title: Inhibitor of apoptosis protein antagonist BV6 – potential for new combinatorial treatment strategies in acute myeloid leukemia

status: Public on Dec 31 2014

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary: Apoptosis is deregulated in most, if not all, cancers, including hematological malignancies. In this study, we wanted to test whether primary acute myeloid leukemia (AML) samples are sensitive for inhibitor of apoptosis (IAP) protein antagonist treatment in vitro, and which AML subgroup might profit most from such a novel therapeutic strategy. We treated diagnostic samples of 67 adult AML patients with either cytarabine (ara-C) or IAP antagonist BV6 and correlated sensitivity with clinical, cytogenetic and molecular markers, and expression levels of selected genes involved in apoptosis. Primary AML samples showed differential sensitivity to treatment with either ara-C (40% sensitive, 17% intermediate, 43% resistant) or BV6 (51% sensitive, 21% intermediate, 28% resistant). Notably, 69% of ara-C resistant samples showed a good to fair response to IAP inhibition. Furthermore, combination treatment of ara-C with BV6 showed additive effects in most samples. Differences in sensitivity to IAP antagonist treatment correlated with significantly elevated expression levels of TNF and lower levels of XIAP in BV6 sensitive samples, as well as with NPM1 mutations. Gene expression profiling pointed to apoptosis-related pathways, which were specifically induced by IAP inhibition in sensitive samples. Thus, our results suggest IAP inhibition as a potential novel therapeutic option in AML.

overall_design: Gene expression was profiled in 24 AML samples [n=12 untreated, diagnostic samples of BV6 resistant (n=6) and sensitive (n=6) cases; n=6 paired samples (BV6 sensitive n=3 and resistant n=3 cases) treated for 24 hours with either DMSO or BV6].

first: Sonja

middle: C

last: Lück


title: CD99 triggering induces a novel processes of death in Ewing's sarcoma cells involving reactivation of p53 functions and RAS upregulation.

status: Public on Feb 01 2015

city: Bologna

first: Andrea

last: Grilli

state: Italy

address: v. di Barbiano 1/10

department: Laboratory of Experimental Oncology

country: Italy

institute: Rizzoli Orthopaedic Institute

summary: CD99 is a transmembrane protein, whose expression is constantly associated to Ewing’s Sarcoma (EWS), a class of pediatric bone tumors with particular poor prognosis. We previously reported that engagement of CD99 leads to massive and rapid EWS cell death through a non-canonical path. Here we report that death occurs through a novel mechanism starting from classical apoptotic features, such as phosphatydilserine exposure on cell surface and mitochondrial depolarization and ending with massive cytoplasmic hypervacuolization (autophagosomes and micropinosomes). Mechanistically, CD99 induces upregulation of IGFI-R and RAS and rapid MDM2 degradation, which leads to p53 reactivation. We propose that upon CD99 engagement and subsequent p53 reactivation, the EWS-ets oncogene becomes insufficient to sustain EWS transformation; in this context, up-regulated RAS, deprived of a cooperating oncogenic stimulus, might contribute to the delivery of fatal rather than pro-survival signal. The most CD99-responsive EWS cells have either wild type or transcriptional active P53, though mutated, and greatly benefit from MDM2 degradation. Due to the low rate of P53 inactivating mutations in EWS patients, these findings sustain CD99-targeting with specific MAbs either to directly kill EWS cells or to increase sensitivity to chemotherapy. By recruiting also RAS, CD99 delivers a signal which exceeds that of drugs designed exclusive to reactivate p53 functions, besides being easily druggable

overall_design: Ewing Sarcoma cell lines 6647 control or treated with the anti-CD99 0662 MAb were profiled to discover mechanisms related to CD99 targeting. Treated cells were compared to control cells after 30, 60 and 120 minutes of exposure to 0662 (10µg/ml); all treatments are in duplicate.

first: Katia

last: Scotlandi


title: TC-1 tumor: WT vs fat-1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary:
expression profile of TC-1 tumor 14 days after s.c.
samples are mixture of 3 tumors respectively

overall_design: TC-1 tumor from WT_vs_TC-1 tumor from fat-1

first: Kensuke

last: Tomio


title: Gene expression of whole hippocampus 24hr post-injury in rat

status: Public on Jan 08 2015

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

country: USA

institute: GenUs BioSystems, Inc.

summary: Traumatic brain injury (TBI) alters and dysregulates the expression of thousands of genes in the brain. Since some of the most common problems in TBI patients are learning and memory deficits, we are studying the effects of TBI on the hippocampus, a region of the brain which is essential for learning and memory and which is known to be particularly vulnerable to TBI. We are interested in understanding how potential neuroprotective drugs alter the TBI-induced gene expression profile. The objective of this study is to elucidate and compare the differential gene expression profiles in the hippocampus of naive, sham-control, TBI and TBI plus drug treated rats. JM6, PMI-006 and E33 are three compounds with neuroprotective, anti-inflammatory and anti-oxidative effects.  Our goal is to determine if different neuroprotective compounds have similar effects on common gene targets. These genes and the cell signaling pathways linked to them would then be the target of new therapeutic strategies for TBI.

overall_design:
Rats were prepared for fluid percussion traumatic brain injury or sham injury (naïve rats had no anesthesia and were not handled in any way and gene expression in their brains serve as baseline data) and 24 hr post-injury, hippocampi were obtained, and stored in RNA later. Total RNA was isolated, quantitified and used for Agilent microarray analysis at GenUs Biosystems. Each group of naive, sham control, TBI and TBI plus JM6, TBI plus PMI-006 and TBI plus E33 (estrogen) has three biological replicates.

[Support/contributor]  The Moody Project for Translational Traumatic Brain Injury Research

first: Helen

middle: L

last: Hellmich

first: Deborah

middle: K

last: Boone

first: Harris

middle: A

last: Weisz

middle: T

first: Karen

middle: E

last: Torres


title: Molecular regulation of enhanced muscle mass in developing Blond Aquitaine foetuses compared to Charolais

status: Public on Aug 01 2015

city: Saint-Genès-Champanelle

first: Isabelle

last: Cassar-Malek

country: France

institute: Inra

summary: Background : The Blonde Aquitaine (BA) is a French beef breed with enhanced muscularity of unknown genetic origin. Targeted sequencing has shown that the BA is not a carrier of any of the bovine MSTN mutations. At the protein level the BA shows a transition to a faster muscle isoform phenotype with a greater proportion of type IIX and a smaller proportion of type I fibres than comparison Charolais (CH). Associated modifications in the activity of oxidative and glycolytic enzymes were also previously detected. Collectively, these changes are often observed in breeds of production species selected for enhanced growth and efficiency, but the underlying molecular mechanisms are unknown. Method : We examined the transcriptome of the Longissimus thoracis muscle at 4 gestational stages (110, 180, 210, and 260 dpc) in BA and CH foetuses. These time points coincide with primary and secondary myogenesis and functional differentiation. Total RNA was hybridised to the Agilent one-colour microarray platform containing 45,220 probes mapped to 17646 protein coding bovine genes. Following normalisation, we used a combination of differential expression (limma method, Smyth & al 2005) and a network theory method based on differential co-expression analysis (Hudson & al 2009) to compare and contrast the two muscle transcriptomes. Conclusions : In both breeds the most developmentally-regulated genes included: embryonic muscle subunit isoforms (e.g. MYL4) whose expression dropped dramatically prior to birth when they are replaced by the adult isoforms; metabolic enzymes (e.g. the mitochondrially-localised sarcomeric creatine kinase CKMT2) that prepare the foetus for functional independence postpartum, and 1 probe out of 4 representing a gene of unknown function (C13H20ORF194) also previously published as highly developmentally regulated in Wagyu by Hereford longissimus muscle (Hudson & al 2013). In contrasting the breeds, MSTN was the 2nd most differentially expressed muscle gene between the breeds, being approximately 4-fold down-regulated in CH at each of the time points. Given MSTN is a growth inhibitor, this result may reflect either divergent muscle mass or fibre composition in foetuses and could account for the low muscle development of BA calves at birth. Among the most differentially connected transcriptional regulators we prioritised expected molecules like MSTN, but also unexpected ones like PROX1, NMI, MBD1, NRIP2 and TAF12. Although not differentially expressed at the transcript level these molecules are transcriptionally rewired between the breeds and may form attractive new candidates for the development of differential muscle mass and fibre composition in cattle.

overall_design: 2 beef breeds: Blond Aquitaine (BA) and Charolais (CH) ; 4 gestational stages per breed (110, 180, 210, and 260 dpc); 3 animals (biological replicats) per stage and per breed, except for BA 180 dpc, BA 260 dpc and CH 110 dpc (only 2 animals due to technical problem during hybridization).

first: I

first: A

last: de la Foye

first: C

last: Boby

first: B

last: Picard

last: Reverter-Gomez

first: N

last: Hudson


title: Fe-FIT-Diff

status: Public on Feb 14 2015

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: au13-06_fit - Fe-FIT-Diff - FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is a regulator of Fe deficiency responses in the root. FIT is a basic helix-loop-helix protein. Here, we investigated the transcriptome changes in response to Fe deficiency (- Fe) versus the control condition (+ Fe) in wild type, the fit-3 loss of function mutant and in FIT overexpression plants.

overall_design: 21 dye-swap - normal vs transgenic comparaison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Petra-

last: Bauer

first: Marie-Laure

last: Martin-Magniette


title: Transcriptomic landscape of developing Presomitic mesoderm (PSM)

status: Public on Jan 01 2015

city: ILLKIRCH

first: philippe

last: moncuquet

address: 1 rue laurent fries

institute: IGBMC

summary: Stem cell-derived tissues have wide potential for modelling developmental and pathological processes as well as cell-based therapy. However, it has proven difficult to generate several key cell types in vitro, including skeletal muscle. In vertebrates, skeletal muscles derive during embryogenesis from the presomitic mesoderm (PSM). Using PSM development as a guide to establish conditions for the differentiation of monolayer cultures of embryonic stem (ES) cells into PSM-like cells without the introduction of transgenes or cell sorting. We generated a high resolution transcriptome expression landscape along the PSM of the mouse embryo, by microdissecting consecutive fragment of the PSM along the antero-posterior axis of the embryo. We took advantage of the observation that during development of embryo, the antero-posterior spatial position of the tissue is directly correlated to its differentiation (time) stage, thus generating an expression time-course of presomitic mesoderm development.

overall_design: Pre Somitic Mesoderm (PSM) were dissected into 7 pieces in Stage E8E9.5 Mouse embryo. The experiment was designed to have biological triplicate in each pieces. The PSM is a symmetric structure, left and right area were obtained from one embryo, another set of dissection was obtained from another embryo.

first: Masayuki

last: Oginuma

first: Philippe

last: Moncuquet


title: Transcriptomic landscape of developing Presomitic Mesoderm (PSM) from Tailbud to somite in E9.5 mouse embryo and in in vitro differentiated Paraxial mesoderm derived from mouse embryonic stem cells (mESCs).

summary: Stem cell-derived tissues have wide potential for modelling developmental and pathological processes as well as cell-based therapy. However, it has proven difficult to generate several key cell types in vitro, including skeletal muscle. In vertebrates, skeletal muscles derive during embryogenesis from the presomitic mesoderm (PSM). Using PSM development as a guide to establish conditions for the differentiation of monolayer cultures of embryonic stem (ES) cells into PSM-like cells without the introduction of transgenes or cell sorting.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: β-arrestin1 is involved in hepatocellular carcinogenesis via an inflammation-mediated Akt signal

status: Public on Apr 11 2015

city: Guangzhou

first: Bin

last: Wu

state: Guangdong

address: No. 600, Tianhe Road, Tianhe District

department: Gastroenterology of The 3rd affiliated Hospital

country: China

institute: Sun Yat-sen University

summary: Hepatocellular carcinoma (HCC), the main form of liver cancer, is the sixth most common cancer and the third most frequent cause of cancer death worldwide1. The exact mechanism of HCC initiation and development is still unclear, though inflammation has been shown to play a key role in this progression. Herein, we performed a gene expression assay to screen for alterative expression of genes among normal liver tissues, HCC tissues and its paracancer tissues with hepatitis.

overall_design: A gene assay to screen the expression of total RNA in liver tissues, including 3 normal liver tissues, 3 HCC paracancer specimens and 3 HCC samples with HBV-induced hepatitis. The normal liver samples were obtained from normal hepatic tissue in three hepatic hemangioma surgical operative patients, and three matched pairs of HCC and its paracancer tissues were respectively obtained from three HCC surgical operative patients without any chemotherapy and radiotherapy.


title: RP58 controls neuron and astrocyte differentiation by downregulating the expression of Id1-4 genes in the developing cortex

status: Public on Dec 08 2014

city: Tokyo

first: Shinobu

last: Hirai

address: Setagaya Kamikitazawa 2-1-6

institute: Tokyo Metropolitan Institute of Medical Science

summary: Appropriate number of neurons and glial cells is generated from neural stem cells (NSCs) by the regulation of cell cycle exit and subsequent differentiation. Although the regulatory mechanism remains obscure, Id (inhibitor of differentiation) proteins are known to contribute critically to NSC proliferation by controlling cell cycle. Here we report that a transcriptional factor, RP58, negatively regulates all 4 Id genes (Id1-Id4) in developing cerebral cortex. Consistently, Rp58 knockout (KO) mice demonstrated enhanced astrogenesis accompanied with an excess of NSCs. These phenotypes were mimicked by the overexpression of all Id genes in wild-type cortical progenitors. Furthermore, Rp58 KO phenotypes were rescued by the knockdown of all Id genes in mutant cortical progenitors but not by the knockdown of each single Id gene. Finally, we determined p57 as an effector gene of RP58-Id-mediated cell fate control. These findings establish RP58 as a novel key regulator that controls the self-renewal and differentiation of NSCs and restriction of astrogenesis by repressing all Id genes during corticogenesis.

overall_design: Sample RNAs were obtained from E16.5 Rp58 KO mouse cerebral cortex or control cortex. Two independent total RNA samples from each mouse strain were mixed and purified using the RNeasy Mini Kit (Qiagen). Oligonucleotide microarray analysis was performed using Panorama Micro Array gene expression chips, each containing approx 22000 probe sets (Sigma-Aldrich) according to the manufacturer's instructions.

first: Akiko

last: Miwa

first: Chiaki

last: Ohtaka-Maruyama

first: Masataka

last: Kasai

first: Shigeo

last: Okabe

first: Yutaka

last: Hata

first: Haruo

last: Okado


title: Deep Sequencing Analysis of miRNAs Expression in Spleen of J subgroup Avian Leukosis Virus Infected and Uninfected Broilers.

status: Public on Dec 01 2014

first: OuYang

last: Hongjia

address: Wushan street 483

department: College of Animal Science

institute: South China Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goals of this study are to investigate the differentially expressed miRNAs between ALV-J infected (WRR+) and uninfected (WRR-)chickens spleens by Illumina deep sequencing.
Methods: 140-day-old female chickens of White Recessive Rock (WRR) were confirmed as J subgroup avian leukosis virus (ALV-J) infection. Total RNA from three ALV-J-infected spleens (designated: WRR1+, WRR2+, WRR3+) and three uninfected normal spleen samples (designated: WRR1-, WRR2-, WRR3-) was isolated by TRIzol following the manufacturer’s instruction (Invitrogen, CA, USA). RNA samples of three individuals within each group were pooled with equal amounts, and then were subjected to Illumina deep sequencing by Illumina Hiseq 2500.
Results: After raw data filtered, 12,150,275 and 15,227,930 reads of 18-32 bp, representing 569,847 and 543,062 unique sequences, were obtained for WRR- and WRR+ libraries, respectively. Through blasting with the chicken reference genome, 360,180 WRR- sequences and 327,391 WRR+ sequences, which accounted for more than 60% of the unique sequences, were perfectly matched.To analyze the miRNA detection efficiency of Illimuna deep sequencing, all the clean reads were blasted with the Rfam data base 10.1, annotated and then removed rRNA, tRNA, snoRNA and other snRNAs. The annotation results revealed that miRNAs accounted for more than 68% of all clean reads in the WRR− and WRR+ libraries. In this study, a total of 476 miRNAs were identified after compared the unique sequences against the chicken miRNAs precursors in miRBase 18.0. Base on unique sequences matched counts, 167 differential expression miRNAs were identified by DEGseq package using Benjamini-q-value of 0.001 as a cut-off. In ALV-J infected spleens, 83 miRNAs showed up-regulated expression and 84 were down-regulated when compared to uninfected samples.
Conclusions: Our study represents the first time to analysis of miRNA Expression in Spleen of J Subgroup Avian Leukosis Virus (ALV-J) Infected (WRR+) and Uninfected (WRR-) Broilers. A total of 167 miRNAs were found to be differentially expressed in ALV-J infected spleens when compared to uninfected chickens. These miRNAs can be considered as candidates for further study ALV-J invasion.

overall_design: Spleen miRNA profiles of 140-day-old ALV-J infected (WRR+) and uninfected (WRR-) female chickens of White Recessive Rock were generated by deep sequencing, using  Illumina Hiseq 2500.

first: Zhenhui

last: Li

first: Nie

last: Qinghua


title: Composition and expression of genes encoding carbohydrate-active enzymes in the straw-degrading mushroom Volvariella volvacea

status: Public on Dec 19 2014

city: Fuzhou

first: Baogui

last: Xie

state: Fujian

address: Shangdian Road

department: Mycological Research Center

institute: mrcfafu

type: Expression profiling by high throughput sequencing

summary: Volvariella volvacea is one of a few commercial cultivated mushrooms mainly using straw as carbon source. In this study, the genome of V. volcacea was sequenced and assembled. A total of 286 genes encoding carbohydrate-active enzymes (CAZymes) in V. volvacea were identified and annotated. Among 15 fungi with sequenced genomes, V. volvacea ranks the seventh in the number of genes encoding CAZymes. In addition, the composition of glycoside hydrolases in V. volcacea is dramatically different from other basidiomycetes: it is particularly rich in members of the glycoside hydrolase families GH10 (hemicellulose degradation) and GH43 (hemicellulose and pectin degradation), and the lyase families PL1, PL3 and PL4 (pectin degradation) but lacks families GH5b, GH11, GH26, GH62, GH93, GH115, GH105, GH9, GH53, GH32, GH74 and CE12. Analysis of genome-wide gene expression profiles of 3 strains using 3'-tag digital gene expression (DGE) reveals that 246 CAZyme genes were expressed even in potato destrose broth medium. Our data also showed that the formation of a heterokaryon strain could dramatically increase the expression of a number of genes which were poorly expressed in its parental homokaryon strains.

overall_design: Using the 3'-tag digital gene expression (DGE), we compared the gene expression profiles among 2 homokaryotic V. volvacea strains PYd15 and PYd21, and one heterokaryotic strain H1521, which is a hybrid strain of PYd15 and PYd21.

first: Bingzhi

last: Chen

first: Fu

last: Gui

first: Youjin

last: Deng

first: Xianyun

last: Sun

first: Mengying

last: Lin

first: Yongxin

last: Tao

first: Shaojie


title: Liver gene expression signatures for type 2 diabetic mice and normal mice

city: Sapporo

first: Hayashi

last: Yasuhiro

address: Kita-12, Nishi-6, Kita-ku

department: Faculty of Pharmaceutical Sciences

institute: Hokkaido University

summary: Over the past decade, considerable progress has been made regarding the discovery of gene targets by nanobiotechnologies. However, a huge gap frequently exists between candidate and therapeutic relevant genes due to the limitations associated with functional analyses. We report herein on the use of an integrated technologies involving a DNA microarray and an in vivo siRNA delivery system to rapidly and efficiently discover gene targets. Using DNA microarrays, we were able to show that the expression of a monoacylglycerol O-acyltransferase 1 (MOGAT1), an enzyme involved in triglyceride synthesis and storage, is elevated in the livers of obese diabetic mice. The in vivo silencing of hepatic Mogat1 via a non-viral siRNA delivery system resulted in a dramatic improvement in systemic glucose and lipid homeostasis. These interdisciplinary approaches have the potential to accelerate not only for identification of target gene, but also drug discovery and development.

overall_design: Gene expression in liver was measured in 4- and 11-week-old KKAy and C57BL/6J mice.

first: Yasuhiro

last: Hayashi

first: Kazuaki

last: Kajimoto

first: Noritada

last: Kaji

first: Yoshinobu

last: Baba

first: Hideyoshi

last: Harashima


title: Control Huh7.5 cell vs HPI cell (HCV-persistently-infected Huh7.5 cell)

first: Satoshi

last: Kondo

summary: Transcriptional profiling of human hepatoma cell lines comparing control uninfected Huh7.5 cells with Huh7.5 cells persistently infected with HCV (HPI cell). The latter maintains and produces HCV.

overall_design: A single experiment, Huh7.5 cell vs. HPI cells.

first: K

last: Sugiyama


title: Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

status: Public on Nov 21 2014

city: Brussels

first: David

last: Brown

address: Boulevard de Waterloo 127

country: Belgium

institute: Institut Jules Bordet

summary: Microarrays have revolutionized breast cancer (BC) research by enabling studies of gene expression on a transcriptome-wide scale. Recently, RNA-Sequencing (RNA-Seq) has emerged as an alternative for precise readouts of the transcriptome. To date, no study has compared the ability of the two technologies to quantify clinically relevant individual genes and microarray-derived gene expression signatures (GES) in a set of BC samples encompassing the known molecular BC's subtypes. To accomplish this, the RNA from 57 BCs representing the four main molecular subtypes (triple negative, HER2 positive, luminal A, luminal B), was profiled with Affymetrix HG-U133 Plus 2.0 chips and sequenced using the Illumina HiSeq 2000 platform. The correlations of three clinically relevant BC genes, six molecular subtype classifiers, and a selection of 21 GES were evaluated.

overall_design: 58 tumors representing the different molecular subtypes [triple negative (ER-/PgR-/HER2-); HER2 positive (HER2+); luminal A (ER+/HER2-/histological grade 1), luminal B (ER+/HER2-/histological grade 3)] were obtained from patients recruited between 2007 and 2011 at the Institut Jules Bordet. RNA was profiled using the Affymetrix HG-U133 Plus 2.0 chips and sequenced on the Illumina platform, producing ~30 million 50 bp paired-end reads per sample. The reads alignment and expression quantification were performed using the Tophat/Cufflinks pipeline and the Ensembl genome version hg19. The Affymetrix microarray data were normalized using fRMA and probesets were selected based on the JetSet reannotation package. This submission represents the gene expression component of the study only.

first: Debora

last: Fumagalli

first: Alexis

last: Blanchet-Cohen

first: Christine

last: Desmedt

last: Gacquer

first: Stefan

last: Michiels

first: Françoise

last: Rothé

first: Samira

last: Majjaj

first: Roberto

last: Salgado

first: Denis

last: Larsimont

first: Marion

last: Maetens

first: Martine

last: Piccart

first: Vincent

last: Detours

first: Christos

last: Sotiriou

first: Benjamin

last: Haibe-Kains


title: Potato virus Y infection hinders potato defence response and renders plants more vulnerable to Colorado potato beetle attack

status: Public on Oct 23 2014

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary:
In the present study molecular interactions between potato plants, Colorado potato beetle (CPB) larvae and Potato virus YNTN (PVYNTN) were investigated by analyzing gene expression in potato leaves.

Grant ID: J4-4165
Slovenian Research Agency ARRS
Growth and defense trade-offs in multitrophic interaction between potato and its two major pests

Grant ID: P4-0165
Slovenian Research Agency ARRS
Biotechnology and Plant Systems Biology

overall_design: mRNA samples of secondary PVYNTN-infected (CPB_PVY) and healthy potato plants (CPB_H) cultivar Igor and of RNAi coi1-silenced (CPB_coi1) and non-transformed (CPB_NT) potato plants cultivar Desiree collected 24 h post CPB infestation and respective control non-infested samples (CONT_PVY, CONT_H, CONT_coi1, CONT_NT).

first: Kristina

last: Gruden


title: Transcriptomic responses to emamectin benzoate in Pacific and Atlantic Canada salmon lice Lepeophtheirus salmonis with differing levels of drug resistance

status: Public on Nov 17 2014

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

summary: This study investigates the baseline or inducible differences in between populations of Atlantic salmon lice Lepeophtheirus salmonis with differing levels of resistance to the parasiticidal drug emamectin benzoate (EMB), as well as the induced effects of EMB exposure to Pacific salmon lice.  F1 generation lice were exposed in bioassays to a dilution series of emamectin benzoate.

overall_design: Two separate experiments were conducted, one for Atlantic and one for Pacific salmon lice (to be analyzed separately). Atlantic pre-adult salmon lice, separated into male and female, and sensitive or resistant to EMB populations, and exposed to a dilution series: 0 (control), 0.1, 25, 300, and 1000 parts per billion EMB. For each combination four biological replicates were included, except male resistant 25 (n = 3) and female resistant 300 (n = 2). Pacific pre-adult lice of both sexes were exposed to a dilution series: 0 (control), 25, 50 parts per billion EMB.

middle: J

last: Sutherland

first: Jordan

middle: D

last: Poley

first: Okechukwu

middle: O

last: Igboeli

first: Johanna

middle: R

last: Jantzen

first: Mark

last: Fast

first: Simon

last: Jones


title: Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to J Subgroup Avian Leukosis Virus (ALV-J) Infection.

status: Public on Nov 15 2014

first: Zhenhui

last: Li

address: Tianhe District Wushan road

summary:
Purpose: The goals of this study are to investigate the differentially expressed genes between ALV-J infected (WRR+) and uninfected (WRR-)chickens spleens by Illumina deep sequencing.
Methods: 140-day-old female chickens of White Recessive Rock (WRR) were confirmed as J subgroup avian leukosis virus (ALV-J) infection. Total RNA from three ALV-J-infected spleens (designated: WRR1+, WRR2+, WRR3+) and three uninfected normal spleen samples (designated: WRR1-, WRR2-, WRR3-) was isolated by TRIzol following the manufacturer’s instruction (Invitrogen, CA, USA). RNA samples of three individuals within each group were pooled with equal amounts, and then were subjected to Illumina deep sequencing by Illumina Genome Analyzer IIx.
Results: Through raw data processed, 49,979,648 and 43,704,401 clean reads with an average length of 101 bp, which represented total residues of 4,859,084,087 and 4,238,826,168 bp, were obtained for WRR- and WRR+ libraries, respectively. Subsequently, the clean reads in the two libraries were assembled. Altogether, 121,493 contigs were assembled with an average length of 927 bp (ranged from 300 bp to 23,402 bp), leading to generation of 82,829 unigenes. The length of unigenes varied from 351 bp to 28,928 bp, with an average length of 1,155 bp. Based on the FPKM value of each gene, 252 DEGs were identified by DEGseq package using Benjamini-q-value of 0.05 as a cut-off. In ALV-J infected spleens, 90 genes showed up-regulated and 162 showed down-regulated expression when compared to uninfected samples.
Conclusions: Our study represents the first time to elucidate the ALV-J infected chickens’spleens at the transcription level by RNA-seq technology. A total of 252 genes were found to be differentially expressed in ALV-J infected spleens when compared to uninfected chickens. These genes can be considered as candidates for further study ALV-J invasion.

overall_design: Spleen mRNA profiles of 140-day-old ALV-J infected (WRR+) and uninfected (WRR-) female chickens of White Recessive Rock were generated by deep sequencing, using Illumina Genome Analyzer IIx.

first: Qinghua

last: Nie


title: Time-dependent global gene expression profile of RAW264.7 cells infected with Mycobacterium tuberculosis H37Rv (Mtb)

status: Public on Dec 23 2014

city: Kolkata

first: Joyoti

last: Basu

address: A.P.C. Road

department: Chemistry

country: India

institute: Bose Institute

summary: Transcriptional profiling of RAW264.7 cells infected with M. tuberculosis H37Rv at an MOI of 10 performed 4 and 24 hours post-infection.

overall_design: RAW264.7 cells were infected with Mtb for 4 hours at an MOI of 10. Cells were washed and treated with gentamycin for 2 hours in order to remove adhered bacteria. Incubation was continued further for  4 and 24 hours followed by total RNA isolation. Total RNA was labelled with Agilent’s quick-Amp labelling kit (p/n: 5190-0444) to generate fluorescent complementary RNA by using T7 promoter based linear amplification. The control sample was labelled with Cy3 while the infected samples were labelled with Cy5 and hybridized to an  Agilent oligo microarray kit.

first: Manikuntala

last: Kundu

first: Zhumur

last: Ghosh


title: Genome-wide identification of PIF1-binding sites and direct-target genes of PIF1 transcriptional regulation in skotomorphogenesis

status: Public on Oct 02 2014

city: Albany

first: james

middle: m

last: tepperman

state: CA

address: 800 Buchanan St.

department: Plant and Microbial Biology

institute: Plant Gene Expression Center/UC Berkeley

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF1 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis.

overall_design: Three biological replicates data of PIF1-binding sites were collected by comparing the parallel ChIP samples from Myc-epitope-tagged-PIF1 (P1M) overexpressing transgenic seedlings and the wild-type (WT) control.

first: Anne

last: Pfeiffer

first: Yu

last: Zhang

first: Peter

middle: H

last: Quail


title: Effect of Helicobacter pylori on ATM-dependent DNA damage responses [cell lines]

status: Public on Aug 23 2014

city: Yufu

first: Katsuhiro

last: Hanada

state: Oita

address: 1-1 Idaigaoka, Hasama-machi

department: Faculty of Medicine

institute: Oita University

summary:
Carcinogenic bacteria, Helicobacter pylori, induce DNA double-strand breaks in infected host cells. Therefore, we have investigated which genes are upregulated after the infection.
Although Helicobacter pylori infection is etiologically related to the inflammation-related malignancy, gastric cancers, it role in the molecular pathogenesis of disease remains unclear. In vitro studies have suggested the infection may cause breaks in double-stranded DNA. We used microarray analysis of H. pylori-infected human gastric biopsies to investigate the effect of H. pylori on gene expression genes involved in DNA repair and DNA damage response. Micro-array analysis and immunohistochemistory showed that ATM (ataxia-telangiectasia mutated) was upregulated in H. pylori gastritis but down regulated in the premalignant lesion, intestinal metaplasia. Studies in gastric cancer cell lines showed that H. pylori-infection induced activation of ATM and formation of γ-H2AX.  γ-H2AX formation was present following infection with bout cag pathogenicity island (PAI)- positive and negative strains but more robust with cag PAI positive strains consistent with the fact that both cag PAI positive negative strains are associated with gastric cancer but the risk is higher with cag PAI positive strains.  Eradication of H. pylori infection is associated with a reduction in cancer risk even in the most high risk populations.  These data provide a plausible molecular mechanism for a direct bacterial-host interaction increasing cancer risk.

overall_design: To identify tumor suppressors affected by H. pylori-infection, microarray screening was used to compare the gene expression profiles of AGS cells, a gastric cancer cell line, infected with various  mutants of H. pylori.

first: Yoshio

last: Yamaoka


title: Genome-wide identification of PIF-binding sites and direct-target genes of PIF transcriptional regulation in skotomorphogenesis

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


title: Arabidopsis AGO5 contributes to a POL II-based RNA silencing pathway directing epigenetic marks

status: Public on Jul 27 2014

city: Cambridge

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

summary: To characterise the Arabidopsis AGO5 protein, we report the AGO5 associated sRNAs, ago5 mutant total sRNAs and digital gene indexing tags with altered abundance in the ago5 mutant.

overall_design: Examination of AGO5 associated sRNAs, population of total sRNAs in the ago5 mutant and characterisation of RNA transcripts with altered abundance in the ago5 mutant.

first: Ericka

last: Havecker

first: Laura

middle: M

last: Taylor-Wallbridge

first: Paola

last: Fedito

first: Thomas

last: Hardcastle

first: Susanne

middle: B

last: HeimstÃ¤dt

first: Ruth

last: Dunn

first: David

last: Baulcombe


title: Gene expression profiles of human hepatocellular carcinoma (validation set)

status: Public on Jul 31 2014

city: Taipei

first: Jui-Yu

last: Hsieh

address: No. 155, Sec 2, Li-Nong Street

country: Taiwan

institute: National Yang-Ming University

summary: Hepatocellular carcinoma (HCC) in young subjects is rare but more devastating. We hypothesize that genes and etiological pathways are unique to young HCC (yHCC; ≤40 years old at diagnosis) patients. We therefore compared the gene expression profiles between yHCCs and HCCs from elderly patients.

overall_design: In this dataset, a total of 31 gene expression profiles of HCC samples were collected. Four of them are classified as stage T1 (early HCC) and 6 of them were classified as stage T3 (late HCC).

first: Hsei-Wei

last: Wang

first: SSu-Yi

last: Huang

first: Tsung-Han

first: Gar-Yang

last: Chau

first: Chien-Yi

last: Tung

first: Chien-Wei

last: Su

first: Jaw-Ching

last: Wu


title: Loss of neuronal 3D chromatin organization causes transcriptional and behavioral deficits related to serotonergic dysfunction [ChIP-seq]

status: Public on Jul 18 2014

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

summary: The interior of the neuronal cell nucleus is a highly organized 3-dimensional (3D) structure in which regions of the genome that are millions of bases apart participate in specialized sub-structures with dedicated functions. To investigate neuronal chromatin organization and dynamics in vivo, we generated bitransgenic mice that express histone GFP-tagged H2B in principal neurons of the forebrain. Surprisingly, the expression of this chimeric histone in mature neurons causes chromocenter declustering and disrupts the association of heterochromatin with the nuclear lamina. The loss of these structures does not affect neuronal viability but is associated with specific transcriptional and behavioral deficits related to serotonergic dysfunction. Overall, our results demonstrate that the 3D-organization of chromatin in the neuronal nucleus supports an additional level of epigenetic regulation of gene expression that critically influences neuronal function and indicate that some loci associated with neuropsychiatric disorders may be particularly sensitive to changes in chromatin architecture.

overall_design: Genome-wide profiling by high throughput sequencing of H3K27me3 in the adult hippocampus of CaMKII-tTA/tetO-H2BGFP (H2BGFP) and their wild-type littermates mice (WT). Chromatin immunoprecipitation (ChIP) was carried out using pooled hippocampal tissue from 3 mice (one hippocampus per mouse). One DNA library was constructed per genotype. Each DNA library was prepared from pooled immunoprecipitated DNA from 4 independent ChIP assays. In total, tissue from 12 different mice was used to prepare each DNA library. 60% of a lane was used to perform single end (1x50bp) multiplex sequencing in HiSeq 2500 apparatus (Illumina). Each library, was sequenced in duplicate (in two independent sequencing runs. Technical replicates).

first: Jose

middle: P

last: Lopez-Atalaya


title: H2BGFP

overall_design: Refer to individual Series


title: Loss of neuronal 3D chromatin organization causes transcriptional and behavioral deficits related to serotonergic dysfunction [expression]

summary:
The interior of the eukaryotic cell nucleus is a highly organized 3D structure. In mature hippocampal and cortical pyramidal neurons, transcriptionally silent DNA is typically compacted in a few clusters referred to as chromocenters that are strongly stained with DNA intercalating agents like DAPI and whose function is still uncertain. We found that this 3D structure was severely disrupted by the incorporation of the chimeric histone H2BGFP into neuronal chromatin. Experiments in inducible and forebrain restricted bitransgenic mice demonstrated that the expression of this histone alters the higher-order organization of neuronal heterochromatin and causes a complex behavioral phenotype that includes hyperactivity, and social interaction, prepulse inhibition and cognitive defects. This phenotype was associated with highly specific transcriptional deficits that affected several serotonin receptor genes located at the edge of gene desert regions. Pharmacological and electrophysiological experiments indicate that this epigenetically-induced hyposerotonergic state may underlie the behavioral defects. Our results suggest a new role for perinuclear heterochromatin and chromocenter organization in the epigenetic regulation of neuronal gene expression and mental illness.
We used microarrays to detect differential gene expression in transgenic mice expressing histone H2BGFP in the forebrain.

overall_design: We obtained triplicate samples (biological replicates) of either genotype (wild-type and H2BGFP mice). Each sample contained pooled total RNA from the hippocampi of 2 three-month old genotype-matched mice.


title: Toxic effects of BDE209 in human embryonic kidney 293 cells (HEK 293)

status: Public on Apr 21 2014

city: Shanghai

first: Min

last: Li

address: 50 Chifeng Rd., Yangpu District

department: Life Sciences and Technology

institute: Tongji University

summary: PBDEs are widely used in consumer and household products as flame retardants. Many studies have shown that PBDEs could disrupt thyroid hormone homeostasis and adversely affect brain development. Here, we explored the toxical effects of BDE209 on HEK 293 cells and found that BDE209 may have a role in nucleosome remodeling. Many gene sets involved in cancer are enriched at the BDE209-treated sample. This indicates the carcinogenicity of BDE209. Interestingly, the impacts of BDE209 dissoved in DMSO on gene expression are more pronounced than the simple additive effects of BDE209 and DMSO alone.

overall_design: Gene expression profiles of human embryonic kidney 293 cells (HEK 293) cultured in normal medium, and medium containing BDE209 or DMSO were generated by deep sequencing, using Illumina HighSeq2000, respectively..

first: Zhenping

last: Liu

first: Liang

last: Gu

first: Rong

last: Yin

first: Huarong

first: Xiaobai

last: Zhang

first: Tongcheng

last: Cao

first: Cizhong

last: Jiang


title: Genome-wide identification of PIF4-binding sites and direct-target genes of PIF4 transcriptional regulation in skotomorphogenesis

first: james

last: tepperman

summary: Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF4, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF4 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis.

overall_design: Three biological replicates data of PIF4-binding sites were collected by comparing the parallel ChIP samples from Myc-epitope-tagged-PIF4 (P1M) overexpressing transgenic seedlings and the wild-type (WT) control.

first: Hui

last: Shi

first: Yu

first: Peter

last: Quail


title: Molecular mechanisms of partial resistance to Aphanomyces euteiches in Medicago truncatula (affy_molecularmechanism_medicago)

status: Public on Feb 28 2014

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary: affy_molecularmechanism_medicago - affy_molecularmechanism_medicago - -Aphanomyces euteiches (Ae), a soilborne oomycete, is the causal agent of pea root rot, a major disease on various cultivated legume species. To gain insight into the mechanism underlying partial resistance to this pathogen, a pathosystem has been developed using the model legume Medicago truncatula (Mt). Two Mt accessions A17 and F83005.5 have been shown to display differential responses upon infection with Ae (partially resistance and susceptibility, respectively). Genetic analyses using a RIL population derived from a cross between those two lines lead to the identification of, prAe1, a major QTL involved in the observed partial resistance. Near isogenic lines (NIL) NR2 and NS2 whose genomes are identical except at the prAe1 locus (resistant alleles for NR2, susceptible alleles for NS2) have been generated, and the same differential response toward Ae has been found. The aim of this experiment is to analyse and compare NR2 and NS2 transcriptomes at 1 and 6 days after Ae inoculation to identify gene networks that are regulated in a prAe1 dependent manner.--Fifteen-day-old NR2 or NS2 plants were grown in vitro on M medium. The entire roots were then inoculated (or not = 0dpi) with a A. euteiches zoospores (75000zsp/ml) and harvested one or six days after inoculation. Three independent repeats were performed.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 18 arrays - Medicago; resistance  vs susceptibility comparison,time course,treated vs untreated comparison

first: Christophe

last: Jacquet

first: Stephanie

last: Huguet

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Gene expression profiles of human hepatocellular carcinoma (training set 1)

first: Jui-Yu

last: Hsieh

overall_design: In this dataset, a total of 87 gene expression profiles of tissue samples were collected, which containing 48 primary HCC samples, as well as those of 39 non-cancerous tissues, from 61 patients. HCC tissues were collected from 16 young HCC and 32 elder HCC patients.

first: Hsei-Wei

last: Wang

first: SSu-Yi

last: Huang

first: Tsung-Han

first: Gar-Yang

last: Chau

first: Chien-Yi

last: Tung

first: Chien-Wei

last: Su

first: Jaw-Ching

last: Wu


title: Liver profiles of mid-lactating goats using  Agilent Array

status: Public on Aug 29 2014

city: Nanjing

first: Dong

last: Haibo

state: Jiangsu

department: Nanjing Agricultural University

institute: Nanjing Agricultural University

summary: Dairy ruminants are often fed high grain diets to meet the energy demand for high milk production. As a result, body metabolism occurs change and  milk quality was suppression. As the vital organ that controls metabolism, the liver contributes to the input of substrate precursors to the mammary gland. To further investigate the role of genes in feeding high concentrate diet metabolic characters, a comparison of mRNA expression profiles in liver of feeding high-concentrate diet (60% concentrate of dry matter, HC) and low-concentrate diet (40% concentrate of dry matter, LC) was carried out.When compaired with LC goats, 43 genes were significantly down-regulated and 112 genes were significantly up-regulated (fold change >2 and p value < 0.01) in the liver of HC among the 115 probes. Through Co-expression network analysis to find K-core regulatory factors (genes). These genes were mainly involved in immune and inflammatory responses (n = 8), lipid metabolism (n = 5), protein metabolism (n = 26), carbohydrate metabolism (n = 7). These results were further described in the unpublished paper

overall_design: Eight mid-lactating goats (LC, n=3;HC, n=5). Liver samples were immersed in liquid nitrogen immediately after collection and then stored at -70 °C. Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions. samples were named as LC1-3 and HC1-3, representing 3 respective liver RNA samples each from LC and HC goats. Microarray experiment was performed by a service provider

first: Haibo

last: Dong

first: Yingdong

last: Ni


title: DNA microarray analysis of labial salivary glands in IgG4-related disease – comparison with Sjögren’s syndrome

status: Public on Jun 23 2014

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary:
<Objective> To compare gene expression in labial salivary glands (LSG) of IgG4-related disease (IgG4-RD) with Sjögren’s syndrome (SS).
<Methods> Gene expression was analyzed by DNA microarray in LSG of IgG4-RD (n=5), SS (n=5), and healthy controls (n=3). Differentially expressed genes (DEGs) in IgG4-RD and SS were identified, and gene-annotation enrichment analysis of these DEGs was performed using Gene Ontology (GO) annotation. Validation of the result was performed by quantitative PCR using LSG from IgG4-RD (n=9), SS (n=10), and controls (n=4).
<Results> Gene expression patterns in IgG4-RD, SS, and healthy controls were quite different with each other in hierarchical clustering as well as principal component analysis. In IgG4-RD, 1771 up-regulated probe sets (corresponding to 1321 up-regulated genes) and 1785 down-regulated probe sets (corresponding to 1320 down-regulated genes) were identified as DEGs (false discovery rate <0.05). GO term analysis indicated that the up-regulated set of DEGs in IgG4-RD encoded proteins that function in cell proliferation, extracellular matrix organization, and organ development. PCR validated significantly higher expression of lactotransferrin (LTF) in IgG4-RD than SS (P<0.05), and chemokine (C-C motif) ligand 18 (CCL18) in IgG4-RD than SS and controls (P<0.05).
<Conclusion> The results clearly showed that the gene expression pattern in LSG of IgG4-RD is different from that of SS.

overall_design: LSG samples were collected from 5 Japanese patients with IgG4-RD, as well as from 5 Japanese patients with SS who had been followed up at University of Tsukuba Hospital (Ibaraki, Japan). All patients with IgG4-RD satisfied the comprehensive diagnostic criteria for IgG4-related disease (IgG4-RD) 2011 proposed by the All Japan IgG4 team [3]. The diagnosis of IgG4-RD was based on the presence of all three items; 1) clinical examination showing characteristic diffuse/localized swelling or masses in single or multiple organs, 2) Hematological examination shows elevated serum IgG4 concentrations (135 mg/dl), 3) Histopathologic examination shows: (1) Marked lymphocyte and plasmacyte infiltration and fibrosis. (2) Infiltration of IgG4+ plasma cells: ratio of IgG4+/IgG+ cells > 40% and >10 IgG4+ plasma cells/HPF. All patients with SS satisfied the Japanese Ministry of Health criteria for the diagnosis of SS (1999) [4]. These criteria included four clinicopathological findings: lymphocytic infiltration of the salivary or lacrimal glands, dysfunction of salivary secretion, keratoconjunctivitis sicca, and presence of anti-SS-A or SS-B antibodies. The diagnosis of SS was based on the presence of two or more of the above four items. Approval for this study was obtained from the local ethics committee and a signed informed consent was obtained from each subject.

first: Hiroto

last: Tsuboi

first: Mana

last: Iizuka

first: Hiromitsu

last: Asashima

first: Yuya

last: Kondo

first: Akihiko

last: Tanaka

first: Masafumi

last: Moriyama

first: Isao

last: Matsumoto

first: Seiji

last: Nakamura

first: Toshio

last: Yoshihara

first: Keiko

last: Abe

first: Takayuki

last: Sumida


title: Characterization of Pythium transcriptome and gene expression analysis for different fermentation stage

status: Public on Dec 30 2014

city: wuhan

first: zhu

last: yuanmin

state: hubei

department: College of Life Science and Technology

institute: Huazhong University of Science and Technology

summary: We performed transcriptome assembly and gene expression analysis using short-read sequencing technology combined with a tag-based digital gene expression (DGE) system. The results generated a total number of 13,288,892 reads (accumulated length of 1,196,000,280 nt), 169,579 contings and 23,796 unigenes. Based on similarity search with known proteins, a total of 9,398 unigenes were identified with a cut-off E-value of 10-5. Assembled sequences were annotated with gene descriptions, such as gene ontology (GO) and clusters of orthologous group terms (COG). In addition, we obtained approximately 6 million raw tags and a larger number of genes at different fermentation stages (48 h, 100 h and 144 h). The related genes of growth characteristic and lipid biosynthesis were analyzed in detail. Some genes associated with the lipid biosynthesis were selected randomly to confirm digital gene expression (DGE) results by quantitative real-time PCR (qRT-PCR). The transcriptome improves our genetic understanding of Pythium splendens RBB-5 greatly and makes a large number of available gene sequences for further study. Notably, the transcriptome and DGE profiling data of Pythium splendens RBB-5 provide the comprehensive insight into gene expression profiles at different fermentation stages and lay a foundation for further study of optimizing lipid content and growth speed at the molecular level.

overall_design: analysis of 3 different fermentation stages in Pythium splendens.

first: Longjiang

last: Yu

first: Yuanmin

last: Zhu


title: Bile acid flux is necessary for normal liver regeneration

status: Public on Feb 05 2014

city: Portland

first: Willscott

middle: Edward

last: Naugler

state: OR

address: 3181 SW Sam Jackson Park Blvd

department: Med/GI&Hepatology

institute: Oregon Health & Science University

summary: Bile acid return from the intestine and attendant signaling is necessary for liver regeneration after partial hepatectomy or CCl4 injury

overall_design: Three groups of rat liver were examined at 4 time points (0, 4h, 12h, 24h) after partial hepatectomy; RNA from whole rat liver was isolated and deep sequencing was performed using the Illumina TruSeq platform


title: The RNA helicase CrhR as a regulatory factor

status: Public on Jun 17 2014

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

country: Germany

institute: University of Freiburg

summary: DEAD-box RNA-helicases catalyze the correct folding of structured RNAs and the formation of RNP complexes. The cyanobacterium Synechocystis sp. PCC 6803 encodes a single DEAD-box RNA helicase, CrhR (Slr0083) whose inactivation has severe effects on cellular physiology and morphology, particularly under cold stress. In order to identify potential RNA targets of CrhR, custom microarrays containing sequences corresponding to non-coding small RNAs (UTRs, ncRNAs, asRNAs, iRNAs) and all mRNAs were constructed. The RNAs exhibiting CrhR-dependent alteration of expression constitute both mRNA and small RNA transcripts. CrhR therefore is not a global regulator of RNA metabolism but instead interacts with a specific subset of the total RNA repertoire in Synechocystis, a CrhR-specific RNA regulon that functions predominately at low temperature. RNA half-life analyses indicated that expression of regulon members is controlled by a mechanism that does not involve CrhR-dependent RNA turnover. Biochemically, CrhR is able to anneal but not unwind an asRNA-mRNA target in vitro, providing evidence that regulation occurs through an RNA duplex intermediate. The data reveal a novel mechanism regulating the differential expression of operon members, crhR mutation disrupts a negative regulatory feedback loop involving CrhR regulation at an early stage of transcription in affected operons. We propose that CrhR is functioning as a RNA chaperone, similar to Hfq in enterobacteria, but regulating both post-transcriptional events and transcription termination, by altering sRNA metabolism.

overall_design: We monitored gene expression of an Synechocystis PCC6083 WT and a partial crhR knockout at 30°C and after 3h of culturing at 20°C. Each sample was done in biological triplicates.

first: Albert

last: Rosana

first: Marion

last: Eisenhut

first: Danuta

last: Chamot

first: Wolfgang

last: Hess

first: George

middle: W

last: Owttrim


title: Plant Viroid Detection Microarray

status: Public on Dec 31 2013

city: Beijing

first: Yongjiang

last: Zhang

institute: Chinese Academy of Inspection and Quarantine

summary: 40mer probes were designed to detect plant viroids infection at the genus level. This microarray platform is able to detect a wide spectrum of all the 8 reported viroid genera, including 37 known plant viroid species.

sample_organism:
Tomato apical stunt viroid
Tomato planta macho viroid
Citrus exocortis viroid
Potato spindle tuber viroid
Hop stunt viroid
Peach latent mosaic viroid
Apscaviroid cicatricimali
Avocado sunblotch viroid
Chrysanthemum stunt viroid
Columnea latent viroid
Hop latent viroid
Chrysanthemum chlorotic mottle viroid
Coleus blumei viroid 1
unclassified viroids
Citrus dwarfing viroid

platform_organism: Hostuviroid Pospiviroid Cocadviroid Apscaviroid Coleviroid Avsunviroid Pelamoviroid Elaviroid

overall_design: Viroid samples were extracted from infected plant hosts and plasmids. Total RNA was extracted and hybridized to the microarray.

first: Jun

last: Yin

first: Shuifang


title: Translational profiling in multiple myeloma to identify novel therapeutic targets

status: Public on Jul 04 2014

city: Seattle

first: Nicholas

last: Burwick

state: WA

address: 1100 Fairview Ave N , D5/100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: The goal of this study is to identify translationally-regulated mRNAs in multiple myeloma following treatment with dexamethasone

overall_design: The overall design is to treat the multiple myeloma cell line MM1.S with 1uM dexamethasone for 0 or 4 hours and collect total RNA and fractionated polysome pooled RNA (in 3 fractions)

first: Akiko

last: Shimamura


title: Gene expression profiles of human hepatocellular carcinoma

first: Jui-Yu

last: Hsieh

type:
Expression profiling by array
Third-party reanalysis


title: microRNA profiling in Marek's disease virus induced lymphoma and infected spleen by deep sequencing

status: Public on Dec 30 2013

first: Ling

last: Lian

address: Room 129, Animal Science Department, 2nd Yuanmingyuan West Road, Haidian District

institute: China Agricultural University

summary: To investigate specific miRNA expression profiles of Marek's disease virus (MDV)-infected samples, we performed deep sequencing for miRNAs in four small RNA libraries, including MDV-infected tumorous spleen, MD lymphoma from liver, and non-infected spleen and lymphocytes from controls. A total of 7.76x106, 6.36x106, 6.36x106, and 7.60x106 counts were obtained in four libraries, respectively. The sequences were blasted with chicken and MDV genomes and miRBase 16.0 to identify known and novel miRNAs. In total, 187 and 16 known mature miRNAs were identified in the chicken and MDV, respectively. Deep sequencing detected 942 novel chicken miRNA candidates, of which 646 were in tumorous spleen. These results indicate that MDV infection induced new host miRNA candidates and increased diversity of miRNAs. Of 942 miRNA candidates, 276 of 533 were verified by customized microarray, and 17 of them were further confirmed by qPCR.

overall_design: Four samples examined: MDV-infected tumorous spleen, MD lymphoma from liver, Non-infected spleen, Non-infected lymphocytes

first: Yanmei

last: Chen

first: Lujiang

last: Qu

first: Changjun

last: Liu

first: Ning

last: Yang


title: APC/CCCS52A2 repressed phytosulfokine signaling restricts root QC cell proliferation through ERF115 degradation

status: Public on Nov 04 2013

city: Gent

first: Ken

last: Heyndrickx

address: Technologiepark 927

department: Department of Plant Biotechnology and Bioinformatics

institute: Ghent University

summary: The quiescent center (QC) plays an essential role during root development by creating a  microenvironment that preserves the stem cell fate of its surrounding cells. Strikingly, in  order to retain root structure, QC cells only occasionally self-renew, displaying a  proliferation rate far below that of all other cells within the root meristem. Previously, the  APC/CCCS52A2 ubiquitine ligase and brassinosteroid signaling pathways have been found to  antagonistically control Arabidopsis thaliana QC cell proliferation. Here, we demonstrate  that both pathways converge on the ERF115 transcription factor that acts as a rate-limiting  factor of QC cell division through transcriptional control of the autocrine phytosulfokine  PSK5 peptide hormone. ERF115 marks QC cell division but is restrained through  proteolysis by the APC/CCCS52A2 ubiquitine ligase, whereas QC proliferation is driven by  brassinosteroid-dependent ERF115 expression. Combined, these two antagonistic  mechanisms delimit the ERF115-PSK5 activity and QC renewal. Our results reveal a  unique cell cycle regulatory mechanism that accounts for the low proliferation rate of QC  cells within a surrounding population of highly mitotic active cells.

overall_design: ChIP-seq analysis of genes bound by the ERF115 transcription factor, using mock ChIP with wild type cells as negative control. Analyzed by Illumina HiSeq

first: Jefri

last: Heyman

first: Lieven

last: De Veylder

first: Jelle

last: Van Leene

first: Klaas

last: Vandepoele

first: Geert

last: De Jaeger


title: Analysis of gene expression in sublines of DU145 human prostate cancer cells created through in vivo metastatic selection

status: Public on Oct 29 2013

city: Boston

first: Jacqueline

last: Banyard

state: MA

address: 300 Longwood Ave

department: Surgery

institute: Boston Childrens Hospital

summary:
DU145 human prostate cancer cells were injected into the prostate of nude mice and cells metastasizing to lymph node (LN1) grown and experiment repeated to make LN2-4.
DU145 human prostate cancer cells were injected into the tail vein of nude mice and cells metastasizing to lung (ivLU1) grown and experiment repeated to make ivLU2-4.

overall_design: 8 groups representing individual cell lines

first: Diane

last: Bielenberg


title: MicroRNA expression in DU145 sublines metastatic to lymph nodes

summary:
Comparison of non-coding RNA profiling by array in sublines of DU145 human prostate cancer cell lines created by in vivo cycling
Cell lines created by removal and growth of metastatic human DU145 tumor cells from mouse lymph node (metastasized from prostate xenograft) for LN cells and extracted from lung after intravenous injection (ivLU cells). Cell line numebr represented number of in vivo cycles of metastatic selection

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Six condition experiment, individual cell line for each sample on array

first: Bruce

last: Zetter


title: Gene expression profiles of human hepatocellular carcinoma (training set 2)

summary: Hepatocellular carcinoma (HCC) in young subjects is rare but more devastating. We hypothesize that genes and etiological pathways are unique to young HCC (yHCC; ≤40 years old at diagnosis) patients. We therefore compared the gene expression profiles between yHCCs and HCCs from elderly patients.

overall_design: 16 young HCC were collected from patients aged less than 40. 16 elder HCC profiles were downloaded from the Expression Project for Oncology (expO) of the International Genomics Consortium, with accession number GSE2109 in GEO database.

first: Hsei-Wei

last: Wang

first: SSu-Yi

last: Huang

first: Tsung-Han

first: Gar-Yang

last: Chau

first: Chien-Yi

last: Tung

first: Chien-Wei

last: Su

first: Jaw-Ching

last: Wu


title: Down-regulation of CD9 by methylation decreased bortezomib sensitivity in multiple myeloma

status: Public on Mar 13 2014

city: Hangzhou

first: Xiaotong

last: Hu

address: Qingchun East Road #3

institute: Zhejiang University

summary:
Bortezomib therapy has been proven successful for the treatment of relapsed and/or refractory multiple myeloma (MM). However, both intrinsic and acquired resistance has already been observed. In this study, we explored the relationship between CD9 expression and bortezomib sensitivity in MM
Both intrinsic and acquired resistance has already been observed. In this study, we explored the relationship between CD9 expression and bortezomib sensitivity in MM. We found that down-regulation of CD9 by methylation decreased bortezomib sensitivity in multiple myeloma.

overall_design: A six chip study using total RNA recovered from three separate wild-type cultures of U266 cells and three separate cultures of U266 with CD9 overexpression. Each chip measures the expression level of 45,033 genes from Homo sapiens with fourteen 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.


title: Transcriptional consequences of manipulating the candidate schizophrenia susceptibility gene miR-137 in human neural progenitor cells

status: Public on Feb 10 2014

city: Cardiff

first: Matthew

middle: James

last: Hill

address: Maindy Road

institute: Cardiff University

summary: In the largest published genome-wide association study (GWAS) of schizophrenia to date (PGC1), the most significant association (P = 1.6 X 10-11) was observed at an intronic variant (rs1625579) within the MIR137 host gene (MIR137HG). In this study we have performed genome-wide RNA profiling of a human foetal neural progenitor cell line following miR-137 manipulation, in order to identify gene expression changes through which genetic variation at the MIR137HG locus could confer susceptibility to schizophrenia.

overall_design: Total RNA extracted from human neural progenitor cells manipulated with either mir137 inhibitor or mimic. 4 replicates per group. Genome wide transcript levels were then measured using gene expression microarrays.

first: Jacek

middle: G

last: Donocik

first: Richard

last: Killick

first: Rosamond

last: Nuamah

first: Charles

last: Mein

first: Ricardo

last: Sainz-Fuertes

first: Nicholas

last: Bray


title: Molecular signatures differentiate immune states in Type 1 Diabetes families

status: Public on May 13 2014

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary: The complex milieu of inflammatory mediators associated with many diseases is often too dilute to directly measure in the periphery, necessitating development of more sensitive measurements suitable for mechanistic studies, earlier diagnosis, guiding selection of therapy, and monitoring interventions.  Previously, we determined that plasma of recent-onset (RO) Type 1 diabetes (T1D) patients induce a proinflammatory transcriptional signature in fresh peripheral blood mononuclear cells (PBMC) relative to that of unrelated healthy controls (HC). Here, using an optimized cryopreserved PBMC-based protocol, we analyzed larger RO T1D, HC, and healthy T1D sibling cohorts. In addition, we examined T1D progression by looking at longitudinal samples.

overall_design: UPN727 cells were stimulated with Auto-antibody-negative (AA-) High HLA Risk Siblings plasma (n=30), Auto-antibody-negative (AA-) Low HLA Risk Siblings plasma (n=42), Recent onset T1DM plasma cultured with IL1RA (n=42), or longitudinal series plasma on T1DM progressor (n=27 chips, 5 series), on auto-antibody-positive (AA+) High HLA Risk Siblings (n=54 chips, 9 series), on auto-antibody-negative (AA-) High HLA Risk Siblings (n=60 chips, 12 series), on auto-antibody-negative (AA-) Low HLA Risk Siblings (n=31 chips, 6 series). Gene expression analysis was perfromed in order to evaluate the transcriptional signature associated with T1D.

first: Yi-Guang

last: Chen

first: Mary

last: Kaldunski

first: Shuang

last: Jia

first: Joanna

last: Kramer

first: Rhonda

last: Geoffrey

first: Mark

last: Roethle

first: Jeffery

last: Woodliff

first: Carla

last: Greenbaum

first: Xujing


title: Plant Leaves: Pinellia pedatisecta vs Pinellia ternata

city: hangzhou

first: miao

last: dong

address: No.2 street

institute: Zhejiang Sci-Tech University

summary: miRNA expression profiling of Pinellia pedatisecta leaves comparing Pinellia ternata leaves in the same condition. Then we compared the accumulation of known miRNA families using microarray signals to identify further the differential miRNA expression between Pinellia pedatisecta and Pinellia ternata.

sample_organism:
Pinellia pedatisecta
Pinellia ternata

platform_organism:
Pinellia pedatisecta
Pinellia ternata

overall_design: Pinellia pedatisecta vs Pinellia ternata, independently grown and harvested. Each sample are mixed. One replicate per array.

first: Tao

last: Xu

first: Miao

last: Dong


title: Transcriptional changes in Zea mays seedlings treated with insect elicitor (volicitin).

status: Public on Sep 19 2013

city: San Antonio

first: Jurgen

last: Engelberth

state: Texas

address: One UTSA Circle

institute: University of Texas at San Antonio

summary: Insect elicitors, in particular fatty acid amides like volicitin, have been known to induce defense-related gene expression. Here we investigated transcriptional changes in response to volicitin 60min after treatment locally and in distal parts of the treated leaf.

overall_design: 3-Week old Zea mays seedling (inbred line B73) were treated with pure volicitin (1nmol per plant). Controls were untreated. Plants were for 60 min. The second leaf was then taken and a segment of 1 cm cut around the damage site and shock-frozen in liquid N2. 3 segments from 3 individual leaves were pooled for one biological replicate and then stored at -85°prior to RNA extraction. For distal gene expression analysis a 1cm segment was cut about 3 cm leaf upwards from the volicitin application site and also frozen in  liquid N2. 3 segments from 3 individual leaves were pooled for one biological replicate and then stored at -85°prior to RNA extraction. 2 biological replicates were performed for each treatment with one dye swap (second sample).


title: Identification and functional analysis of SHISA2 overexpressed in high-grade prostate cancer cells.

status: Public on Sep 13 2013

city: Nankoku

first: Kenji

last: Tamura

address: Kohasu, Oko-cho

department: Urology

institute: Kochi University

summary: We identified a novel molecular target and diagnostic biomarker, SHISA2, as an overexpressed gene in high-grade prostate cancer (PC) cells. To understand the association of SHISA2 overexpression with the aggressiveness of high-grade PC, we performed gene expression analysis using a cDNA microarray.

overall_design: Gene expression patterns of PC-3 cells transfected with the two shRNA expression vectors (siSHISA2 and siCONTROL) were compared.

first: Hatsune

last: Sakoda

first: Taro

last: Shuin


title: The distant Microbial communities in Tibetan alpine meadow based on Geochip 4.0

status: Public on Nov 16 2013

first: Yunfeng

last: Yang

state: Beijing

address: Qinghuayuan Street

department: School of Environment

institute: Tsinghua University

summary: Due to its high altitude and extreme climate conditions, the Tibetan plateau is a region vulnerable to the impact of climate changes and anthropogenic perturbation, thus understanding how its microbial communities function may be of high importance. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, aiming to explore potential microbial responses to climate changes and anthropogenic perturbation. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities in treatment site were distinct, compared with those in control site, e.g. shrubland vs grassland, grazing site vs ungrazing site, or warmer site vs colder site. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes.

overall_design: sixty-three samples were collected from four elevations (3200,3400,3600 and 3800 m) along a Tibetan alpine meadow, varied in treatments of grassland or shurbland, grazing or ungrazing, in situ or transplanted; Three replicates in each treatment

first: Houjuan

last: Chu


title: Comparison after 4 and 52 h (Chloro-Sap)

status: Public on Nov 01 2014

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: cea12-02_chlorosap - comparison after 4 and 52h - To observe the effects of guanosine penta/tetraphosphate on gene expression - Plants of four different genotypes (43A10.6, 44B1.3, H1 P3.2 and Col-0) were grown for ten days on MS/2 plates with 1% sucrose under 80µE light in long-day conditions (16 hours of light, 8 hours of dark). Plants were treated at 10:30 in the morning (Time 0; 10:30 is 3 and a half hours after the onset of the light period) by flooding with 30uM dexamethasone (in aqueous solution with 0,3 % DMSO and 0,033 % Silwet L-77) for 5 minutes . Samples were taken at 4 hrs and 52 hrs after T0. Aerial parts of the seedlings were rapidly harvested and frozen in liquid nitrogen.

overall_design: 9 dye-swap - normal vs transgenic comparaison,time course

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Ben

last: Field

first: Marie-Laure

last: Martin-Magniette


title: Effect of miR-144 and miR-451 expression on lung epithelial cell responses to influenza infection at 1 and 18 hours.

status: Public on Sep 11 2013

first: Aderem

last: Lab

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary:
Antiviral responses must be regulated to rapidly defend against infection while minimizing inflammatory damage, but the mechanisms for establishing the magnitude of response within an infected cell are not well understood. miRNAs are small non-coding RNAs that negatively regulate protein levels by binding target sequences on their cognate mRNA. Here we identify miR-144 as a negative regulator of the host antiviral response. Ectopic expression of miR-144 resulted in increased replication of three RNA viruses, influenza, EMCV, and VSV, in primary mouse lung epithelial cells.
To elucidate the mechanism whereby miR-144 increases influenza replication within lung epithelial cells, immortalized murine Type I epithelial cells (Let1 cells) stably over-expressing miR-144 were infected with influenza A for 1 or 18 hours and the transcriptional profile was compared with those of infected control cells. This systems biology approach identified the transcriptional network regulated by miR-144 and demonstrated that it controls the TRAF6/IRF7 antiviral response by post-transcriptionally suppressing TRAF6 levels. In vivo ablation of miR-144 reduced influenza replication within the lung.

overall_design: 16 RNA samples from immortalized murine Type I airway epithelial cells (Let1 cells) were analyzed using Agilent microarrays. Cells expressing miR-144, miR-451, or a vector control (GFP) were analyzed after infection with PR8 influenza virus (MOI=5) for 1 or 18 hours.

first: Rosenberger

last: Carrie

first: Alan

last: Aderem


title: Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors

status: Public on Feb 26 2015

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

department: Pathology

country: Netherlands

institute: Erasmus MC

summary:
Germ cell tumors (GCT) originate from germ cells at different developmental stages (GCT type I – V) They are thought to inherit their methylation profile from (early embryonic) germ cells which undergo a characteristic epigenetic “reset” during maturation. This study aims to provide insight into the developmental timing and underlying biology of the various subtypes of GCTs and their (embryonic) cells of origin by identifying specific and global methylation differences between GCT subtypes. In total, 91 type I-IV GCTs and four cell lines were profiled using the Illumina HumanMethylation450 BeadChip (450K) platform. The data were pre-processed using a validated pipeline and analyzed using an in-house generated extension of the annotation manifest. Marked methylation differences were identified between GCT subtypes both on the global and local level (i.e. differentially methylated regions, imprinting control regions, promoters, etc). GCT subtypes indeed show major similarities to specific stages of (early) developing embryonic germ cells with regard to their methylation profile. The extended annotation manifest for the Illumina 450K platform and methylation datasets are readily available on GEO (GEO accession: GSE58538, GPL18809), providing an integrated hypothesis generating data source for future research.

File S1. Differentially methylated regions between tumors classes as discussed in Table 1 of the associated publication. All figures. Please investigate using the genomic position as search term.

File S2. Differentially methylated regions between GCT cell lines. DMRforPairs output. Significant results only. Please start from the html file.

overall_design:
91 germ cell tumors of various histologies were investigated for their methylation profile. Methylation detection was performed using Illumina’s HumanMethylation450 BeadChip. 14 type I teratomas (TE) were included of which 6 were located sacral (3 male: I.TE.s.m; 3 female: I.TE.s.f), 4 were located in the testis (I.TE.t) and 3 were located in the ovary (I.TE.o). 30 pure embryonal carcinomas (EC) were included as well as 21 mixed non seminomas (mNS). 12 seminomas of the testis (SE) were included as well as 4 dysgerminomas (their couterpart in the ovary). Finally, 4 spermatocytic seminomas (SS) and three dermoid cysts were analyzed. For a detailed overview the histological classification of germ cell tumors please see the publication linked to this data or associated literature [1-3]. Four cell lines were included, al modelling type II GCTs. Cell lines derived from EC include NT2[4-8], NCCIT [5, 9] and 2102EP[4-8]. TCam-2 closely resembles SE [10-12].
1. Oosterhuis, J.W. and L.H. Looijenga, Testicular germ-cell tumours in a broader perspective. Nat Rev Cancer, 2005. 5(3): p. 210-22.
2. Looijenga, L.H., Human testicular (non)seminomatous germ cell tumours: the clinical implications of recent pathobiological insights. J Pathol, 2009. 218(2): p. 146-62.
3. Woodward, P.J., et al., Testicular germ cell tumors, in World Health Organization Classification of Tumours Pathology and Genetics of the Urinary System and Male Genital Organs., J.N. Eble, et al., Editors. 2004, IARC Press: Lyon. p. 17-278.
4. Andrews, P.W., et al., A comparative study of eight cell lines derived from human testicular teratocarcinoma. Int J Cancer, 1980. 26(3): p. 269-80.
5. Andrews, P.W., et al., Comparative analysis of cell surface antigens expressed by cell lines derived from human germ cell tumours. Int J Cancer, 1996. 66(6): p. 806-16.
6. Wang, N., et al., Nonrandom abnormalities in chromosome 1 in human testicular cancers. Cancer Res, 1980. 40(3): p. 796-802.
7. Fogh, J. and G. Trempe, New Human Tumor Cell Lines, in Human Tumor Cells in Vitro, J. Fogh, Editor. 1975, Springer US. p. 115-159.
8. Fogh, J., Cultivation, characterization, and identification of human tumor cells with emphasis on kidney, testis, and bladder tumors. Natl Cancer Inst Monogr, 1978(49): p. 5-9.
9. Teshima, S., et al., Four new human germ cell tumor cell lines. Lab Invest, 1988. 59(3): p. 328-36.
10. Eckert, D., et al., TCam-2 but not JKT-1 cells resemble seminoma in cell culture. Cell Tissue Res, 2008. 331(2): p. 529-38.
11. de Jong, J., et al., Further characterization of the first seminoma cell line TCam-2. Genes Chromosomes Cancer, 2008. 47(3): p. 185-96.
12. Mizuno, Y., et al., [Establishment and characterization of a new human testicular germ cell tumor cell line (TCam-2)]. Nihon Hinyokika Gakkai Zasshi, 1993. 84(7): p. 1211-8.

middle: A

first: Ad

last: Gillis

first: Lambert

middle: C

last: Dorssers

first: Leendert

last: Looijenga


title: Gene and miRNA expression data in the DU145-LN metastatic cell series

first: Jacqueline

last: Banyard

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: Gaucher Disease: Transcriptome Analyses Using Microarray or mRNA Sequencing in a Mouse Model Treated with velaglucerase alfa or imiglucerase [RNA-Seq]

status: Public on Sep 07 2013

city: Cincinnati

first: nupur

last: dasgupta

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hopital Medical Center

summary: The comparative whole genome transcriptome effects of two similar pharmaceuticals, imig or vela, on a Gaucher disease mouse model, 9V/null, were evaluated by two commonly used platforms, mRNA-Seq and microarray. Also, statistical methods, DESeq and edgeR for mRNA-Seq and Mixed Model ANOVA for microarray, were compared for differential gene expression detection. The biological pathways were similar between two platforms. Cell growth and proliferation, cell cycle, heme metabolism, and mitochondrial dysfunction were the most altered functions associated with the disease process. Although the two biopharmaceuticals have a very similar structure and function, imig- and vela- treatment in the mice differentially affected disease-specific pathways indicating the action of the two drugs on the disease process in the visceral tissues of Gaucher mouse model differ significantly at the molecular level. This study provides a comprehensive comparison between the two platforms (mRNA-Seq and microarray) for gene expression analysis and addresses the contribution of the different methods involved in the analysis of such data. The results also provide insights into the differential molecular effects of two similar biopharmaceuticals for Gaucher disease treatment

overall_design: 9V/null mice (Gaucher mouse model) were injected weekly via tail vein with 60U/kg/wk of imig or vela for 8 wks. Control 9V/null mice were injected with same volume of saline. Wt mice were untreated. Age and strain matched mice were used for the study. Also, statistical methods, DESeq and edgeR for mRNA-Seq and Mixed Model ANOVA for microarray, were compared for differential gene expression detection. Cell growth and proliferation, cell cycle, heme metabolism, and mitochondrial dysfunction were the most altered functions associated with the disease process.  The results also provide insights into the differential molecular effects of two similar biopharmaceuticals for Gaucher disease treatment.

first: Nupur

last: Dasgupta

first: Sunghee

last: Oh

first: You-hai

last: Xu

first: Ying

last: Sun

first: Li

last: Jia

first: Mehdi

last: Keddache

first: Gregory

last: Grabowski


title: Gaucher Disease: Transcriptome Analyses Using Microarray or mRNA Sequencing in a Mouse Model Treated with velaglucerase alfa or imiglucerase


title: Gaucher Disease: Transcriptome Analyses Using Microarray or mRNA Sequencing in a Mouse Model Treated with velaglucerase alfa or imiglucerase [Affymetrix]

summary: The comparative whole genome transcriptome effects of two similar pharmaceuticals, imig or vela, on a Gaucher disease mouse model, 9V/null, were evaluated by two commonly used platforms, mRNA-Seq and microarray. Also, statistical methods, DESeq and edgeR for mRNA-Seq and Mixed Model ANOVA for microarray, were compared for differential gene expression detection. The biological pathways were similar between two platforms. Cell growth and proliferation, cell cycle, heme metabolism, and mitochondrial dysfunction were the most altered functions associated with the disease process. Although the two biopharmaceuticals have a very similar structure and function, imig- and vela- treatment in the mice differentially affected disease-specific pathways indicating the action of the two drugs on the disease process in the visceral tissues of Gaucher mouse model differ significantly at the molecular level. This study provides a comprehensive comparison between the two platforms (mRNA-Seq and microarray) for gene expression analysis and addresses the contribution of the different methods involved in the analysis of such data. The results also provide insights into the differential molecular effects of two similar biopharmaceuticals for Gaucher disease treatment.

overall_design: 9V/null mice (Gaucher mouse model) were injected weekly via tail vein with 60U/kg/wk of imig or vela for 8 wks. Control 9V/null mice were injected with same volume of saline. Wt mice were untreated. Age and strain matched mice were used for the study. Also, statistical methods, DESeq and edgeR for mRNA-Seq and Mixed Model ANOVA for microarray, were compared for differential gene expression detection.Cell growth and proliferation, cell cycle, heme metabolism, and mitochondrial dysfunction were the most altered functions associated with the disease process.  The results also provide insights into the differential molecular effects of two similar biopharmaceuticals for Gaucher disease treatment.


title: Endogenous miRNA targets identified by sequencing of the Soybean degradome

status: Public on Dec 20 2013

city: Guangzhou

first: cunyi

last: yang

address: No. 483 Wushan Road, the Tianhe District of the city

department: College of Agriculture

institute: South China Agricultural University

summary: To identify more targets in soybean, particularly specific targets of Cd-stress-responsive miRNAs, high-throughput degradome sequencing was used. In total, we obtained 8913111 raw reads from the library which was constructed from a mixture of four samples (HX3-CK, HX3-Cd-treatment, ZH24-CK and ZH24-Cd-treatment). After removing the reads without the CAGAG adaptor, 5430126 unique raw-reads were obtained. The unique sequences were aligned to the G. max genome database, and 6516276 reads were mapped to the genome. The mapped reads from the libraries represented 51481 annotated G. max genes.

overall_design: Identification of miRNA targerts in soybean roots

first: Xiaolong

last: Fang

first: Cunyi

last: Yang


title: miRNAs expression in two soybean root with contrasting cadmium tolerance

status: Public on Aug 31 2013

address: NO. 483 Wushan Road Tianhe District

institute: College of Agriculture, South China Agricultural University

summary: MicroRNAs (miRNAs) play crucial roles in regulating the expression of various stress responses genes in plant. To investigate soybean (Glycine max) miRNAs involved in the response to cadmium (Cd), microarrays containing 953 unique miRNA probes were employed to identify differences in the expression patterns of the miRNA between different genotypes, Huaxia3 (HX3, Cd-tolerant) and Zhonghuang24 (ZH24, Cd-sensitive). A total of 26 Cd-responsive miRNAs were identified, of which nine were detected in both cultivars, while five were expressed only in HX3 and 12 were only in ZH24.

overall_design: In the study presented here, four root samples from two contrast soybean cultivars, HX3 (Cd-tolerant) and ZH24 (Cd-sensitive), with or without (Cd) cadmium, harvested at 6, 12, 24, 48, 96 and 144 h after the initiation of Cd treatment, was used to acquire expression profiles of a total of 953 unique genes, leading to the successful construction of supervised.


title: PHF6 knockdown in rat cortical neurons

status: Public on Aug 01 2013

first: Chi

last: Zhang

address: 107 Avenue Louis Pasteur

institute: Harvard Medical School

summary: E18 embryonic rat cortical neurons cultured in vitro are infected with lentivirus expressing control or PHF6shRNA-2, and harvested 5 days after infection

overall_design: pLL3.7 lentivirus expressing control or PHF6shRNA-2 was generated in 293T cells and concentrated using ultracentrifuge. In vitro cultured cortical neurons were infected and RNA was harvested 5 days after infection. PHF6 knockdown was validated by QPCR before sample was processed for microarray analysis.


title: Differential Molecular Effects of Imiglucerase and Velaglucerase Alfa in Gaucher Disease Mice


title: The NRF2-KEAP1 pathway is an early responsive gene network in arsenic exposed lymphoblastoid cells

status: Public on Oct 24 2013

city: Mexico

first: Angelica

last: Martinez

state: DF

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Tlalpan

department: Investigación

country: Mexico

institute: Instituto Nacional de Medicina Genómica

summary:
Inorganic arsenic, a major environmental contaminant, has risen as an important health problem worldwide. More detailed identification of the molecular mechanisms associated with iAs exposure would help to establish better strategies for prevention and treatment. Although chronic iAs exposures have been previously studied there is little to no information regarding the early events of exposure to iAs. To better characterize the early mechanisms of iAs exposure we conducted gene expression studies using sublethal doses of iAs at two different time-points. The major transcripts differentially regulated at 2 hrs of iAs exposure included antioxidants, detoxificants and chaperones. Moreover, after 12 hrs of exposure many of the down-regulated genes were associated with DNA replication and S phase cell cycle progression. Interestingly, the most affected biological pathway by both 2 or 12 hrs of iAs exposure were the Nrf2-Keap1 pathway, represented by the highly up-regulated HMOX1 transcript, which is transcriptionally regulated by the transcription factor Nrf2. Additional Nrf2 targets included SQSTM1 and ABCB6, which were not previously associated with acute iAs exposure.
Signalling pathways such as interferon, B cell receptor and AhR route were also responsive to acute iAs exposure. Since HMOX1 expression increased early (20 min) and was responsive to low iAs concentrations (0.1 M), this gene could be a suitable early biomarker for iAs exposure. In addition, the novel Nrf2 targets SQSTM1 and ABCB6 could play an important and previously unrecognized role in cellular protection against iAs

overall_design: We used human lymphoblastoid cell line (CL-1), immortalized with Epstein-Barr virus. Cell cultures were propagated in RPMI media supplemented with 10% fetal bovine serum (FBS), L-glutammine 2 mM and antiobiotics penicillin and 10 mg/ml streptomycin)  at 37ºC in an atmosphere of 5% CO2. In the case of primary cultures, 1% phytohemaglutinine were added. Cell cultures (1x106) were treated with 5µM sodium arsenite  for 2 and 12 hrs while control cultures were incubated with PBS. Nine biological replicates for each condition were used for microarray analysis. After iAs treatment, total RNA from each biological replicate was isolated with Trizol. From the 9 biological replicates performed on each condition, we generated 3 pools at a concentration of 300 ng/µL, where each pool was processed to a single microarray platform.

first: Emilio

last: Cordova

last: Martinez-H


title: Temperature-dependent alternative splicing of FLM controls flowering in Arabidopsis thaliana

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

institute: Max Planck Institute for Developmental Biology

summary: How plants control the transition to flowering in response to ambient temperature is only beginning to be understood. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles  in this process. FLM is subject to temperature-dependent alternative splicing, producing two  splice variants, FLM-β and FLM-δ, which compete for interaction with the floral repressor SVP.  The SVP/FLM-β complex is predominately formed at low temperatures and prevents precocious flowering. In contrast, the competing SVP FLM-δ complex is impaired in DNA binding and acts as a dominant negative activator of flowering at higher temperatures. Our results demonstrate the importance of temperature-dependent alternative splicing in modulating the timing of the floral transition in response to environmental change.

overall_design: ChIP-seq A. thaliana FLM (3 replicates for gFLM and 2 replicates for FLM splice variants)

first: David

last: Posé

first: Leonie

last: Verhage

first: Levi

last: Yant

first: Johannes

last: Mathieu

first: Gerco

last: Angenent

first: Richard

last: Immink

first: Markus

last: Schmid


title: Differential Molecular Effects of Imiglucerase and Velaglucerase Alfa in Gaucher Disease Mice [RNA-Seq]

first: nupur

last: dasgupta

summary: Gaucher disease type 1 is an inborn error of metabolic disease with the defective activity of the lysosomal enzyme acid b-glucosidase (GCase). Enzyme replacement/reconstitution therapy (ERT), infusions with purified recombinant GCases, is efficacious in reversing hematologic, hepatic, splenic, and bony disease manifestations in Gaucher type 1 patients. However, the tissue specific molecular events in Gaucher disease and their response to therapy are not known yet. To explore the molecular events underlying GCase treatment, we evaluated the tissue-specific gene expression profiles and molecular responses in our Gaucher disease mouse model, which were treated with two FDA approved commercially available GCases, imiglucerase (imig) and velaglucerase alfa (vela). Using microarray and mRNA-Seq techniques, differentially expressed genes (DEGs) were identified in the spleen and liver by the direct comparison of imig- vs. vela- treated mice. Among them three gene expression networks were derived from these spleens: 1) cell division/proliferation, 2) hematopoietic system and 3) inflammatory/macrophage response. Our study showed the occurrence of differential molecular pathophysiologic processes in the mice treated with imig compared with vela even though these two biosimilars had the same histological and biochemical efficacy

overall_design: 9V/null mice (Gaucher mouse model) were injected weekly via tail vein with 60U/kg/wk of imig or vela for 8 wks. To understand the molecular events underlying GCase treatment, we evaluated the tissue-specific gene expression profiles and molecular responses in our Gaucher disease mouse model, which were treated with two FDA approved commercially available GCases, imiglucerase (imig) and velaglucerase alfa (vela).

first: You-hai

last: Xu

first: Nupur

last: Dasgupta

first: Sunghee

last: Oh

first: Ying

last: Sun

first: Li

last: Jia

last: Keddache

first: Sonya

last: Barnes


title: miRNA profiling of plasma samples: patients with unstable coronary artery disease and controls

status: Public on Aug 13 2013

first: Hong

last: Chen

state: China

address: Xizhimen South Street 11, Xicheng District, Beijing

department: Dept. of Cardiology

institute: Peking University People’s Hospital

summary: This study describes a circulating miRNA signature of unstable angina (UA), which may be used as a novel biomarker for unstable coronary artery disease (CAD). The Taqman low-density miRNA array were used to identify distinct miRNA expression profiles in the plasma of patients with typical UA and angiographically documented CAD (UA group, n = 13) compared to individuals with non-cardiac chest pain (control group, n = 13).

overall_design: EDTA-plasma samples were obtained before the cardiac catheterization procedure.The study included 2 groups that were classified according to angiographic evidence and clinical evaluation of chest pain. Patients with chest pain or discomfort but with angiographic exclusion of coronary atherosclerosis were enrolled in the control group (n = 13). Chest discomfort referred to the following complaints: chest pain, pressure, tightness, or heaviness; pain that radiated to the neck, jaw, shoulders, back, or one or both arms; and persistent shortness of breath. Patients with typical unstable angina (UA) and angiographically documented CAD were enrolled in the UA group (n = 13).

first: Jingyi

last: Ren


title: Gene expression data from 16-month and 3-month old male rats, with three different levels of activity over the life span: sedentary, twice weekly physical activity, regular running wheel exercise.

status: Public on Oct 18 2013

city: Oxford

first: Helaine

middle: Mary

last: Alessio

address: 420 S. Oak Street

department: Kinesiology and Health

institute: Miami University

summary:
Gene expression data at rest and immediately post 30 min submaximal exercise in 3 month and 16 month old male rats, some of which were sedentary (SED), had access to a physical activity box twice weekly (PA) and some of which had daily access to a running wheel (EX).
We used microarrays to detail global gene expression underlying select health-related phenotypes and identified differentially expressed genes among the three groups.

overall_design: Young (3 month) and old (16 month) male rats were separated into three different groups: Sedentary (SED), twice-weekly physical activity (PA), and regular exercise (EX). Animals were sacrificed either at rest or after 30 min of sub maximal exercise. Then, a portion of cardiac tissue was collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Ann

middle: E

last: Hagerman


title: Genome-wide GTL1 binding sites in Arabidopsis thaliana

city: Columbus

first: Kengo

last: Morohashi

address: 1060 Carmack Rd

department: Molecular Genetics

institute: The Ohio State University

type: Genome binding/occupancy profiling by genome tiling array

summary: To understand how GTL1 regulates cell growth, we first identified its potential direct targets by the chromatin immunoprecipitation followed by the hybridization on an Affymetrix Arabidopsis Tiling 1.0R array (ChIP-chip). To enrich the genomic region bound by GTL1 in vivo, we harvested whole aerial parts of 12-day-old gtl1-1 plants complemented with the pGTL:GTL1:GFP constructs and immunoprecipitated the chromatin fragments associated with GTL1-GFP proteins using antibodies against GFP. After applying a cut-off P-values of 0.001of MAT (Model-based  analysis of tiling array), we identified a total number of 3,900 putative immediate target genes that showed consistent binding by GTL1.

overall_design: Two IP chips compared to two Input chips.

first: Christian

last: Breuer

first: Erich

last: Grotewold

first: Keiko

last: Sugimoto