken together, our findings indicate that the consequences of antibiotic exposure affecting the gut microbiota can extend to a second generation.

overall_design: C57BL/6 or IL10 deficient pups were born to mothers who were exposed to Control or STAT-perturbed cecal contents. (N = 3/group)

first: Anjelique

last: Schulfer

first: Yelina

last: Alvarez

first: Victoria

last: Ruiz

first: Melody

last: Ho

first: Serina

last: Robinson

first: Tonya

last: Ward

first: Laura

last: Cox

first: Arlin

middle: B

last: Rogers

first: Dan

last: Knights

first: Balfour

last: Sartor

first: Martin

last: Blaser


title: ChIP-seq for Foxg1 in E14-15 cortex

status: Public on Dec 04 2017

city: Santa Cruz

first: Bin

last: Chen

state: CA

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

summary: The goal of the study was to identify the binding site of Foxg1 in wild-type cortex by performing ChIP-seq using a Foxg1 antibody. E14-15 cortical tissues were dissected, lysed and fixed. Chromatin was prepared by sonication. Sequences bound by Foxg1 protein was precipitated using a Foxg1 antibody. Sequencing was performed on Illumina Genome Analyzer II. Foxg1 binding peaks were called using MACS.

overall_design: ChIP for Foxg1, followed by sequencing on Illumina Genome Analyzer II platform

first: Sol

last: Katzman


title: ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2

status: Public on Dec 19 2017

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

summary: Mechanisms regulating mammalian meiotic progression are poorly understood. Here we identify mouse YTHDC2 as a critical component. A screen yielded a sterile mutant, “ketu”, caused by a Ythdc2 missense mutation. Mutant germ cells enter meiosis but proceed prematurely to aberrant metaphase and apoptosis, and display defects in transitioning from spermatogonial to meiotic gene expression programs. ketu phenocopies mutants lacking MEIOC, a YTHDC2 partner. Consistent with roles in post-transcriptional regulation, YTHDC2 is cytoplasmic, has 3’ to 5’ RNA helicase activity in vitro, and has similarity within its YTH domain to an N6-methyladenosine recognition pocket. Orthologs are present throughout metazoans, but are diverged in nematodes and, more dramatically, Drosophilidae, where Bgcn is descended from a Ythdc2 gene duplication. We also uncover similarity between MEIOC and Bam, a Bgcn partner unique to schizophoran flies. We propose that regulation of gene expression by YTHDC2-MEIOC is an evolutionarily ancient strategy for controlling the germline transition into meiosis.

overall_design: RNA-seq was performed on whole-testis RNA samples after polyA capture from three pairs of Ythdc2em1 mutant and wild-type littermates aged 8 dpp, three pairs of mutant and wild-type or heterozygous littermates aged 9 dpp and two pairs of mutant and heterozygous littermates aged 10 dpp. The six 8 and 9 dpp-old mutant and wild-type or heterozygous pairs were from six independent litters. The two 10 dpp-old mutant and heterozygous pairs were from a seventh litter. Animals were derived from crosses between heterozygote carriers, after five or six backcrosses of the Ythdc2em1 founder to B6 mice.

first: Devanshi

last: Jain

first: Rhyan

last: Puno

first: Nathalie

last: Lailler

first: Christopher

last: Mason

last: Lima

first: Kathryn

last: Anderson

first: Scott

last: Keeney


title: Analysis of gene expression in glomeruli of BTBR ob/ob diabetic mice

status: Public on Dec 10 2017

city: Regensburg

first: Dominik

last: Chittka

address: Franz-Josef-Strauss-Allee 11

department: Nephrology

institute: University hospital Regensburg

summary: Although diabetic nephropathy (DN) is the most common cause for end-stage renal disease (ESRD) in western societies, its pathogenesis still remains largely unclear. A different gene pattern of diabetic and healthy kidney cells is one of the probable explanations. Numerous signaling pathways have emerged as important pathophysiological mechanisms for diabetes-induced renal injury. Glomerular cells, as podocytes or mesangial cells, are predominantly involved in the development of diabetic renal lesions. While a lot of gene assays concerning DN are performed with whole kidney or renal cortex tissue, we isolated glomeruli from BTBR ob/ob and wildtype mice at 4 different timepoints (4, 8, 16, 24 weeks) and performed a mRNA microarray to identify differentially expressed genes (DEGs). In contrast to many other diabetic mouse models, these homozygous ob/ob leptin-deficient mice do not only develop a severe type II diabetes, but also diabetic kidney injury with all the clinical and especially histologic features defining human DN. The identified DEGs in diabetic glomeruli were used to investigate biological processes and pathways enriched at different disease stages.

overall_design: Glomeruli were isolated from 4, 8, 16, and 24 weeks old female BTBR wildtype (WT) and BTBR ob/ob (ob) mice. We used 3 animals of each group (WT and ob/ob) at 4 weeks and 4 animals of each group (WT and ob/ob) at 8, 16, and 24 weeks. After cervical dislocation kidneys were explanted and passed through a series of stainless steel sieves (150 µm, 100 µm, 70 µm, 50 µm) to isolate glomeruli. After confirmation of the purity of glomeruli, RNA was extracted  for hybridization on Affymetrix microarray.  Subsequent RNA extraction was conducted using the RNeasy Mini Kit

first: Miriam

last: Banas

first: Simone

last: Reichelt-Wurm

first: Bernhard


title: Evaluation of immunological factors involved in initiation of chronic brucellosis in CD4+ T cells using miRNA array

status: Public on Dec 21 2017

city: Bursa

first: Ferah

last: Budak

address: Gorukle

department: Medical Faculty

country: Turkey

institute: Uludag University

summary: Brucellosis is a serious infectious disease and continues to be an important cause of morbidity. It can be seen almost anywhere in the world and at any age. Acute phase heals or becomes chronic form. Infection of 10-30% of patients becomes chronic, despite early diagnosis and treatment.  Although our knowledge about Brucella virulence factors and the host response increase rapidly, how they can hidden from the immune system and cause chronic disease are still unknown. We aimed to investigate the immunological factors which belong to CD4+ T cells and their roles in the transition of brucellosis from acute to chronic infection. Using miRNA microarray, more than 2000 miRNAs were screened in CD4 + T cells of patients with acute or chronic brucellosis and healthy controls that were sorted from peripheral blood with flow cytometry and validated by RT-qPCR.  Findings were evaluated using GeneSpring GX (Agilent) 13.0 software and KEGG pathway analysis. In comparison to acute cases, expression levels of 28 miRNAs were significantly altered in chronic cases. All of miRNAs were up-regulated in chronic cases in comparison with the control group. Apart from a miRNA (miR-4649-3p), 27 miRNAs were not expressed in the acute cases (p <0.05, fold change> 2).  These miRNAs have the potential to be markers for chronic cases. The differential expressed miRNAs and their predicted target genes that involved in previously MAPK signaling pathway, regulation of actin cytoskeleton, endocytosis, and protein processing in endoplasmic reticulum indicating their potential roles in chronic brucellosis and its progression. It is the first study of miRNA expression analyzes of human CD4+ T cells to clarify the mechanism of inveteracy in brucellosis.

overall_design: Using miRNA microarray, more than 2000 miRNAs were screened in CD4 + T cells of patients with acute or chronic brucellosis and healthy controls that were sorted from peripheral blood with flow cytometry and validated through qRT-PCR.  Findings were evaluated using GeneSpring GX (Agilent) 13.0 software and KEGG pathway analysis.

first: Budak

last: Ferah

first: Bal

last: Haldun

first: Tezcan

last: Gulcin

first: Akalin

last: Halis

first: Yilmaz

last: Abdullah

first: Hiz

last: Pinar

first: Oral

last: Barbaros


title: Long noncoding RNA ROCR contributes to SOX9 expression and chondrogenic differentiation of human mesenchymal stem cells

status: Public on Nov 28 2017

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

institute: Newcastle University

summary: Long non-coding RNAs (lncRNAs) are expressed in a highly tissue-specific manner where they function in various aspects of cell biology, often as key regulators of gene expression. In this study we established a role for lncRNAs in chondrocyte differentiation. Using RNA sequencing we identified a human articular chondrocyte repertoire of lncRNAs from normal hip cartilage donated by neck of femur fracture patients. Of particular interest are lncRNAs upstream of the master chondrocyte transcription factor SOX9 locus. SOX9 is an HMG-box transcription factor which is essential for chondrocyte development by directing the expression of chondrocyte specific genes. Two of these lncRNAs are upregulated during chondrogenic differentiation of MSCs. Depletion of one of these lncRNA, LOC102723505, which we termed ROCR (regulator of chondrogenesis RNA), by RNAi disrupted MSC chondrogenesis, concomitant with reduced cartilage-specific gene expression and incomplete matrix component production, indicating an important role in chondrocyte biology. Specifically, SOX9 induction was significantly ablated in the absence of ROCR, and overexpression of SOX9 rescued the differentiation of MSCs into chondrocytes. Our work sheds further light on chondrocyte specific SOX9 expression and highlights a novel method of chondrocyte gene regulation involving a lncRNA.

overall_design: Human neck of femure fracture hip cartilage chondrocyte mRNA profile generated by RNA-seq

first: Matt

last: Barter

first: David

middle: A

last: Young


title: Small RNA deep sequencing using Illumina HiSeq2500

status: Public on Nov 29 2017

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: 33 miRNAs significantly decreased and 75 miRNAs significantly increased in BCR-ABL+ LSK compared with BCR-ABL- LSK cells, suggesting distinct BCR-ABL-dependent mechanisms of microRNA regulation.

overall_design: LSK cells from non-induced and induced chronic myeloid leukemia (CML) mice were sorted and total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Valencia, CA). Small RNA sequencing was performed using Illumina HiSeq2500 at the COH Integrative Genomics Core following the manufacturer's sample preparation protocol (TruSeq Small RNA Sample Prep kit, Illumina, Inc.) with some modifications.

first: Bin

last: Zhang

first: Dandan

last: Zhao


title: Gene array analysis of primary mouse calvaria osteoblasts without differentiation, with differentiation, or with differentiation plus cabozantinib (XL184)

status: Public on Nov 20 2017

city: Houston

first: Li-yuan

last: Yu-Lee

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We performed a gene array analysis using RNAs prepared from undifferentiated, differentiated, or differentiated + cabozantinib (XL184) treated osteoblasts.

overall_design: Calvarial mouse osteoblasts were prepared from 2-5 day old newborn mice. Osteoblasts were cultured in MEM+10% FBS until confluence (undifferentiated osteoblasts, samples C1 and C2).  Confluent osteoblasts were cultured in differentiation medium for 30 days (differentiated osteoblasts, samples D1 and D2). Confluent osteoblasts were cultured in differentiation medium plus cabozantinib (XL184) for 30 days (sample X1 and X2).

first: Sue-Hwa

last: Lin

first: Li-Yuan


title: Expression analysis of control and Ccp6-depleted D3 ESCs

status: Public on Nov 14 2017

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

summary: Investigation of differentially expressed genes in  Ccp6-depleted D3 ESCs

overall_design: Gene expression profiling using D3 ESCs. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray were performed in accordance with the Affymetrix Mouse Gene2.0 analysis protocol (Affymetrix).

first: Buqing

last: Ye

first: Zusen

last: Fan


title: HydroxyMeDIPseq day 3 differentiated mouse ESCs

city: London

first: Alison

last: Brewer

address: JBC, 125 Coldharbour Lane

department: Cardiology

institute: King's College London

type: Methylation profiling by high throughput sequencing

summary: Graded levels of molecular oxygen (O2) exist within developing mammalian embryos and can differentially regulate cellular specification pathways. During differentiation, cells acquire distinct epigenetic landscapes, which determine their function, however the mechanisms which regulate this are poorly understood. The demethylation of 5-methylcytosine (5mC ) is achieved via successive oxidation reactions catalysed by the Ten-Eleven-Translocation (Tet) enzymes, yielding the 5-hydroxymethylcytosine (5hmC ) intermediate. These require O2 as a co-factor, and hence may link epigenetic processes directly to O2 gradients during development. We demonstrate that the activities of Tet enzymes are differentially dependent upon [O2], and that Tet1 activity, specifically, is inhibited by low levels of O2 which are physiologically relevant in embryogenesis. Further, embryonic stem cells, induced to differentiate, displayed a transient burst of 5hmC, which was both dependent upon Tet1 and inhibited by low (1%) [O2]. A GC-rich promoter region within the Tet3 locus was identified as a significant target of this 5mC-hydroxylation. Further, this region was shown to associate with Tet1, and display the histone epigenetic marks, H3K4me3 and H3K27me3, which are characteristic of a bivalent, developmentally “poised” promoter. We conclude that Tet1 activity, determined by [O2] may play a critical role in regulating cellular differentiation and fate in embryogenesis

overall_design: 2 samples (which were pooled biological triplicates), DNA input and 5hmC enrichment were sequenced on an Illumina MiSeq, single read for 50 cycles

first: Simon

last: Burr


title: Differentially expressed genes after miRNA or siRNA transfection in multiple human cancer cell lines

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (microRNAs or siRNAs) in human cancer, several cell lines ( pancreatic cancer, renal cell carcinoma, oral squamous cell carcinoma, prostate cancer and bladder cancer) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (PANC-1, 786-O, A498, SAS, PC3 and T24) were treated with miRNAs (miR-455-3p, miR-455-5p, miR-451a, miR-144-3p, miR-144-5p, miR-135-5p, miR-135-3p, miR-30a-5p, miR-30a-3p, miR-184, miR-199-3p, miR-107, miR-185-5p, miR-320b and miR-320c), siRNAs (si-PHLDA2).

first: Takayuki

last: Arai


title: Genome-wide analysis of gene expression by IFNβ in Transformed HMEC (Epithelial/non-CSC, Mesenchymal/CSC)

status: Public on Nov 12 2017

city: Cleveland

first: Mary

middle: Rose

last: Doherty

state: Ohio

address: 2103 Cornell Road

department: Pathology

institute: CWRU

summary:
Triple Negative Breast Cancer (TNBC), the deadliest form of this disease, lacks a targeted therapy. TNBC tumors that fail to respond to chemotherapy are characterized by a repressed Interferon/Signal Transducer and Activator of Transcription (IFN/STAT) gene signature and are often enriched for Cancer Stem Cells (CSCs).
We have found that human mammary epithelial cells that undergo an Epithelial-to-Mesenchymal Transition (EMT) following transformation acquire CSC properties. These mesenchymal/CSCs have a significantly repressed IFN/STAT gene expression signature and an enhanced ability to migrate and form tumor spheres.
Treatment with Interferon-Beta (IFNb) led to a less aggressive epithelial/non-CSC-like state, with repressed expression of mesenchymal proteins (VIMENTIN, SLUG), reduced migration and tumor sphere formation, and re-expression of CD24 (a surface marker for non-CSCs), concomitant with an epithelial-like morphology.
The CSC-like properties were correlated with high levels of unphosphorylated Interferon Stimulated Gene Factor 3 (U-ISGF3), which was previously linked to resistance to DNA damage. Inhibiting the expression of IRF9 (the DNA-binding component of U-ISGF3) reduced the migration of mesenchymal/CSCs.
Here we report a positive translational role for IFNb as gene expression profiling of patient derived TNBC tumors demonstrates that an IFNb Metagene signature correlates with improved patient survival, an immune response linked with Tumor Infiltrating Lymphocytes (TILs) and a repressed CSC Metagene signature.
Taken together, our findings indicate that repressed IFN signaling in TNBCs with CSC-like properties is due to high levels of U-ISGF3, and that treatment with IFNb reduces CSC properties, suggesting a novel therapeutic strategy to treat drug-resistant, highly aggressive TNBC tumors.

overall_design: Total RNA was obtained from Transformed HMEC (Ep/non-CSC, MES/CSC) treated with IFNβ for 4h or 96hr or untreated for 0h or 96h

middle: R


title: β-D-N(4)-hydroxycytidine is a potent anti-alphavirus compound that induces high level of mutations in viral genome

status: Public on Nov 13 2017

city: BIRMINGHAM

first: Elena

middle: I

last: Frolova

state: Alabama

address: 1720 2nd Ave South, BBRB373, Box 3

department: Microbiology

institute: University of Alabama at Birmingham

summary: The goal of this project was the analysis of virus variants resistant to β-D-N(4)-hydroxycytidine.

overall_design: Venezuelan equine encephalitis virus TC-83 was passaged on Vero cells for 20 passages in the presence or absence of β-D-N(4)-hydroxycytidine. Virus samples were collected at passages 0, 5 10, 15 and 20. Total virion RNAs were isolated and sequenced.

first: N

last: Urakova

first: V

last: Kuznetsova

first: D

middle: K

last: Crossman

first: A

last: Sokratian

last: Guthrie

last: Kolykhalov

first: M

last: Lockwood

middle: G

last: Natchus

last: Crowley

first: G

last: Painter

first: E

first: I

last: Frolov


title: Whole-transcriptome maps of HepG2 cells after exposure to cationic liposomes and controls

status: Public on Nov 09 2017

city: Shanghai

first: Li

last: Ying

address: Changhai Road No. 225

department: Department of Pharmacy

institute: Eastern Hepatobiliary Surgery Hospital

summary: Cationic liposomes (CLs) are non-viral vectors that play a major role in DNA transfer and gene therapy. The cellular toxicity of CLs has been validated in HepG2 cells. To address the basis of the CLs toxicity, we performed RNA-seq analysis on untreated HepG2 cells and HepG2 cells following exposure to IC50 concentration (120μM) CLs for 24h.

overall_design: Examination of gene expression level in CLs treated HepG2 cells and untreated cells

first: Ying

last: Li

first: Qingshan

last: Chen

first: Hai

last: Zhang

first: Jing

last: Yu

first: Duxin

last: Sun

first: Guoqing


title: Liver array following CMPF treatment

status: Public on Nov 08 2017

city: Toronto

first: Kacey

middle: June

last: Prentice

state: ON

address: 1 King's College Circle, MSB3352

department: Physiology

country: Canada

institute: University of Toronto

summary:
Examining the effect of CMPF treatment in the livers of mice. This study examines both the prevention and reversal of steatosis.
We used arrays to determine the pathways through which CMPF prevents and reverses steatosis

overall_design: In the prevention model, mice were treated for one week prior to being changed to a HFD for 4-5 weeks. The reversal model, mice were fed a HFD for 6 weeks followed by 2 weeks of CMPF treatment.

first: Michael

last: Wheeler


title: Comparison of gene expression between wild-type and SERT knockout ileal mucosa

city: Chicago

first: Christopher

middle: Robert

last: Manzella

state: IL

address: 820 S. Damen Ave.

institute: University of Illinois at Chicago

summary: The serotonin transporter (SERT, SLC6A4), belonging to Na+ and Cl- dependent transporters, functions to regulate the availability of serotonin (5-HT) in various tissues including brain, platelets, and intestine.  Alterations in 5-HT levels and/or SERT expression have been implicated in pathophysiological conditions including anxiety-like behavior, obesity, cardiovascular disorders and GI disorders such as IBD, IBS, and diarrhea. Accordingly, SERT deficiency in mice is pleiotropic with many different phenotypic traits. Transgenic mice with global deletion of SERT exhibit increased anxiety, abnormal GI motility, and obesity associated with hyperglycemia. Additionally, these mice are more susceptible to intestinal inflammation. The mechanism by which SERT deficiency underlies GI related disturbances and exacerbates the severity of gut inflammation is not known. Thus, we evaluated the ileal mRNA expression to identify potential intestinal targets that contribute to disease pathogenesis when the SERT gene is non-functional. For these studies, RNA was extracted from ileum mucosa from age matched (9-10 wk) control and SERT KO mice by Trizol and was subjected to Mouse mRNA and OneArray Profiling. Our microarray data revealed 492 significantly upregulated and 293 downregulated genes in SERT KO ileum. Pathway analysis revealed significant enrichment in cell cycle, signaling, chemotaxis, and epithelial transporters. Genes of interest were validated by RT-PCR, which included CYP1A1 (~20 fold decrease, p < 0.05), CLDN8 (~30% decrease, p < 0.05), and HMGCS2 (~7 fold increase, p < 0.05). Similar changes were found in colon. A remarkable decrease in expression of Cyp1a1, which encodes a cytochrome P450 enzyme, provides a novel role of serotonergic pathways in drug and xenobiotic detoxification.  CLDN8 encodes for claudin 8, which is downregulated in patients with Crohn’s disease. Deficiency of HMGCS2, the mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase, is linked to hypoglycemia.   Our data provides novel clues for differential expression of genes affected by 5-HT and/or SERT deficiency in the intestine.

overall_design: Total RNA from the ileal mucosa of 6 WT and 6 SERT KO mice was pooled pair-wise to create 3 samples from WT and 3 samples from SERT KO mice. Two technical replicates were performed for each sample for 12 total arrays.

first: Megha

last: Singhal

first: Seema

last: Saksena

first: Waddah

last: Alrefai

first: Pradeep

last: Dudeja

first: Ravinder

last: Gill


title: BMAL1-deficiency contributes to mandibular dysplasia by upregulating MMP3

status: Public on Nov 07 2017

city: Wuhan

first: Lili

state: Hubei

address: 1277 Jiefang Avenue

institute: Union Hospital, Tongji Medical College Huazhong University of Science and Technology

summary: Skeletal mandibular hypoplasia (SMH), one of the common types of craniofacial deformities, seriously affects appearance, chewing, pronunciation, and breathing. Moreover, SMH is prone to inducing obstructive sleep apnea syndrome. We found that brain and muscle ARNT-like 1 (BMAL1), the core component of the molecular circadian oscillator, was significantly decreased in mandibles of juvenile SMH patients. Accordingly, SMH was observed in circadian rhythm-disrupted or BMAL1-deficiency mice. RNA sequencing and protein chip analyses suggested that matrix metallopeptidase 3 (MMP3) is the potential target of BMAL1 during the mandibular developmental process. Interestingly, in juvenile SMH patients, we observed that MMP3 level was increased obviously. Consistently, MMP3 was upregulated during the whole growth period of 3 to 10 weeks in Bmal1-/- mice. Given these findings, we set to characterize the underlying mechanism and found that BMAL1-deficiency enhanced Mmp3 transcription through activating p65 phosphorylation. Together our results provide new insight into the mechanism by which BMAL1 is implicated in the pathogenesis of SMH

overall_design: To gain an independent assessment of the regulatory targets of BMAL1 in Bmal1-/- mBMSCs

first: Jiajia

last: Zhao


title: Epigenetic Effects of Maternal Obesity on Wharton's Jelly (WJ) Mesenchymal Stromal Cells (MSCs): Implications For Cellular Therapy. (expression study)

status: Public on Nov 21 2017

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary:
7 WJ-MSC lines from non-obese BMI <25 kg/m2 were compared with 7 WJ-MSC lines obese BMI >30 kg/m2.  No template was used as a negative control
Triplicates for each line were analyses for human whole-genome gene expression profile using HumanHT-12 v4.0 Expression BeadChip (Illumina).

overall_design: RNA (good quality with 8-10 RIN score) from the 14 samples (triplicates from 14 lines) were hybridised to the HumanHT-12 v4.0 Expression BeadChip (Illumina).

first: Dusko

last: ILIC

first: Heba

last: Badraiq


title: microRNA expression data from medial prefrontal cortex (mPFC) of Rat

status: Public on Oct 31 2017

first: Ming

address: Yixue Road 138

institute: Fudan University

summary:
We examined the influence of chronic morphine on microRNA expression profile in the mPFC using miRNA microarray technology.
We found that 97 miRNAs (59 upregulated and 38 downregulated) were altered more than 2-fold in the mPFC from chronic morphine-treated rats.

overall_design: In this dataset, we include the expression data obtained from rat mPFC using a miRNA microarray after chronic morphine treatment.

first: Hualan

last: Yang

first: Ping

last: Zheng


title: Epigenetic Effects of Maternal Obesity on Wharton's Jelly (WJ) Mesenchymal Stromal Cells (MSCs): Implications For Cellular Therapy.

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Analysis of microRNA expression profiles induced by Yiqifumai Powder Injection in rats with chronic heart failure

city: Hangzhou

first: YU

last: ZHAO

address: Yuhangtang Road 388#

institute: College of Pharmeceutical Sciences

summary: To investigate the mechanism of Yiqifumai Powder Injectionthe on treating chronic heart diseases. We have employed a microRNAs microarray to identify the pivotal miRNAs altered by Yiqifumai compared to chronic heart injury and control group samples. 7 miRNAs accord with a 4-fold change (or more) or 1/4 (or less) and reverse rate between 1 and 2 were picked out as the reversible miRNAs for their expression after Yiqifumai treatment reversed significantly compared to model group. Among them, miR-21-3p and miR-542-3p were reported to associate with cardiac hypertrophy and tumer poliferation,respectively and they were validated by RT-PCR, which showed the consistent results as the microarray ones.

overall_design: Yiqifumai Powder Injection regulated 7 differentially expressed miRNAs in treating chronic heart failure rats.

first: Yu

first: Yi

last: Wang


title: Expression profile of early and mid-secretory healthy human endometrium revealed by RNA-seq

city: Tartu

first: Viktorija

last: Kukushkina

address: Riia 23b

country: Estonia

institute: Estonian Genome Center, University of Tartu

summary: Inner uterine lining or endometrium is a unique constantly self-renewed adult tissue that is vital for embryo implantation. As the footrace for universal endometrial receptivity markers continues, RNA-seq remains the most powerful tool for transcriptomic marker discovery. In this study, we aimed to elucidate endometrial maturation mechanisms at transcriptomic level and identify novel robust biomarker candidates for endometrial receptivity.

overall_design: The differential gene expression profiles of early secretory and mid-secretory phase endometrial biopsies obtained from 20 healthy fertile women across one menstrual cycle were analysed using paired sample study design.

first: Marina

last: Suhorutshenko

first: Agne

last: Velthut-Meikas

first: Reedik

last: Mägi

first: Maire

last: Peters

first: Signe

last: Altmäe

first: Kaarel

last: Krjutškov

first: Juan

middle: F

last: Martinez-Blanch

first: Francisco

middle: M

last: Codoñer

first: Felipe

last: Vilella

first: Carlos

last: Simon

first: Andres

last: Salumets

first: Triin

last: Laisk-Podar


title: Obesity Weight Loss Study

status: Public on Oct 28 2017

city: New York

first: Yupu

last: Liang

address: 1230 York Avenue

institute: The Rockefeller University

summary: RNA Sequencing of human adipose tissue before and after diet-induced weight loss

first: Jose

middle: O

last: Aleman


title: Identification of differentially expressed lncRNAs and mRNAs in OLF

status: Public on Oct 27 2017

city: Tianjin

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

institute: Tianjin medical university

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

summary:
Ossification of the ligamentum flava (OLF) is a common spinal disorder among the elderly that causes myelopathy and radiculopathy. Although studies have identified several genes that correlated with OLF, the underlying regulation network is far from clear. To identify transcriptional regulators for OLF, we compared the lncRNAs and mRNAs expression of the ligamentum flava tissues from OLF patients and healthy volunteers through microarray analysis, which revealed a panel of lncRNAs and mRNAs that were specifically regulated in ligament tissues of human undergoing ossification.
To identify transcriptional regulators for OLF, we compared the lncRNAs and mRNAs expression of the ligamentum flava tissues from OLF patients and healthy volunteers through microarray analysis.

overall_design: The lncRNA and mRNA expression profile of 4 OLFs and 4 normal LF tissues were analyzed by microarray analysis.

first: Wei

last: Hong

first: Yuan

last: Xue

first: Yawei

last: Han

first: Liandong

last: Li


title: Expression data from podocytes cultured in vitro treated with thapsigargin +/- forskolin

status: Public on Oct 26 2017

city: Boston

first: Abbe

last: Clark

state: Massachusetts

address: 4 Blackfan Circle, HIM 534

institute: Harvard, Brigham and Women's Hospital

summary: The aim of the study was to gain mechanistic insights of the protective effect of forskolin on thapsigargin-induced podocyte death by assessing, analyzing and comparing the respective gene expression profiles.

overall_design: Gene expression profiles of vehicle (DMSO)-, thapsi-, and thapsi+fors-treated podocytes were analyzed. 3 replicates per condition. Vehicle (DMSO)-treated cells were served as control/reference samples.

first: Anna

last: Greka


title: Transcriptome analysis of T. reesei CBS999.97, backcrossed female fertile strains in QM6a genetic background and QM6a upon mating

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

summary: The aim of this study was to evaluate changes in the transcriptome in the mentioned strains during mating conditions

overall_design: Strains of this study were grown on 2% malt extract medium at 21 °C which facilitates mating, harvesting was done at the contact stage; 2 biological replicates were included

first: Doris

last: Tisch


title: Small RNA sequencing of Pyrobaculum species in exponential and stationary phases

city: Santa Cruz

first: Todd

middle: M.

last: Lowe

address: 1156 High Street

institute: University of California Santa Cruz

summary: A great diversity of small, non-coding RNA (ncRNA) molecules with roles in gene regulation and RNA processing have been intensely studied in eukaryotic and bacterial model organisms, yet our knowledge of possible parallel roles for small RNAs (sRNA) in archaea is limited. We employed RNA-seq to identify novel sRNA across multiple species of the hyperthermophilic genus Pyrobaculum, known for unusual RNA gene characteristics. By comparing transcriptional data collected in parallel among five species, we were able to identify conserved RNA genes fitting into known and novel families and found a large increase in the number of conserved C/D box sRNA genes over what had been previously recognized; many of these genes are encoded antisense to protein coding genes. We also used the genome of Pyrobaculum neutrophilum for comparative genomics. The conserved opposition to orthologous genes across the Pyrobaculum genus suggests similarities to other cis-antisense regulatory systems. We used the improved C/D box sRNA annotations to conduct a deep study of the evolution of archaeal C/D box sRNAs by organizing them into 110 families within the Pyrobaculum based on synteny and conservation of guide sequences. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data provided by this set of C/D box sRNAs enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.

sample_organism:
Pyrobaculum islandicum
Pyrobaculum aerophilum
Pyrobaculum oguniense
Pyrobaculum arsenaticum
Pyrobaculum calidifontis

overall_design:
Cultures were harvested at either stationary or exponential phase.  Total RNA was size selected to everything between 16-70nt.

Please note that the processed data files generated from both stationary and exponential culture samples together are linked to the correponding exponential sample records
For example, the pyrAer1.454best3.stranded.coverage.*.bw files are for both Pae_Exp_smallRNA and Pae_Stat_smallRNA samples and are available from the Pae_Exp_smallRNA records.

first: Lauren

last: Lui

first: David

middle: L

last: Bernick

first: Patrick

middle: P

last: Dennis

first: Andrew

middle: V

last: Uzilov

first: Andrea

last: Corredor

first: Julie

last: Murphy


title: Gene expression analysis of the inflorescence of knu-1 and crc-1 knu-1

status: Public on Sep 30 2017

city: Singapore

first: Yifeng

last: XU

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

summary:
Analyis gene expression in crc-1 knu-1 compared with knu-1
Initiation of the carpel primordia is marked by the termination of floral stem cells. Although genetic evidences have suggested that the YABBY gene CRABS CLAW (CRC) regulates the development of carpel, as well as the floral meristem determinacy as a target of the homeotic protein AGAMOUS, the underlying mechanism remains unclear. Here we show that the tetraspanin-encoding gene TONADO2 (TRN2) and the auxin biosynthesis gene YUCCA4 (YUC4) act as downstream targets of CRC.

overall_design: The knu-1 and knu-1 crc-1 seeds e were  grown at 22°C under continuous light conditions. The inflorescences with flower buds earlier than stage 10 were collected. Three independent sets of knu-1 and crc-1 knu-1 inflorescence mRNA samples were used for this array.

first: Jiangbo

last: Huang

first: Nobutoshi

last: Yamaguchi

last: Xu

first: Toshiro

last: Ito


title: Expression analysis in ductal adenocarcinoma in patients with low and high survival after tumor resection

status: Public on Oct 04 2017

city: valencia

first: Ana Barbara

last: Garcia

state: valencia

address: menendez pelayo 4acc

country: Spain

institute: CIBERDEM-INCLIVA

summary: Analysis of gene expression in pancreatic tumors. Results obtained show an expression gene profile associated with longer survival in patients.

overall_design: Total RNA obtained from paraffined samples of ductal adenocarcinomas from patients with pancreatic cancer. Patients were grouped depending on their survival (higher or lower than 24 months) after tumor resection and their tumor stage.

first: Ana

middle: B

last: Garcia-Garcia

first: Carmen

last: Gomez-Mateo

first: Rebeca

last: Hilario

first: Pilar

last: Rentero

first: Alvaro

last: Martinez-Domenech

first: Veronica

last: Gonzalez-Albert

first: Pablo

last: Marin-Garcia

first: Antonio

last: Ferrandez-izquierdo

first: Luis

last: Sabater

first: Javier

last: Chaves


title: Gene expression profile of neurotoxin exposure in rat midbrain dopaminergic neurons

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: N27 cells are dopaminergic neurons derived from rat midbrain and are extensively employed as a model for neurodegeneration. N27 cells were challenged with 2 neurotoxins associated with Manganism (Manganese Chloride;Mn) and Parkinson's Disease (1-methyl-4-phenylpyridinium ion;MPP+). Mn and MPP+ result in movement dysfunction and are mitochondrial toxins particularly affecting complexes I.This study aimed to understand and differentiate the molecular mechanisms underlying Mn and MPP+ mediated dopaminergic insult by evaluating the differential gene expression pattern in the two models

overall_design: N27 cells were treated with 150 µM and 250 µM of Mn or MPP+ respectively, for 48 h

first: R

last: Mythri

first: N

last: Raghunath

first: M

last: Srinivas Bharath

first: Mohamed

last: Aiyaz

first: Chand

last: Bipin


title: Crosstalk between global regulators CRP and FIS in E. coli.

status: Public on Oct 03 2017

city: Parul

first: Parul

last: Singh

address: 25-28, rue du Docteur Roux

institute: Institut Pasteur

summary: To understand the influence of global transcription regulators Fis and CRP on global gene expression in different growth phases  of E. coli.

overall_design: We have performed RNA-Sequencing experiment in the crp, fis single and double deletion strains in the exponential growth phase.

first: Aswin

middle: S

last: Seshasayee


title: Tracing information flow from Erk to target gene induction reveals mechanisms of dynamic and combinatorial control

status: Public on Sep 15 2017

city: Princeton

first: Jared

middle: E

last: Toettcher

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

summary: In prior work we developed an optogenetic system for delivering highly precise, time-varying inputs to Ras, termed OptoSOS (Toettcher et al., 2013). This system relies on a membrane-targeted photoswitchable protein (Phy-CAAX) and a cytoplasmic Ras activator (PIF-SOScat) whose localization to the membrane can be controlled with light. In this system, Phy/PIF heterodimerization can be triggered on and off by exposure to 650 and 750 nm light, respectively. We found that this system could be used to deliver highly precise levels and dynamics of Ras/Erk signaling both in vitro and in vivo. Here, we aimed to globally assess the transcriptional response to light-activated Ras and compare it to that induced by growth factor stimulation.   We stimulated NIH3T3 OptoSOS cells with either constant activating red light or PDGF and measured transcriptional responses by RNAseq. Total mRNA was collected after 0, 30, 60 and 120 minutes and used to track the dynamics of transcript abundance in both conditions. Genes were defined as upregulated if they satisfied two criteria: (i) induced at least three-fold over unstimulated cells, and (ii) induced at least two consecutive timepoints. By these criteria we detected 118 genes that were upregulated within 2 h by either PDGF or light stimulation, a comparable number of Ras-responsive genes to that found in previous studies.   We found that both PDGF and light induced nearly identical profiles of gene expression, with 100/118 genes induced by PDGF and 110/118 induced by light. At each time point we found excellent agreement between the levels of gene induction in response to both stimuli. This agreement also extended to response dynamics. where hierarchical clustering revealed three classes of dynamic response: an early response peaking within 30 min, an intermediate response peaking at ~1 h, and a late response where gene expression gradually increased over the full 2 h timecourse. In all three classes, we found that light and PDGF led to highly similar expression changes over time. We thus concluded that sole stimulation of the Ras/Erk pathway by light was sufficient to recapitulate at least the first two hours of the PDGF-induced transcriptional response.

overall_design: RNA-seq to measure global transcript abundance at various timepoints after PDGF stimulation or direct optogenetic activation of Ras using the OptoSOS system in NIH3T3 cells (Toettcher et al, Cell 2013). 9 samples were collected using the TruSeq library preparation kit (Illumina), multiplexed, pooled and measured in 3 lanes of an Illumina Hi-Seq 2000. Library quality was assessed by Agilent Bioanalyzer. Roughly 30-50 million reads were measured per sample across all 3 lanes. Baseline transcript abundance was measured in triplicate (0 min controls) and each successive timepoint was measured in a single collection. Genes were considered upregulated if they were induced at least 5-fold in at least two consecutive timepoints relative to their baseline abundance.

first: Maxwell

middle: Z

last: Wilson

first: Pavithran

middle: T

last: Ravindran

first: Wendell

middle: A

last: Lim


title: Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa (RNA-seq)

status: Public on Sep 19 2017

city: Berkeley

first: Areejit

last: Samal

address: 341A Koshland Hall

department: Plant & Microbial Biology

institute: UC Berkeley

summary: The ability to rationally engineer filamentous fungi could greatly facilitate biotechnological enzyme production for the degradation of plant cell wall polysaccharides in biorefinery applications. However, an incomplete and fragmented knowledge base of the biomolecular networks responsible for plant cell wall deconstruction by filamentous fungi impedes experimental efforts in this direction. To expand this knowledge base, we have reconstructed a detailed network of those reactions occurring in the filamentous fungus Neurospora crassa that are important for the degradation of plant cell wall polysaccharides into simple sugars. To build this network, we integrated information from five heterogeneous data types: functional genomics, transcriptomics, proteomics, genetics, and biochemical characterizations. We encapsulated the combined information into a feature matrix and weighed evidence to assign annotation confidence scores for each gene within the network. Comparative analyses of next-generation transcriptome sequencing profiles for N. crassa grown on different substrates corresponding to specific plant cell wall polysaccharides revealed environment-specific modules within the network. Subsequent analyses of next-generation ChIP and RNA sequencing data within the network context shed new light on how N. crassa regulates the plant cell wall degradation network (PCWDN). Specifically, our system-level analyses led to the hypothesis-driven experimental validation of the role transcription factor CLR-2 plays in degradation of the major hemicellulose mannan. In the future, we expect the network to serve as a scaffold for integration of diverse experimental data, leading to elucidation of regulatory design principles for plant cell wall deconstruction by filamentous fungi. In turn, this will guide efforts to rationally engineer novel, industrially relevant fungal hyper-secretion strains.

overall_design: Media shift experiments were performed in triplicate and followed the procedure described earlier in Coradetti et al. (Coradetti et al, 2012) and Znameroski et al. (Znameroski et al, 2012) to ensure optimal comparability with the previously published RNA-seq datasets. First, using shake-flasks (200 rpm), Neurospora crassa cultures were pre-grown from conidia for 16 hrs in 100 mL of Vogels Minimal Medium (VMM) with 2% sucrose. Next, the mycelia were passed over a Whatman glass microfiber filter and washed three times with VMM without a carbon source (NoC). The mycelial mass was then transferred to new shake flasks with 100 mL of VMM containing a specific carbon source 2% xyloglucan (P-XYGLN, Megazyme) or 2% mannan (P-MANCB, Megazyme) or 2% mixed-linkage-glucan (P-BGBM, Megazyme) or 2% starch. After 4 hrs in the new carbon source, the mycelia were harvested over a filter, flash frozen in liquid nitrogen and stored at −80°C.  Total RNA was extracted for library generation using the standard procedures as described in Tian et al. (Tian et al, 2009).

last: Glass


title: Genome-wide analysis of Nrdc-binding sites by ChIP-seq in mouse embryonic fibroblasts

status: Public on Oct 23 2017

city: kyoto

first: Yusuke

last: Morita

state: kyoto

address: kyoto

institute: kyoto university

summary: Nardilysin (Nrdc) is a metallopeptidase of M16 family, which has been recently identified as a transcriptional coregulator. Here, we characterize the role of Nrdc in transcriptional regulation by genome-wide analysis using ChIP-seq and transcriptome.

overall_design: Nrdc-binding sites and histone modifications were examined by ChIP-seq in immortalized mouse embryonic fibroblasts (MEF). MEFs generated from wild-type (+/+) and Nrdc-deficient (-/-) mice were used. MEF-/- cells, in which Nrdc was reintroduced by lenti-virus vector, were also used as control.

first: Morita

last: Yusuke

first: Nishi

last: Eiichiro


title: Nrdc-deficient MEF


title: Antifungal defense of probiotic Lactobacillus rhamnosus GG is mediated by blocking adhesion and nutrient depletion

status: Public on Sep 14 2017

city: Stuttgart

first: Christian

last: Grumaz

address: Nobelstr. 12

department: MBT

institute: Fraunhofer IGB

summary: Candida albicans is an inhabitant of mucosal surfaces in healthy humans but also the most common cause of fungal nosocomial blood stream infections, associated with high morbidity and mortality. As such life-threatening infections often disseminate from superficial mucosal infections we aimed to study the use of probiotic Lactobacillus rhamnosus GG (LGG) in prevention of mucosal C. albicans infections.   Here, we demonstrate that LGG protects oral epithelial tissue from damage caused by C. albicans in our in vitro model of oral candidiasis. Furthermore, we provide insights into the mechanisms behind this protection and dissect direct and indirect effects of LGG on C. albicans pathogenicity. C. albicans viability was not affected by LGG. Instead, transcriptional profiling using RNA-Seq indicated dramatic metabolic reprogramming of C. albicans. Additionally, LGG had a significant impact on major virulence attributes, including adhesion, invasion, and hyphal extension, whose reduction, consequently, prevented epithelial damage. This was accompanied by glucose depletion and repression of ergosterol synthesis, caused by LGG, but also due to blocked adhesion sites. Therefore, LGG protects oral epithelia against C. albicans infection by preventing fungal adhesion, invasion and damage, driven, at least in parts, by metabolic reprogramming due to nutrient limitation caused by LGG.

overall_design: Host pathogen interaction study with probiotic strain

first: D

last: Mailänder-Sánchez

first: C

last: Braunsdorf

last: Mueller

first: S

last: Lorenz

first: P

last: Stevens

first: J

last: Wagener

first: B

last: Hebecker

last: Hube

first: F

last: Bracher

first: K

last: Sohn

last: Schaller


title: Identification of Gon4l-associated genomic regions by DamID-seq

status: Public on Sep 13 2017

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

summary: We report DNA adenine methyltransferase identification (DamID)-sequencing data to identify Gon4l-associated genomic regions in wild-type (WT) tailbud (TB) stage zebrafish embryos. Methylated, and therefore Gon4l-proximal, gDNA was isolated from embryos expressing a Gon4l-Dam fusion and compared to that from embryos expressing GFP-Dam control.

overall_design: gDNA sequencing from WT embryos expressing Gon4l-Dam or control GFP-Dam with biological triplicates.

first: Margot

last: Williams


title: Transcriptome analysis in Nrdc-deficient MEF using RNA-seq

last: Morita

overall_design: Gene expression profiles were examined by RNA-seq in immortalized mouse embryonic fibroblasts (MEF). MEFs generated from wild-type (+/+) and Nrdc-deficient (-/-) mice were used. MEF-/- cells, in which Nrdc was reintroduced by lenti-virus vector, were also used as control.


title: DynaMO, a package identifying transcription factor binding sites in dynamical ChIPSeq/RNASeq datasets, identifies transcription factors driving yeast ultradian and mammalian circadian cycles

status: Public on Sep 26 2017

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

summary: Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. We present a computational method, dynamic motif occupancy (DynaMO), which exploits random forest modeling and clustering based enrichment analysis. DynaMO exploits TF motifs and dynamic ChIP-seq data of chromatin surrogates such as histone modifications to infer important TFs and their spatiotemporal binding in biological processes. Application of DynaMO to the yeast ultradian cycle, mouse circadian clock and human neural differentiation exhibits its accuracy and versatility. We further demonstrate the function of stress response regulators Msn2 and Msn4 as key TFs activating yeast glycolysis genes. Msn2/4 regulates the cellular transition from quiescence to growth by accumulating the intracellular acetyl-CoA level through glycolysis. We anticipate DynaMO will be generally useful for elucidating transcriptional programs in dynamic processes.

overall_design: 6 time point ChIP-seq of Msn2 and Msn4 in YMC; 7 time point WT and 11 time point msn2Δmsn4Δ RNA-seq in YMC

first: Jef

middle: D

last: Boeke

first: Hongkai

last: Ji


title: Regulation and role of the pro-apoptotic transcription factor CHOP in Idiopathic Pulmonary Fibrosis

status: Public on Sep 23 2017

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Idiopathic pulmonary fibrosis (IPF) is a progressive and ultimately fatal interstitial lung disease characterized by alveolar epithelial cell type II (AECII) injury and enhanced fibroblast/myofibroblast proliferation. Recent data show that maladaptive endoplasmic reticulum (ER)-stress leading to AECII apoptosis could play a key role in IPF, although it is still unclear how precisely such response is initiated and signalled. C/EBP homologous protein (CHOP) has been suggested to contribute to a maladaptive ER-stress response in general and has been found to be induced and to be translocated into the nucleus of AECII in IPF in particular.  We here show for the first time a novel mechanism for the regulation of CHOP expression during ER-stress in AECII via AP-1 and c-Ets-1. We found these two transcription factors to be up-regulated in AECII under ER-stress conditions and to interact with each other to jointly bind to the CHOP promoter, thereby inducing CHOP gene expression. Moreover, we show for the first time that singular CHOP overexpression in vitro and in vivo is indeed capable of inducing apoptosis of AECII and, consequently, lung fibroblast proliferation and up-regulation of pro-fibrotic markers. We therefore believe that CHOP plays a key role in AEC injury and consecutive fibrosis.

overall_design: Cell-culture of MLE12 cells, transfected and/or treated with Thapsigargin (TG, 1µM/ml), dual-color hybridizations (always two similar samples were labelled with Cy3 and Cy5 and hybridized on one array).

first: Martin

last: Hühn

first: Andreas

last: Günther


title: Carbon nanotubes, but not graphene oxide, trigger chemokine production in primary human macrophages via MyD88 dependent NF-kB Pathway

city: Stockholm

first: Pekka

middle: Juhani

last: Kohonen

address: Nobelsväg 13, Box 210

department: IMM Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

summary: The growing medical application of engineered nanomaterials (ENMs) necessitates better understanding of their molecular toxicity mechanisms governing immune effects. In the present study, a comprehensive mechanistic in vitro assessment of two carbon-based ENMs, single-walled carbon nanotubes (SWCNTs) and graphene oxide (GO), was performed using primary human monocyte-derived macrophages (HMDM) as a model. HMDM were exposed to SWCNTs and GO at concentrations 10–100 µg/ml for 24 h. Toxicity, reactive oxygen species (ROS) production and uptake of ENM by cells was measured. The changes in gene expression profile of HMDM in response to SWCNTs and GO were studied and the key stress response pathways identified. The transcriptomics and pathway enrichment analysis findings were verified by multiplex immunoassay and functional assays.

overall_design: Primary human monocyte-derived macrophages (HMDM) as a model were treated with GO (graphene oxide), HCS (hollow carbon spheres) and SWCNT (single-walled carbon nanotubes) at concentrations from 10-100 µg/ml for 6 or 24 hours using 1-3 replicates and samples collected for analysis with the Affymetrix Human Genome U219 array.

first: Olesja

last: Bondarenko

first: Sourav

last: Mukherjee

first: Fernando

last: Andón

first: Táňa

last: Brzicová

first: Reija

last: Autio

first: Heli

last: Salminen-Mankonen

first: Riitta

last: Lahesmaa

first: Sanjay

last: Mathur

first: Anna

last: Shvedova

first: Bengt

last: Fadeel


title: Analysis of differentially expressed genes in SMMC-7721 cell line after transfection with miR-215 and siPCAT1

status: Public on Sep 07 2017

city: jinan

first: Yanli

last: Ren

state: shandong

address: huaiyin street

institute: SDCH

summary: This study aimed to identify differential expressed genes before and after tranfection with miR-215 and siPCAT1, using the 7721 liver cancer cell line as a model.

overall_design: There were a total of 3 samples examined.

first: Ming

last: Yang


title: Understanding microRNA regulation involved in metamorphosis of the veined rapa whelk (Rapana venosa)

status: Public on Sep 01 2017

city: Qingdao

first: Hao

last: Song

state: Shandong

address: 7 Nanhai Road

institute: Institute of Oceanology,Chinese Academy of Sciences

summary: The veined rapa whelk (Rapana venosa) is widely consumed in China but is also a predator that is reducing bivalves resources in oceans worldwide. Larval metamorphosis of this species, a pelagic to benthic transition that involves considerable structural and physiological changes, plays a pivotal role in its commercial breeding and natural populations. Thus, the endogenous microRNA that drive this transition attract considerable interest. This study is the first to investigate alterations of miRNA expression during metamorphosis in a marine gastropod by using high-throughput sequencing. A total of 195 differentially expressed miRNAs were obtained, including 65 miRNAs differentially expressed during the transition from pre-competent larva to competent larva (33 up-regulated and 32 down regulated) and 123 miRNAs differentially expressed during competent to post larva transition (96 up-regulated and 27 down regulated). Our data improve understanding of the microRNA function into R. venosa metamorphosis and provide a solid basis for further study.

overall_design: Larval samples from pre-competent larval stage (the three spiral whorls stage), competent larval stage (the four spiral whorls stage) and the post larval stage (juveniles) were collected with three biological replicates (each replicate contains 40~100 individuals).Total RNA was extracted from an individual intestine using the RNeasyMini Kit (Qiagen, USA) according to the manufacturer's instructions. The quality and concentration of RNA were measured using a NanoDrop 1000 spectrophotometer (Thermo). After total RNA extraction, the RNA molecules in a size range of 18–30nt were enriched by polyacrylamide gel electrophoresis (PAGE). Then the 3’adapters were added and the 36-44nt RNAs were enriched. The 5’adapters were then ligated to the RNAs as well. The ligation products were reverse transcripted by PCR amplification and the 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology Co. Limited (Guangzhou, China).

first: Tao

last: Zhang


title: Differential gene expression in MZudu v. WT zebrafish gastrulae

first: Bo

summary: We report RNA-sequencing data from zebrafish embryos lacking both maternal and zygotic expression of udu (which encodes Gon4l) (MZudu) at tailbud (TB) stage. Transcripts were compared to stage-matched wild-type (WT) embryos to identify differentially expressed genes.

overall_design: Sequencing of polyadenylated mRNAs from MZudu mutant and control WT embryos with 2 biological and 2 technical replicates per genotype - each with 3 lanes per sample.

first: Margot

last: Williams


title: Cigarette smoking induces changes in airway epithelial expression of genes associated with monogenic lung disorders

status: Public on Aug 30 2017

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: Smoking-induced lung disease is one of the most prevalent forms of lung disease but  also one of the more diverse. Based on the phenotypic diversity caused by the same environmental stress, we hypothesized that smoking may induce changes in lung cell expression of genes that, with specific variants, are causative of monogenic lung disease, i.e., not that smoking induces a phenocopy of a genetic disease, but smoking may subtly modify the expression of genes known to be associated with genetic disorders with distinct lung disease phenotypes.  To assess this hypothesis, and based on the knowledge that most smoking-related disease phenotypes start in the small airway epithelium, we asked: are the genes associated with the monogenic lung disorders expressed in the small airway epithelium, and if so, does smoking alter the expression of these genes? To accomplish this, we examined small airway epithelium expression of 92 genes known to be associated with 17 monogenic lung disorders in 230 samples of small airway epithelium (SAE) obtained from healthy nonsmokers and healthy smokers without any clinical evidence of disease.  Of the 86 monogenic disorder-related genes we found expressed in the SAE, strikingly, 37 were significantly differentially expressed in normal smokers compared to normal nonsmokers (p<0.05, Benjamini-Hochberg correction for multiple comparisons). The data demonstrates that the effect of smoking on the transcriptome of small airway epithelium includes significantly altered regulation of the genes responsible for known monogenic disorders.

overall_design: This study provides biologic evidence that smoking may induce changes in lung cell expression of genes that are causative of monogenic lung disease .

first: Ann

last: Tilley

first: Jacqueline

last: Salit

first: Michelle

middle: R

last: Staudt

first: Robert

middle: J

last: Kaner

first: Thomas

last: Vincent

first: Francisco

last: Agosto-Perez

first: Jason

middle: G

last: Mezey

first: Benjamin

last: Van De Graaf

last: Raby

first: Ronald

last: Crystal


title: The impact of oil spill to lung health – insights from an RNA-seq study of human airway epithelial cells

status: Public on Aug 24 2017

city: New Orleans

first: Yao-Zhong

last: Liu

state: LA

address: 1440 Canal Street, Suite 1610

department: Biostatistics and Data Science

institute: Tulane University School of Public Health and Tropical Medicine

summary: To reveal the potential effects of oil and oil dispersants on the respiratory system at the molecular level, we evaluated the transcriptomic profile of human airway epithelial cells grown under treatment of crude oil, the dispersants Corexit 9500 and Corexit 9527 and oil-dispersant mixtures. We identified a very strong effect of Corexit 9500 treatment, with 84 genes (response genes) differentially expressed in treatment vs. control samples. We discovered an interactive effect of oil + dispersant mixtures; while no response gene was found for Corexit 9527 treatment alone, cells treated with Corexit 9527 + oil mixture showed an increased number of response genes (46 response genes), suggesting a synergic effect of 9527 with oil on the transcriptomic perturbation of airway epithelial cells. Through GO (gene ontology) functional term and pathway-based analysis, we identified upregulation of genes involved in angiogenesis and immune responses and downregulation of genes  involved in cell junctions and steroid synthesis as the prevailing transcriptomic signatures in the cells treated with Corexit 9500, oil or Corexit 9500 + oil mixture. Interestingly, these key molecular features coincide with those observed in common lung diseases, such as asthma, cystic fibrosis and chronic obstructive pulmonary disease. Our study provides mechanistic insights into the detrimental effects of oil and oil dispersants to the respiratory system and suggested significant health impacts of the recent BP oil spill to those people involved in the cleaning operation.

overall_design: We profiled with RNA-seq six groups of human airway epithelial cells. Each group contains three replicate samples. These groups are oil treatment group, 9500 treatment group, 9527 treatment group, oil+9500 treatment group, oil+9527 treatment group, and control group.


title: Role of OSGIN1 in Mediating Smoking-induced Autophagy in the Human Airway Epithelium [array]

status: Public on Aug 31 2017

summary: Enhanced autophagy is recognized as a component of the pathogenesis of smoking-induced airway disease. Based on the knowledge that enhanced autophagy is linked to oxidative stress and the DNA damage response, both of which are linked to smoking, we used microarray analysis of the small airway epithelium to identify smoking up-regulated genes known to re-spond to oxidative stress and the DNA damage response. This analysis identified OSGIN1 as significantly up-regulated by smoking in both the large and small airway epithelium (1.8-fold, p<0.01, 2.1-fold, p<10-4, respectively), an observation confirmed by an independent small airway microarray cohort, TaqMan PCR and RNAseq. Genome-wide correlation of RNAseq analysis of airway basal/progenitor cells isolated from healthy subjects (n=17) showed a direct correlation of OSGIN1 mRNA levels to multiple classic autophagy genes, including, LC3B, P62, WIPI1 and ATG13 (all rho>0.7, p<0.01). In vitro cigarette smoke extract exposure of nonsmoker primary airway basal/progenitor cells was accompanied by a dose-dependent up-regulation of OSGIN1 and autophagy induction. Lentivirus-mediated enhanced expression of OSGIN1 in human primary basal/progenitor cells induced puncta-like staining of LC3B and up-regulation of LC3B mRNA and protein and P62 mRNA expression level in a dose and time-dependent manner. OSGIN1-induction of autophagosome / amphistome / autolysosome formation was confirmed by co-localization of LC3B with P62 or CD63 (endosome marker) and LAMP1 (lysosome marker). Induction of autophagy by OSGIN1 is accompanied with heightened oxidative stress. Together, these observations support the concept that smoking-induced up-regulation of OSGIN1 is at least one link between smoking-induced stress and enhanced-autophagy in the human airway epithelium.

overall_design: Airway epithelium transcriptome analysis suggested that OSGIN, an oxidative response and cell death induction gene, was up-regulated by cigarette smoking and might be involved in autophagy regulation. In vitro study demonstrated that smoking can increase OSGIN1 expression and enhanced-expression of OSGIN1 led to autophagy, which is accompanied with heightened oxidative stress.

first: Guoqing

last: Wang

first: Haixia

last: Zhou

first: Mohammed

last: Al-Hijji

first: Xuemei

last: Ou

first: Matthew

last: Walters


title: Large-Scale Atlas of Mutant IDH1-Dependent Chromatin State Reprogramming, Reversibility, and Persistence [RNA-seq]

status: Public on Aug 23 2017

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

department: LRI

institute: Cleveland Clinic

summary: Isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) mutations drive the development of gliomas and other human malignancies.  Significant efforts are already underway to attempt to target mutant IDH in clinical trials.  However, how mutation of IDH leads to tumorigenesis is poorly understood. Mutant IDH1 promotes epigenetic changes that promote tumorigenesis but the scale of these changes throughout the epigenome and the reversibility of these changes are unknown.  Here, using both human astrocyte and glioma tumorsphere systems, we generate a large-scale atlas of mutant IDH1-induced epigenomic reprogramming.  We characterize the changes in the histone code landscape, DNA methylome, chromatin state, and transcriptional reprogramming that occur following IDH1 mutation and characterize the kinetics and reversibility of these alterations over time.  We discover coordinate changes in the localization and intensity of multiple histone marks and chromatin states throughout the genome.  These alterations result in systematic chromatin states changes, which result in widespread gene expression changes involving oncogenic pathways.  Specifically,  mutant IDH1 drives alterations in differentiation state and establishes a CD24+ population that features enhanced self-renewal and other stem-like properties.  Strikingly, prolonged exposure to mutant IDH1 results in irreversible genomic and epigenetic alterations.  Together, these observations provide unprecedented molecular portraits of mutant IDH1-dependent epigenomic reprogramming at high resolution.  These findings have significant implications for our understanding the mechanisms underlying mutant IDH function and for optimizing therapeutic approaches to targeting IDH mutant tumors.

overall_design: RNA-sequencing of inducible IDH1 R132H astrocyte and tumorsphere models

first: Sevin

last: Turcan

first: Timothy

last: Chan


title: Role of OSGIN1 in Mediating Smoking-induced Autophagy in the Human Airway Epithelium

first: Yael

last: Strulovici-Barel

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

overall_design: Refer to individual Series


title: Whole genome transcriptional responses to aluminum stress in rice roots

city: Ithaca

first: Susan

middle: R.

last: McCouch

address: 162 Emerson Hall

department: Plant Breeding & Genetics

institute: Cornell University

summary: We used RNA-Seq to perform a whole transcriptome analysis in roots of Azucena (tropical japonica), IR64 (indica), and the near-isogenic lines AZU[IR64121] and IR64[AZU12.1] in control conditions and treated with 80 μM Al3+ activity  for 4 hours

overall_design: Four independent biological replicates per genotype per treatment were analyzed

first: Juan

last: Arbelaez

first: Lyza

last: Maron

last: Jobe

first: Zhangjun

last: Fei

first: Leon

last: Kochian


title: Large-Scale Atlas of Mutant IDH1-Dependent Chromatin State Reprogramming, Reversibility, and Persistence

type: Methylation profiling by genome tiling array


title: Large-Scale Atlas of Mutant IDH1-Dependent Chromatin State Reprogramming, Reversibility, and Persistence [methylation]

overall_design: Bisulphite converted DNA from IDH1 R132H expressing astrocyte and tumorsphere models were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.


title: Tissue-specific DNA methylation is conserved across species and driven by primary sequence conservation

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: Tissue specific differentially methylated regions (DMRs) have been shown to play important roles in tissue specification, but little is known about the conservation pattern of genome-wide DNA methylation distribution that encodes tissue specifity. Using a comparative approach, we identified and compared the tissue-specific DNA methylation patterns of the rat against that of mouse and human across three common tissue types. We found that 10%-40% of this tissue-specific DNA methylation pattern is conserved, and this epigenetic onservation is associated with the conservation of tissue specific TFBS.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
To evaluate the epigenetic evolution of tissue specific DMRs, we generated complete DNA methylome maps for rat blood, brain, sperm, and mouse blood by integrating data from methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq). We have also profiled DNA methylation datasets for mouse brain, sperm, and human blood, brain, sperm, as well as ChIP-seq data in the matching tissue types. These data were collected from the Human Epigenome Roadmap and MouseENCODE consortia;
Mouse Brain: GSE53694 [GSM1299110, GSM1299111]
Mouse Sperm: GSE49623 [GSM1202750-GSM1202753]
Human Blood: GSE16368 [GSM543023]
Human Brain: SRP002318
Human Sperm: GSE30340 [GSM752295, GSM752296]

first: Jia

first: Ting

first: Theodore

last: Cicero

first: Xiaoyun

last: Xing