title: Pathogen Trojan horse delivers bioactive host protein ZmMAC1 to alter maize (Zea mays) anther cell behavior in the male sterile mutant Zmmac1-1.

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: To determine if TH delivery of ZmMAC1 protein results not only in cytological but also molecular cell differentiation in Zmmac1-1, gene expression was determined using RNA sequencing of the infected anthers.

overall_design: There were four biological replicates of fertile anther infected with SG200 (F_SG200a/b/c/d) as control to show normal somatic niche and AR cell progression; two biologcial replicates of Zmmac1-1 sterile anthers infected with SG200 (mac1_SG200a/b) as negative controls lacking the somatic niche and overproducing AR cells; and four biological replicates of Zmmac1-1 sterile anthers infected with SG200 carrying ZmMAC1.

first: Karina

last: van der Linde

first: Reza

last: Hammond

first: Chong

last: Teng

first: Virginia

last: Walbot


title: Transcriptional profiling of leukemic stem cells of AML treated with Wnt inhibitors in vivo

status: Public on Mar 05 2018

city: Dallas

first: Lawrence

last: Lum

state: Texas

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

summary: Epigenetic changes in cancerous cells including alterations in histone methylation facilitate the installation of growth-promoting signaling networks by altering DNA accessibility to transcriptional machinery. The oncofusion protein MLL-AF9 promotes deviant histone methylation and induces acute myelogenous leukemia (AML) in animals. Despite observations supporting a role for WNT signaling in AML pathogenesis, we have a limited mechanistic account of how cancerous growth is sustained in this context. Using chemical antagonists of WNT signaling and genetic ablation of the WNT chaperone Wntless (Wls), we identified the homeobox domain gene Sine oculis 1 (Six1) to be an atypical WNT-controlled target gene in MLL-AF9-transformed leukemic stem cells (LSCs). Elimination of Wls or Six1 in MLL-AF9 LSCs, or their exposure to WNT pathway inhibitors results in extended survival in LSC-transplanted recipient mice suggesting that WNT/SIX1 signaling is critical to MLL-AF9 transformation. Profiling of chromatin accessibility changes using ATAC-seq of MLL-AF9 transformed cells reveals chromatin remodeling in Six1 DNA regions that support binding of the transcriptional effector TCF7L2. Our data suggests de novo installation of a WNT/SIX1 signaling axis is critical to the development of some forms of AML and reveals how epigenetic alterations can re-assemble master regulatory pathways controlling cell fate with cancer-promoting consequences.

overall_design: Total RNA obtained from leukemic stem cells (LSC) sorted from bone marrow cells of AML mice treated with Wnt inhibitors IWR107, IWP2G9 or vehicle control for 4 weeks

first: Lishu

last: Zhang


title: Transcriptional profiling of leukemic stem cells of AML with Wls WT or KO background

overall_design: Total RNA obtained from leukemic stem cells (LSC) sorted from bone marrow cells of AML mice with Wls WT or KO background


title: Enzymatic or in vivo installation of propargyl groups in combination with click chemistry enables enrichment and detection of methyltransferase target sites in RNA

status: Public on Feb 21 2018

city: Muenster

first: Benedikt

middle: Sebastian

last: Nilges

address: Von-Esmarch-Straße 54

department: RNA Biology Group

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

summary: m6A is the most abundant internal modification in eukaryotic mRNA. It is introduced by METTL3-METTL14 and tunes mRNA metabolism, impacting cell differentiation and development. Precise transcriptome-wide assignment of m6A sites is of utmost importance. However, m6A does not interfere with Watson-Crick base pairing making polymerase-based detection challenging. We developed a chemical biology approach for the precise mapping of methyltransferase (MTase) target sites based on the introduction of a bioorthogonal propargyl group in vitro and in cells. We show that propargyl can be introduced enzymatically by wild-type METTL3-METTL14. Reverse transcription terminated up to 65 % at m6A sites after bioconjugation and purification, hence enabling detection of METTL3-METTL14 target sites by next generation sequencing. Importantly, we implemented metabolic propargyl labeling of RNA MTase target sites in vivo based on propargyl-L-selenohomocysteine and validated different types of known rRNA methylation sites.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: enrichment of methylated nucleotides by bioconjugation of propagyl groups in synthetic oligos and rRNA

first: Katja

last: Hartstock

middle: S

first: Anna

last: Ovcharenko

first: Nicolas

last: Cornelissen

first: Nikolai

last: Püllen

first: Ann-Marie

last: Lawrence-Dörner

first: Sebastian

middle: A

last: Leidel

first: Andrea

last: Rentmeister


title: Coordinated regulation of Arabidopsis microRNA biogenesis and red light signaling through Dicer-like 1 and phytochrome-interacting factor 4

status: Public on Feb 27 2018

city: Shanghai

first: Zhenfei

last: Sun

address: Dongchuan Road 500

country: China

institute: Shanghai Jiaotong University

type: Non-coding RNA profiling by high throughput sequencing

summary: Light and microRNAs (miRNAs) are key external and internal signals for plant development respectively. However the relationship between light signaling and miRNA biogenesis pathways remains unknown. Here we found that miRNA processer DCL1/HYL1 interacts with a basic helix–loop–helix (bHLH) transcription factor, phytochrome-interacting factor 4 (PIF4), which mediates the destabilization of DCL1 during dark-red light transition.  PIF4 acts as a transcription factor for some miRNA genes and is necessary for the proper accumulation of miRNAs. DCL1/HYL1 and mature miRNAs play roles in the regulation of plant hypocotyl growth. These results uncovered a previously unknown crosstalk between miRNA biogenesis and red light signaling through the PIF4-dependent regulation of miRNA transcription and processing to affect red light-directed plant photomorhogenesis.

overall_design: Examination of small RNA populations in Arabidopsis Wild Type and pif4-2 mutant or Wild Type and hyl1-2 mutant

first: Z

first: Y

last: Fang


title: Targeted DNA demethylation of the Arabidopsis genome using the Human TET1 catalytic domain.

status: Public on Feb 18 2018

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is important for silencing genes and transposable elements. Changes in DNA methylation can be heritable and thus, the loss or gain of methylation can lead to the formation of stable epialleles. A well characterized example of a stable epiallele in plants is fwa-4, which consists of the loss of DNA cytosine methylation (5mC) in the promoter of the FLOWERING WAGENINGEN (FWA) gene, causing upregulation of FWA and a heritable late flowering phenotype. Here we demonstrate that a fusion between the catalytic domain of the Human demethylase TEN-ELEVEN TRANSLOCATION1 (TET1cd) and an artificial zinc finger (ZF) designed to target the FWA promoter can cause highly efficient targeted demethylation, FWA upregulation, and a heritable late flowering phenotype. Additional ZF-TET1cd fusions designed to target methylated regions of the CACTA1 transposon also caused targeted demethylation and changes in expression. Finally, we have developed a CRISPR/dCAS9 based targeted demethylation system using the TET1cd and a modified SunTag system and demonstrate its ability to target demethylation at and activate the expression of FWA and CACTA1. Our study provides tools for targeted removal of 5mC at specific loci in the genome with high specificity and minimal off-target effects. These tools provide the opportunity to develop new epialleles for traits of interest, and to reactivate expression of previously silenced genes, transgenes, or transposons.

overall_design: 38 RNA-seq, 42 WGBS

first: Javier

last: Gallego-Bartolomé

first: Jason

last: Gardiner

first: Ashot

last: Papikian

first: Basudev

last: Ghoshal

first: Hsuan

middle: Y

last: Kuo

first: Jenny

middle: M

last: Zhao

first: David

middle: J

last: Segal

first: Steven

middle: E

last: Jacobsen


title: RNA-seq Analysis of Suspension Cells of Wild Type, anti sense and Overexpression Transcriptomes

status: Public on Feb 10 2018

city: Beijing

first: Bin

last: Yin

address: Tsinghua East Road

institute: Beijing Forestry University

summary: RNA-seq was performed to examine the differential expressed transcriptomes in anti sense and overexpression suspension cells compare to wild type.

overall_design: To examine the differential expressed transcriptomes in wild type, anti sense and overexpression cell lines, their cells at 5-days after subculturing were collected for RNA-seq analysis. No replicates include in each samples.


title: Comparative Transcriptomics of Choroid Plexus in Alzheimer's Disease, Huntington's Disease and Frontotemporal Dementia: Implications for CSF Homeostasis and Dynamics

status: Public on Feb 08 2018

city: Providence

first: Edward

middle: G

last: Stopa

state: RI

address: 593 Eddy Street

department: Pathology & Laboratory Medicine

institute: Brown University

summary:
Background: In aging and Alzheimer’s disease there are striking changes in CSF composition that may relate to altered choroid plexus function.  Studying CP tissue gene expression at the BCSFB provides further insight into epithelial and stromal responses to aging and diseased states.
Results: Highly significant differences in gene expression occurred in CP of advanced AD patients vs. normal controls.  Immune-related pathways including acute phase response, cytokine/JAK/STAT signaling and cell adhesion were the most significantly enriched among the genes upregulated in AD patients, while methionine degradation, and protein translation genes were most notably downregulated.  While the majority of gene expression changes in AD patients was also observed in FTD and HuD, there were significant differences among the disease groups.  AD had the most unique expression findings, these genes being enriched in upregulated VEGF signaling and immune response proteins, e.g., interleukins.  HuD/FTD patients uniquely displayed upregulated cadherin-mediated adhesion.  Conclusions: This unique database of changes in CP tissue gene expression provides mechanistic insight into the effects of neurodegenerative diseases on CSF dynamics and hydrocephalus, particularly in regards to choroidal immune activation, metabolic homeostasis and resiliency of the CP.

overall_design: Methods: Transcriptome-wide Affymetrix microarrays were used to determine disease-related changes in gene expression within human choroid plexus.  Post-mortem tissue samples of the entire lateral ventricular choroid plexus were from 6 healthy controls and 7 patients with advanced (Braak & Braak stage III-VI) Alzheimer’s disease (AD), 4 with Frontotemporal dementia (FTD) and 3 with Huntington’s disease (HuD).

first: Keith

middle: Q

last: Tanis

first: Miles

middle: C

last: Miller

first: Elena

middle: V

last: Nikonova

first: Alexei

last: Podtelezhnikov

first: Eva

last: Finney

last: Stone

first: Luiz

last: Camargo

first: Lisan

last: Parker

first: Ajay

last: Verma

first: Andrew

last: Baird

first: John

last: Donahue

first: Tara

last: Torabi

first: Brian

last: Eliceiri

first: Gerald

middle: D

last: Silverberg

first: Petra

last: Klinge

first: Conrad

last: Johanson


title: miRNA sequencing on triple negative breast cancer cell lines

status: Public on Feb 07 2018

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

summary: This study consists of miRNA seq data of 26 triple negative breast cancer cell lines

overall_design: We cultured and sequenced 26 TNBC cell lines (BT20, BT549, CAL120, CAL148, CAL51, DU4475, HCC1143, HCC1187, HCC1395, HCC1599, HCC1806, HCC1937, HCC38, HCC70, HDQP1, HS578T, MDAMB157, MDAMB231, MDAMB436, MDAMB453, MDAMB468, MFM223, SUM159, SUM185, SW527) in order to describe the small RNA landscape of these cell lines.

last: Lehmann


title: Degradome sequencing from Arabidopsis tissues non-infected and infected with Tobacco rattle virus (TRV)

status: Public on Mar 01 2018

city: Murcia

first: Livia

last: Donaire

state: Murcia

address: Campus de Espinardo

department: Plant Pathology

country: Spain

institute: Centro de Edafología y Biología Aplicada del Segura

summary: Construction of Parallel analysis of RNA ends (PARE) libraries was done as described by German et al.,  2009. Raw reads consisting of short sequences of 16 to 21 nts after MmeI digestion.

overall_design: Degradome libraries were prepared from infected inflorescences, and from leaves of mock-inoculated and TRV-infected plants

first: Irene

last: Guzmán-Benito

first: Cesar

last: Llave


title: Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes [ChIP-seq]

status: Public on Feb 01 2018

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The NF-κB transcription factors are activated via diverse molecular mechanisms in response to various types of stimuli. A plethora of functions associated with specific sets of target genes could be regulated differentially by this factor, affecting cellular response to stress including an anticancer treatment. Here we aimed to compare subsets of NF-κB-dependent genes induced in cells stimulated with a pro-inflammatory cytokine and in cells damaged by a high dose of ionizing radiation (4 and 10 Gy). The RelA-containing NF-κB species were activated by the canonical TNFα-induced and the atypical radiation-induced pathways in human osteosarcoma cells. NF-κB-dependent genes were identified using the gene expression profiling (by RNA-Seq) in cells with downregulated RELA combined with the global profiling of RelA binding sites (by ChIP-Seq), with subsequent validation of selected candidates by quantitative PCR. There were 37 NF-κB-dependent protein-coding genes identified: in all cases RelA bound in their regulatory regions upon activation while downregulation of RELA suppressed their stimulus-induced upregulation, which apparently indicated the positive regulation mode. This set of genes included a few “novel” NF-κB-dependent species. Moreover, the evidence for possible negative regulation of ATF3 gene by NF-κB was collected. The kinetics of the NF-κB activation was slower in cells exposed to radiation than in cytokine-stimulated ones. However, subsets of NF-κB-dependent genes upregulated by both types of stimuli were essentially the same. Hence, one should expect that similar cellular processes resulting from activation of the NF-κB pathway could be induced in cells responding to pro-inflammatory cytokines and in cells where so-called “damage-induced inflammation” response was initiated by ionizing radiation

overall_design: We sequenced DNA immunoprecipitated from wild type U2OS cells using rabbit polyclonal anti-p65 antibodies. Cells were untreated (control) or stimulated using TNFalpha cytokine for specific time or subjected to ionizing radiation with subsequent recovery. Six ChIP replicates were collected and pooled per each sequenced sample. Input samples were included as negative control (no DNA enrichment was observed in mock-IP samples).

first: Patryk

last: Janus

first: Piotr

last: Widlak


title: The nonhuman primate kidney transcriptome during fetal development

status: Public on Jan 20 2018

city: San Antonio

first: Laura

middle: L

last: Cox

department: Genetics

institute: Texas Biomedical Research Institute

summary: Little is known about the repertoire of nonhuman primate kidney genes expressed throughout development. The present work establishes an understanding of the primate renal transcriptome at different stages of fetal development and defines the framework of gene expression in the context of renal maturation, which provides a basis for identifying deviations in transcriptome expression resulting from suboptimal conditions during renal development. The baboon kidney transcriptome was characterized at 60 days gestation (DG), 90DG, 125DG, 160DG and adulthood (6-12 years) using human genome arrays to identify differential gene expression in the context of biological pathways and hierarchical clusters. Whole genome expression profiling showed 11,331 genes that were expressed during kidney development, 4,698 of which were differentially expressed among the developmental time points. Pathway analysis indicated activation of annotated pathways previously reported to be important to kidney development and pathways not reported as relevant to kidney development. QRT-PCR for genes central to these pathways validated expression profiles and revealed differences between males and females at specific times in gestation. Hierarchical clustering indicated that two clusters best fit the data, one containing genes that increased in expression from 60DG to adult and one that decreased. Cluster analysis also revealed gene splice variants with discordant expression profiles during development. For example, SMAD4, which is central to Wnt signaling, TGF-β signaling and cell cycle, showed up-regulation of the full-length splice variant during development and down-regulation of a shorter variant that is missing DNA binding and protein heterotrimerization domains suggesting decreased inhibition of cell proliferation, which may impact renal cell number and maturation. This study provides the first detailed genetic analysis of the developing primate kidney, and our findings of discordant expression of gene splice variants suggest that gene arrays likely provide a simplified view and demonstrate the need to study the fetal renal proteome.

overall_design: Papio hamadryas whole kidneys were selected at successive stages of primate kidney development for RNA extraction and hybridization on Affymetrix microarrays.

first: Kimberly

last: Spradling-Reeves

first: Jeremy

middle: P

last: Glenn

first: Kenneth

last: Lange

first: Ashley

last: Melchoir

first: Natalia

last: Kuhn

first: Jacqueline

last: Coalson

first: Mark

last: Nijland

first: Peter

middle: W

last: Nathanielsz


title: RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation [ChIP-Seq]

status: Public on Feb 19 2018

summary: Cellular response to ionizing radiation involves activation of the p53-dependent pathways and activation of the atypical NF-κB pathway. Mechanisms of the crosstalk between these two transcriptional networks include (co)regulation of common gene targets. Novel genes potentially (co)regulated by p53 and NF-κB were found using high-throughput genomics screening in human osteosarcoma U2-OS cells irradiated with a high dose (4 and 10 Gy). Radiation-induced expression in cells with silenced TP53 or RELA (coding the p65 NF-κB subunit) genes was analyzed by RNA-Seq while radiation-induced binding of p53 and RelA (p65) in putative regulatory regions was analyzed by ChIP-Seq, then selected candidates were validated by qPCR. A subset of radiation-modulated genes whose expression was affected by silencing of both TP53 and RELA, and a subset of radiation-upregulated genes where radiation stimulated binding of both p53 and RelA were identified. Competition for the same transcriptional coactivators of p53 and NF-κB was the most probable mechanism of a frequent antagonistic effect of the TP53 and RELA silencing. However, this mode of regulation was noted for 3 genes where radiation-induced binding of both p53 and RelA was observed, namely IL4I1, SERPINE1, and CDKN1A. This suggested a possibility of a direct antagonistic (co)regulation by both factors: activation by NF-κB and inhibition by p53 of IL4I1, and activation by p53 and inhibition by NF-κB of CDKN1A and SERPINE1. On the other hand, radiation-induced binding of both p53 and RelA was observed in a putative regulatory region of RRAD gene whose expression was downregulated both by TP53 and RELA silencing, which suggested a possibility of direct (co)activation by both factors.

overall_design: We sequenced DNA immunoprecipitated from wild type U2OS cells using rabbit polyclonal anti-p65 antibodies or rabbit polyclonal anti-p53 antibody. Cells were untreated (control) or subjected to ionizing radiation with subsequent recovery. Six ChIP replicates were collected and pooled per each sequenced sample. Input samples were included as negative control (no DNA enrichment was observed in mock-IP samples).

first: Katarzyna

last: Szoltysek


title: ChIP-seq analysis of histone H3K4me3, H3K27Ac and RNA polymerase II (RNApol II) in HuH-7 cells.

status: Public on Jan 25 2018

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

summary: The RNA-seq profile of the novel LIN28B variant suggested an alternative transcription initiation (ATI) site approximately 20 kb upstream of LIN28B-WT. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed significant enrichment of histone H3K4me3, H3K27Ac and RNA polymerase II (RNApol II) near the ATI site.

overall_design: Examination of histone H3K4me3, H3K27Ac and RNA polymerase II (RNApol II) in HuH-7 cells.

first: Weijie

last: Guo


title: Expression data from skin biopsies in patients with systemic sclerosis treated with beta-catenin inhibitor (C82) and placebo

status: Public on Jan 01 2018

city: Boston

first: Julio

last: Mantero

state: MA

address: 72 E Concord St

department: Rheumatology

institute: Boston University School of Medicine

summary:
Wnt signaling pathway is thought to have a role in skin fibrosis in  Systemic slcerosis. This Randomized, Placebo-Controlled trial examines the effect of beta catenin inhibition on skin expression.
We used microarrays to explore  gene expression changes in the C82 trial

overall_design: Patietns with diffuse cutaneous systemic sclerosis had biopsis before treatment and at day 28.

first: Robert

last: Lafyatis


title: Genome-wide CRISPR screen identifies TSC1 and DEPDC5 that control HIV-1 latency via the mTOR Signaling pathway

status: Public on Jan 30 2018

first: SHAN

last: JIN

address: Scientific Research Center 2901 Cao Lang Road, Jin Shan District, Shanghai, P.R.China

institute: FUDAN University

summary: Identification of factors that control HIV-1latency

overall_design: CRISPR activation technology was used to identify genes that control HIV-1 latency. The complete sgRNA library (plasmid sample) were packaged into lentivirus and used to transduce C11 cells (transduced sample). The proportion of GFP positive C11 cells increased after infection with CRISPRV2.0. GFP positive cells were sorted for 4 rounds and enriched genes. In three independent biological replicates( samples Screen1, 2, and 3),  the sgRNAs enriched in Initial,GFP negative andGFP postive populations were sequenced.

first: Shan

last: Jin

first: Xiaoyan

last: Zhang


title: Global changes in gene expression in human dermal fibroblasts after CSL silencing

status: Public on Dec 04 2017

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

summary:
Senescence of stromal fibroblasts has been linked to establishment of cancer associated fibroblasts (CAF) and aging-associated increase of tumors. However, in clinically occurring carcinomas, density and proliferation of CAFs are frequently increased rather than decreased. We previously showed that genetic deletion or down-modulation of the canonical Notch effector CSL/RBP-J-kappa in skin dermal fibroblasts is sufficient for CAF activation with consequent development of multifocal keratinocyte tumors. We now show that CSL deletion or knockdown induces senescence of primary fibroblasts derived from dermis, oral mucosa, breast and lung. CSL functions in these cells as a constitutive direct repressor of multiple senescence- and CAF-effector genes. At the same time, it physically interacts with p53, repressing its activity, with p53 activation providing a failsafe mechanism against compromised CSL function. Concomitant loss of CSL and p53 overcomes fibroblasts senescence, enhances CAF effector gene expression and, in vivo, promotes stromal and cancer cell expansion. Together, these findings support a CAF activation/stromal evolution model under convergent CSL/p53 control.
We used microarrays to detail the global changes in gene expression in human dermal fibroblasts after CSL silencing

overall_design: HDFs were infected with two different shRNA lentiviruses against CSL in parallel with a control virus. Total RNA was extracted 9 days post-infection, followed by microarray hybridization and analysis as previously described (Lefort et al., 2013)controls

first: Maria-Giuseppina

last: Procopio

first: Csaba

last: Laszlo

first: Dania

last: Allabban

first: Pino

last: Bordignon

first: Seung-Hee

last: Jo

first: Paola

last: Ostano

first: Ugo

last: Ala

first: Paolo

last: Provero

first: Vic

last: Neel

first: Witek

last: Kilarski

first: Melody

last: Swartz

first: Cathrin

last: Brisken

first: Karine

last: Lefort

first: G

last: Dotto


title: Triple negative breast cancer subtypes and pathologic complete response rate to neoadjuvant chemotherapy

status: Public on Nov 17 2017

city: Malaga

first: Angela

last: Santonja

state: Malaga

address: Campus de teatinos s/n

department: Hospital Universitario Virgen de la Victoria

institute: Instituto de Investigación Biomédica de Málaga (IBIMA)

summary: Triple negative breast cancer  is a heterogeneous disease with distinct molecular subtypes that differentially respond to chemotherapy and targeted agents. The purpose of this study was to explore the clinical relevance of Lehmann triple negative breast cancer subtypes by identifying any differences in response to neoadjuvant chemotherapy among them.

overall_design: We performed a retrospective analysis in paraffined pre-treatment tumor biopsies from 119 triple negative breast cancer patients (88 patients treated with neoadjuvant anthracyclines and/or taxanes and 31 with anthracyclines and/or taxanes plus carboplatin). We determined Lehmann subtypes by gene-expression profiling with the GeneChip® Human Transcriptome Array 2.0. (Affymetrix). Data were normalized with the Robust Multichip Analysis (RMA) algorithm in the Affymetrix Expression Console (EC, v.1.4.1) and annotated in the statistical computing environment R (v.3.2.3) using hg19 human genome built. Duplicated genes were mean summarized.

first: Alfonso

last: Sánchez-Muñoz

first: Ana

last: Lluch

first: M

middle: R

last: Chica-Parrado

first: Joan

last: Albanell

first: José

middle: I

last: Chacón

first: Lourdes

last: Calvo

last: Jerez

first: Juan

last: de la Haba

first: Vanessa

last: de Luque

first: Cristina

last: Fernández-De Sousa

first: Luis

last: Vicioso

first: Yéssica

last: Plata

first: César

last: Ramírez-Tortosa

first: Martina

last: Álvarez

first: Casilda

last: Llácer

first: Irene

last: Zarcos

first: Eva

last: Carrasco

first: Rosalía

last: Caballero

first: Miguel

last: Martín

first: Emilio

last: Alba


title: RNA-seq analysis of HuH-7, NCI-H1299 and HEK-293T cells

status: Public on Jan 24 2018

first: Shenglin

last: Huang

summary: The diversity and complexity of the cancer transcriptome hold the potential to yield tumor-specific transcripts (TSTs) in cancer. We report a novel LIN28B variant, LIN28B-TST, which is specifically expressed in hepatocellular carcinoma (HCC) and many other cancer types. LIN28B-TST initiates from a de novo alternative transcription initiation site. We found that LIN28B-TST was expressed in HuH-7 HCC cells and NCI-H1299 lung cancer cells, while wild-type LIN28B (LIN28B-WT) was expressed in HEK-293T human embryo kidney cells.

overall_design: Celluar RNAs were generated by deep sequencing using Illumina Hiseq.

first: Weijie

last: Guo


title: Expression data from root of sir1-1 and serat tko Arabidopsis mutants.

status: Public on Aug 16 2017

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: Cysteine is one essential amino acid for plants and its limitation is known to have a significant impact on plant growth and yield. In this study we performed global transcriptome analyses to investigate the responses to cysteine precursor limitation.

overall_design: Arabidopsis thaliana plants were grown hydroponically under short-day conditions (8h light / 16h dark cycles) under full nutrient supply of Hoagland medium. Arabidopsis root material was harvested when the plants reached the age of 7 weeks (from sowing) and used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates from each condition were analyzed.

first: Anna

last: Speiser

first: Marleen

last: Silbermann

first: Markus

last: Wirtz

first: Ruediger

last: Hell

first: Carsten

last: Sticht


title: Expression data from TGRL lipolysis products treated normal human astrocytes

status: Public on Aug 22 2017

city: Davis

first: Hnin

middle: H

last: Aung

state: CA

address: 451 E Health Science Dr., GBSF 5404

department: Internal Medicine

institute: University of California, Davis

summary:
Lipotoxicity is a metabolic disorder that results from accumulation of lipids, particularly fatty acids, in non-adipose tissue leading to cellular dysfunction, lipid droplet formation, activate the ATF3 stress pathway, induce secretion of inflammatory cytokines, and increase APP. Our observations are consistent with neurovascular lipotoxicity that could play a role in cognitive decline with aging.
We used microarrays to determine the TGRL lipolysis products induced gene expression and to understand the mechanism underline the vascular inflammation.

overall_design: Total RNA was isolated from normal human astrocytes cells treated with media (M), Lipoprotein lipase (L), triglyceride-rich lipoprotein (TGRL or T), or  TGRL lipolysis products (TL) treatment. Affymetrix microarrays analyses of the pooled total RNA samples (n = 3 per group for Media, LpL, TGRL, and TGRL lipolysis products treatments) were performed.

first: Jennifer

last: Rutkowsky

first: John

last: Rutledge

first: Linda

last: Lee


title: Expression data from shoots of Arabidopsis grown under sulfur limitation.

summary:
Sulfate in one essential nutrient for plants and its limitation is known to have a significant impact on plant growth and yield. In this study we performed global transcriptome analyses to investigate the responses to long term sulfate deficiency at the shoot level.
The shoot global transcriptomic responses to sulfur deprivation.

overall_design: Arabidopsis thaliana plants were grown hydroponically under short-day conditions (8h light / 16h dark cycles) under full nutrient supply or under the limitation of sulfur. Arabidopsis root material was harvested when the plants reached the age of 7 weeks (from sowing) and used for RNA extraction and hybridization on Affymetrix microarrays. Four biological replicates from each condition were analyzed.

first: Ilaria

last: Forieri


title: Impact of the knock down of sulfite reductase on the transcriptome of Arabidopsis thaliana.

summary: Sulfite reductase (SiR) plays an essential role in the assimilatory sulfur reduction pathway by catalyzing the reduction of sulfite to sulfide. The T-DNA insertion mutant line sir1-1 shows lower amounts of SiR transcript, protein and lower activity and is severely affected in growth. In this study we performed global transcriptome analysis to investigate the impact of the mutation in the shoot of 7-week-old plants.

overall_design: Wild type and sir1-1 mutant plants were grown on soil under short day conditions until they reached the 7th week from sowing.

first: Arman

last: Samami


title: miRNAs in extracellular vesicles prepared from patients with multiple sclerosis

status: Public on Nov 18 2017

city: Kodaira

first: Kimitoshi

last: Kimura

state: Tokyo

address: 4-1-1 Ogawahigashi

department: Department of Immunology, National Institute of Neuroscience

country: Japan

institute: National Center of Neurology and Psychiatry

summary: Differences in the levels of miRNAs in extracellular vesicles (EVs) between multiple sclerosis (MS) patients and healthy individuals were detected by means of microarray analysis.

overall_design: In this study, miRNAs were extracted from EVs in the plasma of 4 relapsing-remitting MS patients and 4 sex- and age-matched healthy controls, and applied to array analysis.

first: Hirohiko

last: Hohjoh

first: Takashi

last: Yamamura


title: Sequential gene regulatory events leading to glucocorticoid-evoked apoptosis of CEM human leukemic cells [HG_U95Av2]

status: Public on Oct 14 2017

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary:
Glucocorticoid (GC)- sensitive cells are killed by receptor (GR)-filling concentrations of GC for a sufficient time.
We used 3 closely related clones (2 sensitive, 1 resistant) from the CEM line of ALL cells to test the hypothesis that over time, a distinct set of regulated genes would be found in sensitive clones, with cross-talk to other significant pathways

overall_design:
CEM C1-15(resistant), CEM C1-6 (spontaneous revertant to sensitive) are subclones of resistant clone CEM C1.  CEM C7-14 is a subclone of sensitive clone CEM C7.  C1 and C7 were cloned from the original CEM ALL line.  Samples were obtained 2, 8, 12 an 20 hr after addition of 10E-6 M dexamethasone (Dex) to triplicate cultures, RNA extracted and analyzed for transcript expression levels

**Please note that the submitter was unable to locate the raw data CEL files. Thus raw data is not included in the current records.**

first: M

middle: S

last: Webb

first: Aaron

last: Miller

first: Tamara

last: Howard

first: Betty

last: Johnson

first: Sergei

last: Chumakov

first: Yuriy

last: Fofanov

first: Trang

last: Nguyen-Vu

first: C

last: Lin

first: E

middle: B

last: Thompson


title: LSD1 inhibitor-induced changes in gene expression profile in T-cell acute lymphoblastic leukemia cells

status: Public on Aug 15 2017

city: Shimotsuke

first: Yusuke

last: Furukawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

institute: Jichi Medical University

summary: We screened for the changes in gene expression induced by an LSD1 inhibitor to elucidate the mechanism of its cytotoxic effect on T-cell acute lymphoblastic leukemia (T-ALL).

overall_design:
We isolated mRNA from the T-ALL cell line MOLT4 cultured with vehicle alone or LSD1 inhibitor, and subjected them to gene expression profiling using an  Agilent GeneChip Array.

Please note that experiments were technically performed as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed dat was provided for each single channel (Cy3 and Cy5 signals; i.e. one raw data file for two sample records).

first: Jiro

last: Kikuchi


title: Identification and analysis of microRNAs in the SAM and leaves of Populus tomentosa

status: Public on Jun 22 2017

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: High-throughput sequencing was performed to build four sRNA libraries (each sample with two replications) derived from shoot tips and mature leaf tissues of P. tomentosa. Millions of small RNA (sRNA) reads were obtained, and many known and novel miRNAs in SAM and leaf libraries were established. Several miRNAs that were differentially expressed between the SAM and its surrounding tissues, and their targets involved in important biological processes were identified and analyzed. Our study provide insights for better understanding the regulatory mechanisms of miRNAs involved in the SAM of woody plants.

overall_design: Small RNA sequencing in SAM and leaves of P. tomentosa

first: Jiawen

last: Cui


title: The redox-sensitive regulatory module of cyclophilin 20-3, 2-cysteine peroxiredoxin and cysteine synthase in the high light acclimation response in Arabidopsis thaliana

status: Public on Jul 31 2017

first: Carolina

last: Delatorre

summary:
Previous data suggest that 2-cysteine peroxiredoxin, cyclophilin 20-3 and the cysteine synthase complex work as a dynamically interacting module (here named COPS-module) and are involved in stress response. In this study we performed global transcriptome analyses to investigate the responses to short-term high light in wildtype and mutants deficient in each protein of COPS-module.
The global transcriptomic response in leaves to 6 h high light in Col.0 and mutants deficient in each protein of COPS-module.

overall_design: Arabidopsis thaliana mutant lines and wildtype plants were grown in soil under short-day (8h light / 16h dark cycles) and normal light conditions. When the plants reached the age of 4 weeks they were tranferred to high light for 6 h or maintained in normal light. The leaf material of treated plants was used for RNA extraction and hybridization on Affymetrix microarrays. Four biological replicates from each condition were analyzed.

first: Sara

last: Müller

first: Karl-Josef

last: Dietz

first: Shanshan

last: Wang

first: Markus

last: Wirtz

first: Rüdiger

last: Hell


title: Regulation of NRF2 signaling by O-GlcNAcylation of KEAP1

status: Public on Jun 26 2017

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

summary: O-GlcNAcylation is an essential, nutrient-sensitive post-translational modification, but its biochemical and phenotypic effects remain incompletely understood. To address this knowledge gap, we investigated the global transcriptional response to perturbations in O-GlcNAcylation. Unexpectedly, many transcriptional effects of O-GlcNAc transferase (OGT) inhibition were due to the activation of NRF2, the master regulator of redox stress tolerance. Moreover, we found that a signature of low OGT activity strongly correlates with NRF2 activation in multiple tumor expression datasets. Guided by this information, we identified KEAP1 (also known as KLHL19), the primary negative regulator of NRF2, as a direct substrate of OGT. We show that O-GlcNAcylation of KEAP1 at serine 104 is required for the efficient ubiquitination and degradation of NRF2. Interestingly, O-GlcNAc levels and NRF2 activation co-vary in response to glucose fluctuations, indicating that KEAP1 O-GlcNAcylation links nutrient sensing to downstream stress resistance. Our results reveal a novel regulatory connection between nutrient-sensitive glycosylation and NRF2 signaling, and provide a blueprint for future approaches to discover functionally important O-GlcNAcylation events on other KLHL family proteins in various experimental and disease contexts.

overall_design: DESIGN:  MDA-MB-231 cells treated with small molecular inhibitors targeting OGT (5SGlcNAc) or OGA (Thiamet-G)

first: Po-Han

last: Chen

first: Tim

last: Smith

first: Michael

last: Boyce

middle: A


title: effect of n nutrition of arabidopsis response to erwinia infection-MULTIPASS

status: Public on Apr 12 2017

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: ra14-05_multipass - effect of n nutrition of arabidopsis response to erwinia infection - Effect of N nutrition of Arabidopsis response to Erwinia infection - Comparison of Arabidopsis responses to Erwinia infection in relation to nitrogen nutrition (sufficient vs limited).

overall_design: 4 dye-swap - normal vs disease comparison,treated vs untreated comparison

first: Christian

last: Meyer

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Global expression changes of LNCaP and PC3 cells in response to acute Notch activation

status: Public on Mar 08 2017

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

summary: Adenocarcinomas of the prostate arise as multifocal heterogeneous lesions as the likely result of genetic and epigenetic alterations and deranged cell-cell communication. Notch signaling is an important form of intercellular communication with a role in growth/differentiation control and tumorigenesis. Contrasting reports exist in the literature on the role of this pathway in prostate cancer (PCa) development. We report here that Notch1 expression is significantly reduced in a substantial fraction of human PCas, while it is unaffected or even increased in others. Global analysis of gene expression shows that increased Notch1 expression in PCa cells or samples, while counteracting to a significant extent the abnormal program of gene expression that is characteristically altered in clinically occurring tumors, enhances some other aberrant aspects of this program. In particular, down-modulation of Notch1 expression and activity in immortalized normal prostate epithelial cells increases their proliferation potential, while increased Notch1 activity in PCa cells suppresses growth and tumorigenicity. While control of p21Cip1/WAF1 expression by increased Notch1 activity through a Smad3-dependent mechanism can explain the growth inhibitory effects, pro-oncogenic genes, like EPAS1 and CXCL6, are concomitantly up-regulated by Notch in PCa cell lines resistant to Notch1 growth inhibition, in agreement with enhanced tumorigenic behavior.

overall_design: LNCaP and PC3 cell lines overexpressing activated Notch1 versus controls. Each sample was tested in duplicate

first: Karine

last: Lefort

first: Giovanna

last: Chiorino


title: Isolation of putative stem cells present in human adult olfactory mucosa

status: Public on Mar 17 2017

city: schlieren

first: tamara

last: tanos

address: Wagistrasse 27

country: Switzerland

institute: InSphero

summary: The olfactory mucosa (OM) has the unique characteristic of pursuing almost continuous neurogeneration during adulthood in response to external injuries to maintain olfactory function due to the presence of stem cells. The easily accessibility of the OM in humans is a feature that makes these stem cells relevant candidates for the development of regenerative therapies. In this report we present an in depth characterization of patient derived OM together with the characterization of their respective OM derived cultures. In addition, we present a method for the enrichment and isolation of OM stem cells that can be used for future translational sought studies regarding plasticity, neuro-regeneration or disease modeling.

overall_design: several patient OM derived cell cultures were collected and analyzed individually for array employing the GeneChip® Human Genome U133A 2.0 array from affimatrix

first: T

last: Tanos

first: A

last: Rubio


title: Genome-wide analysis of early gene expression by primary human articualr chondrocytes to the pro-inflammatory stimulus of IL-1+OSM

status: Public on Mar 07 2017

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

country: United Kingdom

institute: Newcastle University

summary:
Analysis of early gene expression and how this correlates to MMP gene expression seen at 24 hours. The hypothesis.
Results provide important information of the early gene expression that precedes the catabolic expression of MMPs in chondrocytes.

overall_design: Total RNA obtained from human articualr chondrocytes subjected to 1, 1.25 or 24 hours stimulation by IL-1+OSM compared to unstimulated control chondrocytes.

last: Rowan

first: Chris

last: MacDonald


title: Paclitaxel resistance in triple negative breast cancer involves novel functional genomic aberrations in the ABCB1 gene.

status: Public on Feb 28 2017

city: Montreal

first: Elaheh

last: Ahmadzadeh

state: Please select

address: 3220 Ridgewood, apt 319

country: Canada

institute: McGill University

summary:
Five Triple Negative Breast Cancer cell lines were exposed to increasing concentration of Paclitaxel untill they acquired resistance. In order to identify changes in gene expression associated with resistance to PTX, we performed gene expression profiling on parental and resistant cell lines.
Of ~22000 genes surveyed by microarray analysis, 5.0%, 3.7%, 9.0%, 7.3%, and 5.4% of the genes showed changes in expression of 2-fold or greater (p value < 0.05) in BT20, SUM149, MDA-MB-231, MDA-MB-436 and MDA-MB-468 cell lines, respectively.

overall_design: Parental and resistant cells growing were seeded at a density of 0.8x106 per well in 6 well-plates and incubated without drug for 24 hours. Cells were harvested and total RNA from parental and resistant cell lines were extracted using the AllPrep DNA/RNA Mini kit. Four independent RNA extraction from different cell passage was performed for all cell lines except for MDA-MB-468. Three independent replicate is presented for MDA-MB-468 P and MDA-MB-468 R. .

first: François

last: Lefebvre


title: Expression data from Class 1 and Class 2 human Wilms tumors.

status: Public on Feb 20 2017

city: New York

first: Emily

last: Hsu

state: NY

address: 1130 St. Nicholas Ave.

department: ICG

institute: Columbia University

summary: Oncogenic stabilizing mutations in the beta-catenin gene CTNNB1 are common in one class of human Wilms tumors. To model these tumors, we crossed mice carrying an inducible Cre recombinase (Rosa26-CreERT2) with a conditional gain-of-function beta-catenin allele (Ctnnb1Ex3flox). We obtained kidneys at embryonic day 13.5 and placed them in organ culture with tamoxifen. Multiple small tumors formed in the Ctnnb1∆Ex3 kidneys while the control kidneys developed normally. Immunostaining for Sall1, a marker of condensing metanephric mesenchyme, indicated that the tumors arise from this tissue compartment, analogous to the origin of human Wilms tumors. Expression profiling identified a set of induced genes overlapping with those up-regulated in human Wilms tumors with CTNNB1 mutations, including genes encoding feedback inhibitors of Wnt/beta-catenin signaling, the epithelial-mesenchymal transition (EMT) inducers, and the transcription factor E2-2 (ITF2/TCF4). A conditional deletion of E2-2 showed that this gene is important for growth of the nephroblastomas, in part via promoting an epithelial to mesenchymal transition downstream of beta-catenin. Given these cross-species validations, and genetic proof of the oncogenic function of a key downstream target gene, we expect that this rapid and efficient organ culture model will be useful for further studies to dissect and inhibit oncogenic Wnt/beta-catenin signaling.

overall_design: The expression of 8 Class 1 Wilms tumors was compared with 5 Class 2 Wilms tumors.

first: Iveta

last: Yotova

first: Benjamin

last: Tycko


title: Autocrine Complement Inhibits IL10-Dependent T-cell-Mediated Antitumor Immunity to Promote Tumor Progression

status: Public on Mar 01 2017

first: You-Wen

last: He

address: 207 Resarch Drive

department: Immunology

summary: In contrast to its inhibitory effects on many cells, IL-10 activates CD8+ tumor infiltrating lymphocytes (TILs) and enhances their antitumor activity. However, how IL-10 globaly regualte TIL CD8+ T cell function is stil not clear. To understand the transcriptional regulation of TIL CD8+ T cell by IL-10, we performed a microarray analysis using in vitro expanded HUMAN LUNG CANCER TIL CD8 T cells with or without IL-10.

overall_design: TILs from human lung cancer were in vitro expanded as described anywhere for 20 days with 6000µ/ml rIL-2 and/or 100µ/ml rIL-10. The expanded TILs were activated by 3µg/ml anti-CD3 and anti-CD28 for 6hrs. The CD8+ TILs were enriched by negative selection kit (Stem cell).

first: Yu

last: Wang


title: Transdifferentiation Of Human Dermal Fibroblasts Towards The Cardiac Cell Lineage

status: Public on Feb 08 2017

first: Nicolas

last: Christoforou

address: 136 Hudson Hall, Box 90281

department: Biomedical Engineering

summary: Transdifferentiation has been recently described as a novel method for converting human fibroblasts into induced cardiomyocyte-like cells. Such an approach can produce differentiated cells to study physiology or pathophysiology, examine drug interactions or toxicities, and engineer tissues. Here we describe the transdifferentiation of human dermal fibroblasts towards the cardiac cell lineage via the induced expression of transcription factors (TFs) GATA4, TBX5, MEF2C, MYOCD, NKX2-5, and delivery of microRNAs miR-1 and miR-133a. Cells undergoing transdifferentiation expressed ACTN2 and TNNT2 and partially organized their cytoskeleton in a cross-striated manner. The conversion process was associated with significant upregulation of a cohort of cardiac-specific genes, activation of pathways associated with muscle contraction and physiology, and downregulation of fibroblastic markers. We used a genetically encoded calcium indicator and readily detected active calcium transients although no spontaneous contractions were observed in transdifferentiated cells. Finally, we determined that inhibition of Janus kinase 1, inhibition of glycogen synthase kinase 3, or addition of NRG1 significantly enhanced the efficiency of transdifferentiation. Overall, we describe a method for achieving transdifferentiation of human dermal fibroblasts into induced cardiomyocyte-like cells via transcription factor overexpression, microRNA delivery, and molecular pathway manipulation.

overall_design: Human dermal fibroblasts (HDFs) were induced to transdifferentiate for 2 weeks. Group 1: Cardiac TF and microRNA, Group 2: Cardiac TF only, Group 3: Control (M2rtTA only). Conversion occurred using transdifferentiation medium supplemented with JAK1 inhibitor and sodium butyrate. Total RNA was isolated using the RNeasy Mini kit (Qiagen, 74104). Its quality was assessed using the Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, Santa Clara, CA) and NanoDrop 8000 spectrophotometer (Thermo Scientific / NanoDrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX) from total RNA, hybridized to GeneChip® Human Genome U133A 2.0 arrays in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip® Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols (Affymetrix, Santa Clara, CA). This work was performed at the Duke University microarray core facility.


title: Expression data from control and drought treated wheat plants

status: Public on Feb 27 2017

city: Mohali

first: Jitendra

last: Kumar

state: Punjab

address: National Agri-Food Biotechnology Institute (Department of Biotechnology, Government of India) C-127, Industrial Area S.A.S. Nagar, Phase 8 Mohali-160071, Punjab, India

country: India

summary:
Comparative analysis of transcriptome in two wheat genotypes with contrasting levels of draught tolerance.
We used microarrays to investigate the global gene expression in response to drought stress.

overall_design: Wheat leaf tissues were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Sudhir

last: Singh


title: Active estrogen receptor-alpha signaling in ovarian cancer

status: Public on May 15 2017

city: Pittsburgh

first: Courtney

last: Andersen

state: PA

address: 204 Craft Avenue, Rm A430

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh

summary: High-grade serous ovarian cancer (HGSOC) is an aggressive disease with few available targeted therapies.  Despite high expression of estrogen receptor-alpha (ER) in ~80% of HGSOC and some small but promising clinical trials of endocrine therapy, ER has been understudied as a target in this disease.  Results: Proliferation is ER-regulated in HGSOC cells in vitro and in vivo, and is in part dependent on 3-D context.  Transcriptomic studies identified genes shared by cell lines and PDX explants as ER targets. The selective ER down-regulator (SERD) fulvestrant is more effective than tamoxifen in blocking ER action.  ER H-score was predictive of efficacy of endocrine therapy, and this prediction could be further improved by inclusion of target gene expression, especially that of IGFBP3.  Conclusion: Laboratory models corroborate intertumor heterogeneity of endocrine response in HGSOC but identify features associated with functional ER and endocrine responsiveness. Assessing ER function (e.g. IGFBP3 expression) in conjunction with ERH-score may help select patients who would benefit from endocrine therapy. Our preclinical data suggest that SERDs might be more effective than tamoxifen.

overall_design: PEO1 and PEO4 ovarian cancer cells were hormone-deprived in IMEM + 10% charcoal stripped esrum for three days.  After deprivation, cells were treated with vehicle (EtOH), 1 nM estradiol (E2), 1 uM 4-hydroxytamoxifen (Tam), 1 uM ICI182,780 (ICI), Tam + E2, or ICI + E2 for 3 hours.  Cells were lysed and RNA isolated usin gthe Illustra RNAspin Mini kit (GE).

first: Matthew

middle: J

last: Sikora

first: Michelle

middle: M

last: Boisen

first: Tianzhou

last: Ma

first: Alec

last: Christie

first: George

last: Tseng

first: Yongseok

last: Park

first: Uma

last: Chandran

first: Paul

last: Haluska

first: Gina

last: Mantia-Smaldone

first: Kunle

last: Odunsi

first: Karen

last: McLean

first: Adrian

last: Lee

first: Esther

last: Elishaev

first: Robert

last: Edwards

first: Steffi

last: Oesterreich


title: Expression data from blood of healthy controls and ns vitiligo patients

status: Public on Jan 31 2017

city: Buffalo

first: Rama

last: Dey-Rao

address: 6086 CTRC Bldg, 875 Ellicott Street

department: Dermatology

institute: University at Buffalo

summary:
Vitiligo Blood Transcriptomics Provides New Insights into Disease Mechanisms and Identifies Potential Novel Therapeutic Targets Abstract   Background: Significant gaps remain regarding the pathomechanisms underlying the autoimmune response in vitiligo (VL), where the loss of self-tolerance leads to the targeted killing of melanocytes. Specifically, there is incomplete information regarding alterations in the systemic environment that are relevant to the disease state.  Methods: We undertook a genome-wide profiling approach to examine gene expression in the peripheral blood of VL patients and healthy controls in the context of our previously published VL-skin gene expression profile. We used several in silico bioinformatics-based analyses to provide new insights into disease mechanisms and suggest novel targets for future therapy.   Results: Unsupervised clustering methods of the VL-blood dataset demonstrate a “disease-state”-specific set of co-expressed genes. Ontology enrichment analysis of 99 differentially expressed genes (DEGs) uncovers a down-regulated immune/inflammatory response, B-Cell antigen receptor (BCR) pathways, apoptosis and catabolic processes in VL-blood. There is evidence for both type I and II interferon (IFN) playing a role in VL pathogenesis. We used interactome analysis to identify several key blood associated transcriptional factors (TFs) from within (STAT1, STAT6 and NF-kB), as well as “hidden” (CREB1, MYC, IRF4, IRF1, and TP53) from the dataset that potentially affect disease pathogenesis. The TFs overlap with our reported lesional-skin transcriptional circuitry, underscoring their potential importance to the disease. We also identify a shared VL-blood and -skin transcriptional “hot spot” that maps to chromosome 6, and includes three VL-blood dysregulated genes (PSMB8, PSMB9 and TAP1) described as potential VL-associated genetic susceptibility loci. Finally, we provide bioinformatics-based support for prioritizing dysregulated genes in VL-blood or skin as potential therapeutic targets.   Conclusions: We examined the VL-blood transcriptome in context with our (previously published) VL-skin transcriptional profile to address a major gap in knowledge regarding the systemic changes underlying skin-specific manifestation of vitiligo. Several transcriptional “hot spots” observed in both environments offer prioritized targets for identifying disease risk genes. Finally, within the transcriptional framework of VL, we identify five novel molecules (STAT1, PRKCD, PTPN6, MYC and FGFR2) that lend themselves to being targeted by drugs for future potential VL-therapy.
We used microarrays to detail the global programme of gene expression underlying the disease state in vitiligo and established differentially expressed genes by comparing gene expression values from diseased patients to healthy controls.

overall_design: Blood was drawn from vitiligo patients and healthy controls (Weill Cornell Medical College Institutional Review Board: WCM IRB # 0998-398) for RNA extraction from sepearted PBMCs and subseuent hybridization on Affymetrix microarrays.  We sought to compare normalized, background subtracted genome-wide gene expression values between patients and controls and to that end conducted microarray experiments. The patients and controls were not undergoing any therapy during sampling and the patients were clearly diagnosed with ns vitiligo in the clinic.

first: A

last: Sinha


title: Identification of potential ABBV-075 responsive markers in human PBMCs

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

summary: To identify genes that are modulated by BET inhibitors in blood, we determined global gene expression changes in ABBV-075-treated human PBMC samples

overall_design: Freshly isolated human PBMC cells from 5 donors were treated with DMSO or 0.2 uM ABBV-75 (triplicates for each treatment).  Samples were collected 6 hours post treatment and subjected to total RNA extraction and miroarray analysis.

last: Hessler

first: Xiaoyu

last: Lin

first: Xiaoli

last: Huang


title: Association of Interferon- and Transforming Growth Factor  -Regulated Genes and Macrophage Activation With Systemic Sclerosis-Related Progressive Lung Fibrosis

status: Public on Jan 01 2017

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

summary: OBJECTIVE: Systemic sclerosis (SSc)-related interstitial lung disease (ILD) is one of the leading causes of mortality. We undertook this study to analyze the gene expression of lung tissue in a prospective cohort of patients with SSc-related ILD and to compare it with that in control lungs and with 2 prospective clinical parameters in order to understand the molecular pathways implicated in progressive lung disease.  METHODS: Lung tissue was obtained by open lung biopsy in 28 consecutive patients with SSc-related ILD and in 4 controls. High-resolution computed tomography (HRCT) and pulmonary function testing (PFT) were performed at baseline and 2-3 years after treatment based on lung histologic classification. Microarray analysis was performed, and the results were correlated with changes in the HRCT score (FibMax) and PFT values. Quantitative polymerase chain reaction (qPCR) and immunohistochemistry were used to confirm differential levels of messenger RNA and protein.  RESULTS: Lung microarray data distinguished patients with SSc-related ILD from healthy controls. In the lungs of patients with SSc-related ILD who had nonspecific interstitial pneumonia (NSIP), expressed genes included macrophage markers, chemokines, collagen, and transforming growth factor β (TGFβ)- and interferon (IFN)-regulated genes. Expression of these genes correlated with progressive lung fibrosis defined by the change in FibMax. Immunohistochemistry confirmed increased markers of collagen (COL1A1), IFN (OAS1 and IFI44), and macrophages (CCL18 and CD163), and the positive correlation with the change in FibMax was confirmed by qPCR in a larger group of SSc patients with NSIP. Several genes correlated with both the change in FibMax (r > 0.4) and the change in % predicted forced vital capacity (r < -0.1), including IFN and macrophage markers, chemokines, and heat-shock proteins.  CONCLUSION: These results highlight major pathogenic pathways relevant to progressive pulmonary fibrosis in SSc-related ILD: macrophage emigration and activation, and up-regulated expression of TGFβ- and IFN-regulated genes

overall_design: Gene expression from lung biopsies was measured in 7 patients with SSc-ILD and 4 controls

first: Romy

last: Christmann

last: Lafyatis


title: Role of DLX3 in primary human keratinocytes

status: Public on Feb 09 2017

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary:
DLX3 is expressed by differentiated cells in human skin and it has a functional role in epidermal maturation.
We used microarray data analysis to assess gene expression in keratinocytes as consequence of DLX3 expression. We identified  a specific subset of genes which are involved in cell cycle regulation and modulate the differentiation program in epidermal cells.

overall_design: Normal human epidermal keratinocytes (NHEK) were isolated from foreskin and maintained in proliferating media. Cells were transfected with a retroviral vector expressing DLX3 (DLx3/Flag). No transduced keratinocytes (KERA) or Empty Vector (VECTOR) transduced cells were considered as controls. RNA samples were collected 24 hours later used for hybridization on Affymetrix microarrays.

first: E

last: Palazzo

first: M

last: Kellett

first: C

last: Cataisson

last: Gormley

first: P

last: Bible

first: V

last: Pietroni

first: N

last: Radoja

first: J

last: Hwang

last: Blumemberg

first: S

last: Yuspa

last: Morasso


title: Identification of genes that are modulated by BET inhibitors in cancer cells to identify robust pharmacodynamic marker for monitoring target engagement of BET family bromodomain inhibitors in tumors and surrogate tissue

last: Lu

summary: Competitive inhibitors of acetyl-lysine binding to the bromodomains of the BET (bromodomain and extra terminal) family are being developed for the treatment of solid and heme malignancies.  BET family member BRD4 function at enhancers/super-enhancers has been shown to sustain signal-dependent or pathogenic gene expression programs.

overall_design: Microarray study which included biological triplicates of the DMSO (Vehicle), MS417 (BETi) and C1 3 and 6 hr treated MiaPaCa-2 and NCI-H1299 cell line samples (n=36).  C1 treatment is included as a inactive compound for the BETi.

first: Lisa

last: Roberts-Rapp

first: Tamar

last: Uziel


title: Digital Restriction Enzyme Analysis of Methylation (DREAM) of normal colon genomic DNA.

city: Philadelphia

first: Takahiro

last: Sato

address: 3307 North Broad Street

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

summary: We analyzed levels of 5-methyl cytosine nnnn CCCGGG target sites by sequential restriction digest by SmaI and XmaI enzymes, ligating Illumina adaptors to the restriction fragments and reading methylation-specific signatures at the ends of restriction fragments by paired ends Illumina high throughput sequencing.

overall_design:
Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of normal colon genomic DNA. Genomic DNA spiked in with unmethylated, partially methylated and fully methylated standards was sequentially cut at CCCGGG sites with the methylation-sensitive enzyme SmaI (blunt ends) and its methylation-tolerant neoschizomer XmaI (5'CCGG overhangs), creating different end sequences that represented methylation status of the CCCGGG sites. These end sequences were analyzed by Illumina high throughput sequencing. Methylation status at individual CCCGGG sites across the genome was determined by counting the methylated reads with the CCGGG signature and unmethylated reads with the GGG signature at the beginnings of the sequencing reads after alignment to the human genome.
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This record is incomplete: Submitter cannot locate the raw data.

first: Matteo

last: Cesaroni

first: Shoghag

last: Panjarian

first: Anthony

last: Tran

first: Jozef

last: Madzo

first: Yasuyuki

last: Okamoto

first: Hanghang

last: Zhang

first: Xiaowei

last: Chen

first: Jaroslav

last: Jelinek

first: Jean-Pierre

last: Issa


title: Gene expression profiles of NCI-H929 cells after knockdown of RRM1 and RRM2

city: Boston

first: Mehmet

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Purpose: Overexpression or polymorphisms of ribonucleotide reductase (RR) are described in many solid tumors, and its expression is highly correlated with survival. However, the biologic significance in multiple myeloma (MM) has not yet been elucidated. Here, we identify the role of RR in MM pathogenesis.   Experimental Design: Here we studied the potential utility of RRM1 knockdown effect in multitple myeloma in vitro and in vivo.  Results: Knockdown of RRM1 (large subunit) triggered significant growth inhibition, associated with apoptotic cells death, in MM cells, regardless of the existence of bone marrow microcnrivonment. To validate the role of RRM1 of xenograft model, tumor growth was significantly reduced in RRM1-knocked-down MM cells versus control MM cells. Gene expression profiling showed that p53 regulated genes were upregulated after RRM1 knockdown. Immunoblot and QRT-PCR validated that p53 pathways were acviated as well. Clofarabine (CLO), a purine nucleoside analog which inhibits both DNA polymerases and RRM1, is a potential therapeutic agent in MM. CLO induced growth arrest in p53 wild-type cell lines, but not in p53 mutant or null cells. Moreover, CLO treatment with combined with DNA damaging agents triggered synergetic cell death even in p53 mutant MM cells.   Conclusions: Our results therefore demonstrate that RRM1 is a novel therapeutic target in patients with MM, and provide the basis for clinical evaluation of RRM1 inhibitor, alone or in combination with DNA damaging agents, to improve patient outcome.

overall_design: Myeloma cell line (NCI-H929) was transduced with either siRNAs targeting RRM1, RRM2 or scramble (control) in duplicate. The gene expression profiles of RRM1 and RRM2 knockdown cells were compared with that of control cells. A total of 6 RNA samples (2 RRM1 knockdown, 2 RRM2 knockdown, and 2 control) were analyzed.

first: M

last: Sagawa

middle: K

last: Munshi

first: T

last: Hideshima

first: K

last: Anderson


title: A Molecular Profile of Colorectal Cancer to Guide Therapy [HMEC]

status: Public on Dec 31 2016

first: David

last: Hsu

address: 905 S. LaSalle St. Rm 3008

department: Medical Oncology

summary: Here we describe the generation and application of a gene expression signature for the Rheb pathway.   Affymetrix array data obtained from human mammary epithelial cells over expressing Rheb or GFP were used to generate a Rheb/mTOR activation signature.  To test the capacity of the signature to predict patient response to everolimus we treated patient-derived colorectal cancer explants (PDCCEs) predicted to have high and low Rheb pathway activity withthe mTOR inhibitor everolimus.

overall_design: This study utilized a total of 20 affymetrix data files generated from 20 independent human mammary epithelial cell culture samples treated with adenovirus overexpressing either Rheb (n=10) or GFP (n=10). From these data, a Rheb gene expression signature was created and used to predict Rheb/mTOR activity in patient derived colorectal cancer explants (PDCCEs).  PDCCEs were then tested for response to the mTOR inhibitor everolimus.

first: Joshua

last: Uronis

first: Jeffrey

last: VanDeusen

first: Ellie

last: Proussaloglou

first: Takuya

last: Osada

first: Xiao

middle: Y

last: Yang

first: Christopher

last: Mantyh

first: Michael

last: Morse

first: H

last: Lyerly

first: Bryan

last: Clary

last: Gatza

last: Datto

last: Chang


title: caArray_willm-00144: Gene Expression Profiling for Molecular Classification and Outcome Prediction in Infant Leukemia Reveals Novel Biologic Clusters and Pathways for Treatment Failure

status: Public on Dec 23 2016

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: 126 infant leukemia cases registered to NCI-sponsored Infant Oncology Group/Children's Oncology Group treatment trials were studied using oligonucleotide microarrays containing 12,625 probe sets (Affymetrix U95Av2 platform)

overall_design:
willm-00144
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG_U95Av2
Organism: Homo sapiens (ncbitax)
Material Types: synthetic_RNA, whole_organism, total_RNA
Disease States: leukemia


title: Artesunate shows potent anti-tumor activity in B-cell lymphoma by inducing ER-stress response

status: Public on Feb 07 2017

city: Oslo

first: Thea

middle: Kristin

last: Vatsveen

address: Ullernschauseen 70

department: Cancer Research

institute: Oslo University Hospital

overall_design: Total RNA was isolated using MiRNeasy (Qiagen, Hilden, Germany) after 4 and 12 h treatment with artesunate (5 µM) in BL-41, Oci-Ly-2 and SU-DHL-4. D1 and d3 refer to technical replicates. The microarray analyses were performed on Illumina’s HumanHT-12 v4 Expression BeadChip platform (Illumina, San Diego, CA). The differential gene expression analysis was done using the limma package 26 in R (version 3.3.1). The differentially expressed genes were selected based on two criteria: a log fold change larger than the absolute value of 0.5, and an adjusted p-value (FDR) of less than 0.01. The probes were collapsed according to gene symbol, using the annotation file for the Illumina’s HumanHT-12 v4 Expression BeadChip platform. When several probes mapped to the same gene on the Microarray, the probe with lowest log fold change was selected. The pathways and networks most enriched for the differentially expressed genes were identified running by Ingenuity Pathway Analysis (IPA) software (Qiagen) with default settings.

last: Våtsveen

first: Marit

last: Myhre

first: Chloé

last: Steen

first: Sébastien

last: Wälchli

first: Ole

middle: C

last: Lingjærde

first: Baoyan

last: Bai

first: Toril

last: Holien

first: Anders

last: Sundan

first: Else

last: Inderberg

first: Erlend

last: Smeland

first: June

last: Myklebust

first: Morten

last: Oksvold


title: Expression data of differentially regulated genes in ESR1 depleted human endometrial stromal cells during differentiation.

status: Public on Dec 22 2016

city: Urbana

first: Milan

last: Bagchi

address: 407 S. Goodwin Ave

department: MIP

institute: UIUC

summary:
Estrogen and progesterone are important regulators of human endometrial differentiation. These steroid hormones act, at least in part, through their nucelar receptors. Role of estrogen receptor alpha (ESR1) during human endometrial differentiation is still unclear.
We used microarray analysis to detail the gene expression regulated by ESR1 during differentiation of human endometrial stromal cells.

overall_design: Human endometrial stromal cells were transfected with nontargeting control siRNA or siRNA targeting ESR1 for 48h. Then, cell were  treated with differentiation cocktail composed of estrogen, progesterone and a cAMP analog. At 24 hours, total RNA was isolated and used for microarray analysis.

first: Hatice

last: Kaya


title: Gene expression profiles of MCF7 cells treated with traditional Chinese medicine components

status: Public on Mar 26 2017

city: Shanghai

first: chao

last: lv

state: None Selected

address: No. 325, Guohe Rd

department: School of Pharmacy

institute: Second Military Medical University

summary:
At present, the DNA microarray application to study traditional Chinese medicines (TCMs) has received more and more attention. Furthermore, kinds of TCMs were too large, and ingredients in TCMs were also extremely abundant, which afforded an extraordinary source for drug development. To pursue a suitable approach on the research of TCM components, we produced gene expression profiles of 102 TCM ingredients treating MCF7 cells. All selected molecules were main ingredients in Chinese herb and TCM formula. In addition, the gene expression profiles data can be analyzed in combination with public database connectivity map (CMAP) and other bioinformatics methods, which could identify the underlying pharmacological mechanisms and molecular targets/pathway of numerous components.
This study indicated that the gene expression profiles data of TCM components was a very convenient and useful approach for researchers engaged in study of TCMs.

overall_design: Currently, we produced the gene expression profiles of MCF7 cells to 102 different molecules in TCMs, vehicle control (DMSO), and mixture of four compounds (tanshinone IIA, salvianic acid A sodium, protocatechuic aldehyde, salvianolic acid B). Two biological replicates for each group and the data set includes profiles for 212 samples.

first: Chao

last: Lv

first: Xueting

last: Wu

first: Xia

last: Wang

first: Juan

last: Su

first: Huawu

last: Zeng

first: Shan

last: Lin

first: Runhui

last: Liu

first: Xuan

last: Li

first: Honglin

first: Weidong

last: Zhang


title: Expression data from side population cells of the human OSCC cell line SCC172

city: Thiruvananthapuram

first: Vinitha

last: Richard

state: Kerala

address: Thycaud P.O.

department: Cancer Research Program

institute: Rajiv Gandhi Centre for Biotechnology

summary: A cancer stem cell cannot be identified solely based on surface markers as none of the markers used to isolate stem cells in various normal and cancerous tissues is expressed exclusively by stem cells. Our experimental results have also identified additional fractions representing true stem-like cells in oral squamous cell carcinoma (OSCC), refuting the concept that cancer stem cells (CSCs) are a rare population, and we have also developed an in vitro model to explore the stem cell concept in oral epithelial tumorigenesis. This model expounds four distinct fractions within a homogenous cell line SCC172 that is morphologically similar (85% cells expressing CSC markers), yet varying in all functional aspects of cell cycle, dye retention, chemoresistance, tumor-forming potential, self renewal, apoptosis resistance and regulation at molecular levels. Relating to our CSC shift model, we analysed the concept of biological heterogeneity in terms of four fractions SP1, SP2, MP1 and MP2 and associated it with variations among patients in a clinical scenario.

overall_design: We used microarray expression profiling to determine the transcriptional profiles of representative tumorigenic SP1 and non-tumorigenic non-SP/MP1 fractions. Three batches of approximately 6x10^5 of SP1 and non-SP (MP1) cells were sorted by flow cytometry on different days as biological replicates after ensuring maximum resort purity. Only two SP1 replicates are included in this submission.

first: M

last: Pillai


title: Expression data from A549 lung adenocarcinoma cells and TUSC3 knocked out A549 cells

city: Austin

first: Bum-Kyu

last: Lee

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

summary:
Cancer metastasis is a multistep processes based on reciprocal interanctions between tumor cells and their surroundings. From this experiments, we aim to investigate the contribution of TUSC3 deficency in lung cancer metastasis.
We performed gene expression transcriptome analysis to identify genes and/or noncoding RNAs regulated by TUSC3 gene

overall_design: The A549 TUSC3 knockout cells were generated by a CRISPER knockout construct and then control cells or the knockout cells were stimulated by Tunicamycin, an ER stress inducer. After that, the cells were harvested and preapred for the analysis

first: Young-Jun

last: Jeon

first: Carlo

last: Croce


title: Genome wide gene-expression analysis of the spider mite Tetranychus urticae after transfer from their common host (bean) to either cotton, maize or soy

status: Public on Oct 10 2016

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

summary:
A genetically diverse strain (labelled as London) of the phytophagous mite Tetranychus urticae was transferred from its common host (bean) to other host plants (cotton, maize or soy).
Three different host plant species were included in the experimental set-up: cotton (Gossypium spp.), maize (Zea mays cv. Ronaldinio) and soy (Glycine max cv. Merlin). Five generations after host-transfer, total RNA of all mite populations (London, London-SOY, London-MAIZE and London-COTTON) was collected and used in a genome-wide gene expression microarray (Sureprint G3 microarray, Agilent)
Microarray analysis revealed large-scale differential expression of genes coding for enzymes of detoxification families, secreted proteins with unknown functions and regulatory enzymes.

overall_design: Three major comparisons were investigated: 4 biological replicates of soy adaptation (London-SOY vs London), 4 biological replicates of maize adaptation (London-MAIZE vs London) and 3 biological replicates of cotton adaptation (London-COTTON vs London).

first: Wim

last: Jonckheere

first: Wannes

last: Dermauw

first: Thomas

last: Van Leeuwen


title: Serum miRNA in liver disease

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary:
Aiming to develop novel biomarker for cancer prediction after surgical resection
In title X-Y: X represents a patient number. Y represents the order in which the blood was collected during surgical treatment.

overall_design: 98 HCC related patients

first: Yoshiki

last: Murakami

first: Saori

last: Itami


title: Expression data from primary human hepatocyte oxygenated co-cultures infected by HCV and human liver biopsies from HCV patients.

status: Public on Oct 07 2016

city: Cambridge

first: Naomi

last: Habib

state: MA

address: 75 Ames st

department: Zhang

institute: Broad Institute

summary:
Viruses lack the basic machinery needed to replicate and therefore must hijack host metabolism to propagate. Virus-induced metabolic alterations have yet to be systematically studied in the context of the host transcriptional regulation, offering insight into host-pathogen metabolic interplay. In this work we identified Hepatitis C Virus (HCV)-responsive regulators by coupling system-wide metabolic flux analysis with targeted perturbation of nuclear receptors in primary human hepatocytes. We find HCV-induced up-regulation of glycolysis, ketogenesis and drug metabolism, controlled by activation of HNF4α, PPARα, FXR and PXR, respectively. Pharmaceutical inhibition of HNF4α reversed HCV-induced glycolysis, blocking viral replication while increasing apoptosis in infected cells showing a viral-induced dependence on glycolysis. In contrast, pharmaceutical inhibition of PPARα or FXR reversed HCV-induced ketogenesis, but increased viral replication demonstrating a unique host anti-viral response. Our results show that viral-induced changes to host metabolism can be detrimental to its lifecycle demonstrating a distinct biological complexity.
In this dataset, we include the expression data obtained from primary human hepatocyte oxygenated co-cultures infected or not infected by HCV and human sanp frozen liver biopsys from HCV patients at earley stages.

overall_design: We compared the 4 naïve and HCV-infected primary hepatocytes samples, and compared the 5 human liver biopsy samples to 19 normal liver samples from GSE14323.

first: Yaakov

last: Nahmias


title: Expression data of U2OS ER-HA-E2F1 cells induced by OHT with and without knockdown of NFYB

status: Public on Sep 09 2016

city: Durham

first: Jen-Tsan

last: Chi

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

summary:
E2F1 induces numerous genes, including transcription factors, upon activation. The transcription factors then further cooperates with E2F1 to regulate the target genes and enhance the transcriptional effect.
We used microarrays to analyze genes upregulated upon E2F1 activation by OHT with and without knockdown of NFYB and identified genes that are targets of both transcription factors.

overall_design: NFYB was knocked down by siRNA by transfection. Cells were serum starved for 24 hours before induction of E2F1 by 80nM OHT. Samples were collected before induction and at 4 and 8 hours after induction

first: Xiaolei

last: Jiang

first: Igor

last: Shats


title: Microarray analysis of gene expression from inoculated wheat leaves by XT4699, XT-Rocky and XT 4699hrcC-

status: Public on Oct 05 2016

city: Manhattan

first: Sanzhen

last: Liu

state: KANSAS

address: 4024 Throckmorton Plant Sciences Ce

department: Plant Pathology

institute: Kansas State University

summary:
TAL effectors are special family of type III effectors which can activate host gene expression at transcriptional level. The different induced genes in inoculated wheat leaves of wild type strain vs type III mutant are potential targets of TAL effectors.
We observed around 250 differently induced genes (>10 fold) in the microarray analysis of gene expression of inoculated samples by XT4699 vs XT4699hrcC-

overall_design: Microarray analyses of wheat leaf samples that were inoculated with strains XT4699 (wild type), XT-Rocky (wild type), and XT4699hrcC- (type III mutant of XT4699) were performed to identify changes in host gene expression.  First fully expanded leaves of 10-day-old ‘Chinese Spring’ wheat plants were inoculated with three different bacterial suspensions (XT4699, XT-Rocky, XT4699hrcC-) with optical density of 0.5 at 600 nm using a needleless syringe. RNA samples were isolated 24 h after inoculation using Trizol reagents (Invitrogen) as described by the manufacturer. Three biological replicates (pooled from three independently inoculated leaves) were used for each treatment.

first: Frank

last: White

first: Zhao

last: Peng

first: Ying

last: Hu


title: Large scale analysis of apple development within HIVW apple progeny

status: Public on Sep 26 2016

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

institute: IRHS

summary: Based on sensorial analysis, 8 apple genotypes with contrasted fruit texture for mealiness were selected among a progeny. Apple samples were collected at 60 days after flowering (60DAF), 110 days after flowering (110DAF), harvest (Rec), and after 1 or 2 months of cold storage (1M and 2M respectively).

overall_design: The 8 apple hybrids were analysed in 38 dye-swap made of 4 mealy vs non-mealy pairs (I062 vs V083, W029 vs V034, H097 vs I095, I016 vs H74) for each time point (60DAF, 110DAF, Rec, 1M, 2M) when possible. Biological replicates are fruits from 2 plots (PH and P12).

first: Emmanuelle

last: Dheilly

first: Marie-Charlotte

last: Guillou

first: Jean-Pierre

last: Renou

last: Orsel


title: Expression profiles in CD44- and CD44+ hepatocellular carcinoma HuH7 cells  Sep 01, 2016   pending   None

status: Public on Sep 01 2016

city: Yonago

first: Tomohiko

last: Sakabe

state: Tottori

address: Nishi-cho 86

institute: Tottori University

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

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

overall_design: Refer to individual Series


title: caArray_willm-00090: Gene Expression Profiling Reveals Novel Genes for Improved Risk Classification and Outcome Prediction in Pediatric Acute Lymphoblastic Leukemia: Identification, Cloning, and Validation of OPAL1

first: Mervi

last: Heiskanen

summary: Affymetrix HG_U95Av2 oligonucleotide microarrays were used to perform gene expression profiling of 254 cases of pediatric ALL in order to determine genes predictive of outcome that may be useful in refining risk classification.

overall_design:
willm-00090
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG_U95Av2
Organism: Homo sapiens (ncbitax)
Material Types: synthetic_DNA, synthetic_RNA, organism_part, whole_organism
Disease States: Pre-treatment leukemia diagnostic sample


title: A Window of Opportunity Study of Valproic Acid in Breast Cancer Testing a Gene Expression Biomarker

status: Public on Dec 17 2016

city: Salt Lake City

first: Adam

last: Cohen

state: Utah

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute, University of Utah

summary:
Purpose: Valproic acid(VPA) has anti-cancer activity attributed to histone deacetylase inhibition(HDACi). We published the Genomically–Derived Sensitivity Signature for VPA(GDSS-VPA), a gene expression biomarker predicting breast cancer sensitivity to VPA in vitro and in vivo.  We conducted a window-of-opportunity study examining the tolerability of VPA and the ability of the GDSS-VPA to predict biologic changes in breast tumors from VPA.
Methods: Eligible women had untreated breast cancer with breast tumors over 1.5 cm.  After a biopsy, women took VPA for 7-12 days, increasing from 30mg/kg/day PO divided BID to a maximum of 50mg/kg/day.  After VPA treatment, serum VPA level was measured followed by breast surgery or a biopsy.  Tumor proliferation was assessed by Ki-67 immunohistochemistry. Peripheral blood mononuclear cells(PBMCs) histone acetylation was assessed by Western blot.
Results:  Thirty women were evaluable.  The median age was 54(range 31-73).  52% of women tolerated 50mg/kg/day, but 10% missed more than two doses due to adverse events(AEs).  Grade 3 AEs included one patient with vomiting and diarrhea and one with fatigue.  The end serum VPA level correlated with change in PBMC histone acetylation(rho=0.451, p=0.024).  50% of women with triple-negative breast cancer(TNBC) had a Ki-67 reduction of at least 10%, compared with 17% of other women.   GDSS-VPA correlated with a Ki-67 decrease of at least 10%(AUC 0.66).
Conclusions:  Most women tolerate VPA. VPA treatment caused a decrease in proliferation of breast tumors. The genomic biomarker correlated with decreased proliferation. HDACi is a valid strategy for drug development in TNBC using gene expression biomarkers.

overall_design: RNA was extracted from breast tumors before and after treatment for 7-12 days with valproic acid

middle: L

first: Andrea

last: Bild


title: mRNA profile of CD8 T cells from chronic HBV patients

status: Public on Jul 01 2016

first: You-Wen

last: He

address: 207 Resarch Drive

department: Immunology

summary:
The low frequency of HBV-specific CD8+ T cells in the peripheral blood of CHB patients has limited studies of the mechanisms underlying HBV-induced T cell exhaustion. Similar to the expansion defect displayed in HBV-specific CD8+ T cells, TCR-induced proliferation of global CD8+ T cells is impaired in a fraction of chronic HBV (CHB) patients. Thus, examining the molecular regulation of global CD8+ T cell function in CHB patients may provide insight into the exhaustion of HBV-specific CD8+ T cells.
We used microarrays to detail the global programme of gene expression of CD8 T cells from CHB patients who have not received anti-viral treatment.

overall_design: Fifteen milliliters of blood was drawn from eachof three CHB patients and three healthy donors. PBMCs were enriched using Ficoll, and CD8+ T cells were purified using positive selection beads to a purity of >95% (Miltenyi Biotec, Auburn, CA). Total RNA was extracted using a mirVana isolation kit (Life Technologies, Carlsbad, CA).

first: Yu

last: Wang


title: Chromatin accessibility maps of chronic lymphocytic leukemia identify subtype-specific epigenome signatures and transcription regulatory networks

status: Public on Jun 26 2016

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ATAC-seq assay, and we also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting dataset, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations. Our analysis identified sample-specific variation on top of a shared core of CLL regulatory regions. IGHV mutation status – which distinguishes the two major subtypes of CLL – was accurately predicted by the chromatin profiles, and gene regulatory networks inferred for IGHV-mutated vs. IGHV-unmutated samples identified characteristic differences between these two disease subtypes. In summary, we found widespread heterogeneity in the CLL chromatin landscape, established a community resource for studying epigenome deregulation in leukemia, and demonstrated the feasibility of chromatin accessibility mapping in cancer cohorts and clinical research.

overall_design:
Genome-wide profiling of chromatin states and gene expression levels in 88 CLL samples from 55 individuals gave rise to 88 ATAC-seq profiles, 40 ChIPmentation profiles (10 samples, each with 3 different antibodies and matched immunoglobulin control), and 10 RNA-seq profiles.

Raw sequence data has been deposited at the EBI's European Genome-phenome Archive (EGA) under the accession number EGAS00001001821 (controlled access to protect patient privacy).

first: Andre

middle: F

last: Rendeiro

first: Christian

last: Schmidl

first: Jonathan

last: Strefford

first: Renata

last: Walewska

first: Zadie

last: Davis

first: Matthias

last: Farlik

first: David

last: Oscier


title: Circulating microRNA profiles in patients with type-1 autoimmune hepatitis

status: Public on Aug 01 2016

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

summary: Recent studies have demonstrated that micro (mi)RNA molecules can be detected in the circulation and can serve as potential biomarkers of various diseases. This study used microarray analysis to identify aberrantly expressed circulating miRNAs in patients with type 1 autoimmune hepatitis (AIH) compared with healthy controls. Patients with well-documented and untreated AIH were selected from the National Hospital Organization (NHO)-AIH-liver-network database. They underwent blood sampling and liver biopsy with inflammation grading and fibrosis staging before receiving treatment. To further confirm the microarray data, circulating expression levels of miR-21 and miR-122 were quantified by real-time quantitative polymerase chain reaction in 46 AIH patients, 40 patients with chronic hepatitis C (CHC), and 15 healthy controls. Consistent with the microarray data, serum levels of miR-21 were significantly elevated in AIH patients compared with CHC patients and healthy controls. miR-21 and miR-122 serum levels correlated with alanine aminotransferase levels. Circulating levels of miR-21 and miR-122 were significantly reduced in AIH patients with liver cirrhosis, and were inversely correlated with increased stages of fibrosis. By contrast, levels of circulating miR-21 showed a significant correlation with the histological grades of inflammation in AIH. We postulate that aberrantly expressed serum miRNAs are potential biomarkers of AIH and could be implicated in AIH pathogenesis. Alternations of miR-21 and miR-122 serum levels could reflect their putative roles in the mediation of inflammatory processes in AIH.

overall_design: Case-control study, steroid treatment

first: K

last: Migita


title: microRNA expression profiles in CD44- and CD44+ hepatocellular carcinoma HuH7 cells

summary: To investigate the significance of CD44+ hepatocellular carcinoma (HCC) HuH7 cells, microRNA (miRNA) expression profiles of CD44-positive HuH7, CD44-negative HuH7, and human nomal hepatocyes were analyzed. Results provide the insight into the significance of CD44-positive HCC cells as the liver CSCs.

overall_design: CD44-positive and CD44-negative HuH7 cells were sorted by flow cytometry. Total RNA were extracted from CD44-positive HuH7, CD44-negative HuH7 cells, and human normal hepatocytes. Total RNA isolated from each cell labeled using 3D-Gene miRNA labeling kit (TORAY) and hybridized onto the 3D-Gene human miRNA V20 (TORAY).

first: Goshi

last: Shiota


title: Implementing whole genome array for clinical use in academic centers: A randomized trial comparing neoadjuvant standard chemotherapy to genomic-driven chemotherapy in operable breast cancer (REMAGUS04 trial)

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary:
REMAUS04 is a phase III trial comparing DNA array-based chemotherapy (by DLD30 score and TOP2A expression) to standard neoadjuvant chemotherapy, in patients with HER2-negative breast carcinoma not eligible for conserving surgery.
We evaluated whether whole genome array approach is feasible in daily practice, and if the use of a genomic score (DLD30/TOP2A) improves chemotherapy efficacy.

overall_design: DNA arrays were performed within 15 days after tumor biopsy. Only samples with >30% cancer cells, a RIN>6 and good cDNA quality were eligible for hybridization on arrays U133Av2.

first: Monica

last: ARNEDOS

first: Marie-Eglantine

last: DUJARIC

first: Florence

last: LEREBOURS

first: Samar

last: ALSAFADI

last: GENTIEN

first: Suzette

last: DELALOGE

first: Philippe

last: VIELH

first: Audrey

last: RAPINAT

first: Emmanuel

last: BARILLOT

first: Fabien

last: VALET

first: Etienne

last: BRAIN

first: Brigitte

last: SIGAL-ZAFRANI

first: Fabrice

last: Andre

first: Jean-Yves

last: Pierga


title: Effects of starter microbiota and early life feeding of medium chain triglycerides on the gastric transcriptome profile of 3 weeks old caesarean derived pigs

status: Public on Sep 21 2016

city: bologna

first: PAOLO

middle: o

last: BOSI

state: BOLOGNA

address: Viale Fanin, 46

department: DISTAL

institute: UNIVERSITY OF BOLOGNA

summary:
An early settlement of a complex gut microbiota can protect against gastro-intestinal dysbiosis, but the effects of neonatal microbiota colonization and early life feeding of medium chain triglycerides on the maturation of the porcine gastric mucosa are largely unknown.
The transcriptome of the oxyntic mucosa of  24 caesarian-derived pigs previously associated with microbiota of different complexity and fed a diet fortified or not with medium chain fatty acids was studied.
Pigs received pasteurized sow colostrum at birth (d0), 2 mL of starter microbiota (10^7 CFU of each Lactob. Amylovorus (LAM), Clostr. glycolicum, and Parabacteroides spp.) on d1-d3 of age and either a placebo inoculant (simple association, SA) or an inoculant consisting of diluted feces of an adult sow (complex association, CA) on d3-d4 of age. Then  half of pigs was fed a moist diet (CON) or, for the remaining half, CTRL fortified in medium chain triglycerides with 7% coconut oil ( MCT). Gastric samples were obtained at on euthanised pigs at 3 weeks of age.

overall_design: The analysis of whole mRNA transcript expression was done by Affymetrix©Porcine Gene 1.1 ST array strips, a Robust Multichip Analysis was performed on the CEL files, and Transcripts ID’s were associated to human gene names, based on Sus scrofa Ensemble.

first: Paolo

last: Trevisi

first: Davide

last: Priori

first: Vincezo

last: Motta

first: Diana

last: Luise

first: Alfons

last: Jansman

first: Sietse-Jan

last: Koopmans

last: Bosi


title: Effects of starter microbiota on the gastric transcriptome profile of 2 weeks old caesarean derived pigs

summary:
An early settlement of a complex gut microbiota can protect against gastro-intestinal dysbiosis, but the effects of neonatal microbiota colonization on the maturation of the porcine gastric mucosa are largely unknown.
The transcriptome of the oxyntic mucosa of  12 caesarian-derived pigs previously associated with microbiota of different complexity  was studied.
Pigs received sow blood serum at birth (d0), 2 mL of starter microbiota (10^7 CFU of each Lactob. Amylovorus (LAM), Clostr. glycolicum, and Parabacteroides spp.) on d1-d3 of age and either a placebo inoculant (simple association, SA) or an inoculant consisting of diluted feces of an adult sow (complex association, CA) on d3-d4 of age. Then   pigs were fed a moist diet . Gastric samples were obtained at on euthanised pigs at 2 weeks of age.

overall_design: The analysis of whole mRNA transcript expression was done by Affymetrix©Porcine Gene 1.1 ST array strips, a Robust Multichip Analysis was performed on the CEL files, and Transcripts ID’s were associated to human gene names, based on Sus scrofa Ensemble