title: Ex vivo mouse model for hepatic schistosomiasis

status: Public on Dec 12 2014

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

summary: An ex vivo approach to studying hepatic schistosomiasis used thick naive mouse liver sections and sterile culturing. This tissue is unfixed, unfrozen, and alive for subsequent in vitro studies. We have cultured and monitored these sections for up to 48 hrs noting unchanged gross hepato-cellular morphology, and no significant increases in hepatotoxicity as demonstrated by media liver enzyme concentrations. Liver slices were treated with soluble egg antigen from Schistosoma japonicum eggs and cultured for 48hrs. Transcriptional changes were then analysed by microarray.

overall_design: The gene expression profile of the naive mouse liver slices cultered with and without the additional of soluble egg antigen (SEA) from Schistosoma japonicum eggs. Microarray analysis was performed on cRNA synthesised from total RNA. The liver of female 6 week old C57BL/6 mice were removed and then sectioned at 250um thickness using a  vibrotome. Sections were cultered at 37oC and 5%CO2 in in William’s Medium E containing 25 mM glucose, 10 mg/ml gentamycin and 10% FBS. SEA was added at 10ug/ml and sections sampled at timepoints 0, 4hr, 24hr and 48hrs. Illumina mouse ref8_V2 arrays were used and fold changes compared to whole intact, precut tissue.

first: Donald

last: McManus


title: Neonatal Skeletal Progenitors

status: Public on Jan 29 2015

city: Stanford

first: Charles

middle: Chan

last: KF

state: CA

address: 265 Campus Drive

country: USA

institute: Stanford

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

overall_design: Refer to individual Series

middle: K

last: Chan

first: Michael

middle: T

last: Longaker

first: Irving

middle: L

last: Weissman


title: PDGF and FGF treatment in E13.5 MEPMs

status: Public on Nov 11 2014

city: San Francisco

first: Harish

last: Vasudevan

address: 555 Mission Bay Blvd South, Room 452H

department: Radiation Oncology

institute: University of California San Francisco

type: Expression profiling by high throughput sequencing

summary: Receptor tyrosine kinase signaling is critical for mammalian craniofacial development, but the key downstream transcriptional effectors remain unknown. We demonstrate that SRF is induced by both PDGF and FGF signaling in mouse embryonic palatal mesenchyme cells, and Srf neural crest conditional mutants exhibit facial clefting accompanied by proliferation and migration defects. Srf and Pdgfra mutants interact genetically in craniofacial development, but Srf and Fgfr1 mutants do not. This signal specificity is recapitulated at the level of cofactor activation: while both PDGF and FGF target gene promoters show enriched genome-wide overlap with SRF ChIP-seq peaks, PDGF selectively activates a network of MRTF-dependent cytoskeletal genes. Collectively, our results identify a novel role for SRF in proliferation and migration during craniofacial development and delineate a mechanism of receptor tyrosine kinase specificity mediated through differential cofactor usage, leading to a unique PDGF-responsive SRF-driven transcriptional program in the midface.

overall_design: Serum Starved MEPMs (4 replicates), 1 hr PDGF treated MEPMs (4 replicates), 1 hr FGF treated MEPMs (3 replicates)

middle: N

first: Philippe

last: Soriano


title: C.elegans treated with control or elt-2 RNAi during adulthood and exposed to E. coli or P. aeruginosa

status: Public on Dec 04 2014

city: Berkeley

last: Shapira

address: 3060 Valley Life Sciences Bldg room 5163

department: Integrative Biology

institute: UC Berkeley

summary:
Transcriptional profiling of adult C.elegans exposed to E.coli or to GFP-expressing P. aeruginosa (strain PA14).
For P. aeruginosa exposure, worms were separated into 2 groups - fully colonized (green) or non-colonized (dark).

overall_design:
Six conditions ( control or elt-2 RNAi ; E.coli, P. aeurginosa colonized, and P. aeurginosa non-colonized).
2-color arrrays, each sample co-hybridized with the same reference RNA sample from mixed stage C.elegans cultures
Worms were either sorted using the wormsorter (WS) or were hand picked (HP) under a fluorescent stereoscope

first: Kwame

last: Twumasi-Boateng


title: Comparative expressional analyses between a diffuse-type gastric cancer cell line HSC-60 and its highly metastatic subline 60As6 by microarray

status: Public on Dec 31 2014

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

country: Japan

institute: National Cancer Center Reseach Institute

summary: Although peritoneal dissemination is a major obstacle in treating diffuse-type GC patients, the mechanism is still unclear. To address this phenomenon from the viewpoint of molecular biology, we established a highly peritoneal-metastatic cell line, 60As6, from a diffuse-type GC derived cell line, HSC-60, through a six-times iterative in vivo selection consisting of an orthotopic inoculation of the tumor cells and the isolation of highly-metastatic ones from the ascites of immunodeficient mice. To assess the biological differences between HSC-60 and 60As6 cells, we compared gene expression profiles for both cell lines by microarray analysis. Down-regulation of three gastric pit cell differentiation markers and some cytokeratins were found in 60As6. By contrast, several stem cell markers were up-regulated in this cell line. The expression profile suggests that 60As6 has a strong mensencymal phenotype, which is a characteristic of epithelial cell-derived CSCs.

overall_design: We conducted microarray analyses two times by using GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). The procedures were conducted according to the suppliers’ protocols. The expression value (average difference: AD) of each gene was calculated using GeneChip Analysis Suite version 5.0 software (Affymetrix). The mean of AD values in each experiment was 1000 to reliably compare variable multiple arrays. By Wilcoxon u-test (p < 0.05) and a 2-fold change, 684 genes were selected as specific genes for 60As6 and 60As6Luc cells, and 1150 genes were selected as specific genes for HSC-60 and HSC-60Luc cells.

first: Rie

last: Komatsuzaki


title: Gene expression data from substantia nigral regions of MPTP-intoxicated mouse brain by acupuncture

status: Public on Dec 27 2014

city: Seoul

first: Sabina

last: Lim

address: #1 Hoegi-dong Dongdaemoon-gu

country: South Korea

institute: East-West Medical Research Institute, Kyung Hee University

summary:
Parkinson’s disease (PD) is a representative neurodegenerative disease that is characterized the death of dopamine-generating cells in the substantia nigra (SN). Acupuncture stimulations at GB34 and LR3 resulted in the enhanced survival of dopaminergic neurons in the SN in the parkinsonism animal models. SN is known as an important player in brain function, in particular, movement. Behavioral tests showed that acupuncture stimulations improved the motor dysfunction in a previous study by almost 87.7%. This study investigated the changes of gene expression profiles in the SN regions of the relatively chronic parkinsonism model and demonstrated the genes that may be related to the inhibitory effect of acupuncture on the change in gene expression in the SN induced by an 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) intoxication using a whole transcript array.
We investigated gene expression profile changes in the substantia nigral region of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced parkinsonism models after acupuncture at the acupoints GB34 and LR3

overall_design: C57BL/6 mice were divided into four experimental groups; ① C: Control, ② M: MPTP-treatment only, ③ MA: MPTP- and acupuncture-treatment at acupoints GB34 and LR3, ④ MNA: MPTP- and acupuncture-treatment at non-acupoints. Total RNA was isolated from two brains' substantia nigral regions of each experimental group (4 experimental group × 2 samples of each experimental group = total 8 samples).

first: Sujung

last: Yeo

first: Yeon-Mi

last: Hong

first: Yeong-Gon

last: Choi


title: Identification of gene expression pattern for glioma stem cells in low grade glioma

status: Public on Dec 01 2014

city: Saint Louis

first: Yi-Hsien

last: Chen

state: Missouri

address: 4566 Scott Avenue

department: Neurology

institute: Washington University School of Medicine

summary:
Gioma stem cells from Nf1-associated optic gliomas and NSCs from third ventricle zone show differencies in gene expression patterns and physiological functions.
We used microarrays to identify differential gene expression between glioma stem cells and the control counterparts including the wild type and Nf1-/- neural stem cells from the third ventricle.

overall_design: Cultured glioma stem cells were isolated from mouse optic gliomas. Wild-type and Nf1-/- TVZ NSCs were generated from postnantal day 1 Nf1flox/flox pups. We sought to obtain neural stem cells from three independent cultures. There are 9 samples in total. 3 wild-type TVZ NSCs, 3 Nf1-/- TVZ NSCs, 3 glioma stem cells.

first: Da-Yong

last: Lee

first: David

middle: H

last: Gutmann


title: Pachymic acid inhibits growth and induces apoptosis of pancreatic cancer in vitro and in vivo by targeting ER stress

city: Indianapolis

first: shujie

last: cheng

state: IN

address: 1800 N Capitol Ave, E504

department: Methodist Research Institute

institute: Indiana University Health

summary:
Background: Pachymic acid (PA) is a purified triterpene extracted from medicinal fungus Poria cocos. In this paper, we investigated the anticancer effects of PA on human chemotherapy resistant pancreatic cancer cells.

Methods: Gemcitabine-resistant pancreatic cancer cells PANC-1 and MIA PaCa-2 were used, along with a xenograft model of MIA PaCa-2 cells implanted in mice. Apoptosis was assessed by quantitation of cytoplasmic histone-associated DNA fragments and expression of cleaved PARP. Differential expression of genes was identified using comparative DNA microarray analysis. Protein levels were determined by immunoblotting. Toxicology studies in vivo were assessed by detecting pathological changes in organs and liver enzyme profiles in plasma. Tumor tissues were analyzed by quantification of apoptotic bodies, qRT-PCR and immunoblotting.

Principal Findings: PA induced endoplasmic reticulum (ER) stress in chemotherapy resistant pancreatic cancer cells through activation of heat shock response and unfolded protein response related genes, which further triggered apoptosis. The involvement of ER stress was confirmed by increasing expression of XBP-1s, ATF4, Hsp70, CHOP and phospho-eIF2α. Moreover, 25 mg kg−1 of PA significantly suppressed MIA PaCa-2 tumor growth in vivo without toxicity, which correlated with induction of apoptosis, ER stress related genes and proteins expression.

Conclusions: Growth inhibition and induction of apoptosis by PA in chemotherapy resistant pancreatic cancer cells were associated with ER stress activation both in vitro and in vivo.

overall_design: Pancreatic cancer cell line treated with pachymic acid vs. control (untreated)

first: Shujie

last: Cheng

first: Jeanette

last: McClintick

first: Daniel

last: Sliva


title: Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition, based on hierarchical binding affinities

status: Public on Nov 10 2014

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

type: Non-coding RNA profiling by high throughput sequencing


title: Expression data from fracture hematoma tissue of young and old rats after 3days of rigid or semi-rigid fixation of an osteotomy

city: Berlin

first: Andrea

last: Ode

address: Augustenburger Platz 1

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary:
The long-term healing outcome of bone regeneration is known to depend not only on mechanical stability, but also on age and, more importantly, on the overlap of both parameters. Although especially the early healing period determines the healing outcome, it so far remains unclear which factor - mechanical loading or age - dominates this phase and how these factors interact on the molecular level in the early fracture hematoma.
We used microarrays to detail the global programme of gene expression underlying the influence of fixation stability in young and old rats and identified distinct classes of regulated genes during this process.

overall_design: At day three post-osteotomy, gene expression analyses of fracture hematoma tissue were performed for four groups of Sprague-Dawley rats with a 1.5-mm osteotomy gap in the femora with varying age (12 vs. 52 weeks - biologically challenging) and fixator stiffness (ridig vs. semi-rigid - mechanically challenging).

first: Patrick

last: Strube


title: Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition, based on hierarchical binding affinities (iCLIP)

summary: Target competition (ceRNA crosstalk) within miRNA-regulated gene networks has been proposed to influence biological systems. To assess target competition, we characterize and quantitate miRNA networks in two cell types. Argonaute iCLIP reveals that hierarchical binding of high to low affinity miRNA targets is a key characteristic of in vivo activity. Quantification of cellular miRNA and mRNA/ncRNA target pool levels indicates that miRNA-Target pool ratios and an affinity partitioned target pool accurately predict in vivo Ago binding profiles and miRNA susceptibility to target competition. Using single-cell reporters, we directly test predictions and estimate ~3,000 additional high affinity target sites can affect active miRNA families with low endogenous miRNA-Target ratios, such as miR-92/25. In contrast, the highly expressed miR-294 and let-7 families are not susceptible to increases of nearly 10,000 sites. These results show differential susceptibility based on endogenous miRNA-Target pool ratios and provide a physiological context for ceRNA competition in vivo.

overall_design: iCLIP in mouse embryonic stem cells expressing a single Ago family member, either dox-inducible FLAG-HA-hAgo2 (TT-FHAgo2) or untagged hAgo2 (TTAgo2).


title: Alterations in circulating miRNAs following early-stage breast cancer resection

status: Public on Nov 01 2014

city: Odense

first: Annette

middle: Raskov

last: Kodahl

address: Sdr. Boulevard 29

department: Oncology R

country: Denmark

institute: Odense University Hospital

summary: Introduction: Circulating microRNAs (miRNAs) exhibit remarkable stability and may serve as biomarkers in several clinical cancer settings. The aim of this study was to investigate changes in the levels of specific circulating miRNA following breast cancer surgery and evaluate whether these alterations were also observed in an independent data set.  Methods: Global miRNA analysis was performed on prospectively collected serum samples from 24 post-menopausal women with estrogen receptor-positive early-stage breast cancer before surgery and 3 weeks after tumor resection using global LNA-based quantitative real-time PCR (qPCR).   Results: Numbers of specific miRNAs detected in the samples ranged from 142 to 161, with 107 miRNAs detectable in all samples. After correction for multiple comparisons, 3 circulating miRNAs (miR-338-3p, miR-223 and miR-148a) exhibited significantly lower, and 1 miRNA (miR-107) higher levels in post-operative vs. pre-operative samples (p<0.05). No miRNAs were consistently undetectable in the post-operative samples compared to the pre-operative samples. Subsequently, our findings were compared to a dataset from a comparable patient population analyzed using similar study design and the same qPCR profiling platform, resulting in limited agreement.   Conclusions: A panel of 4 circulating miRNAs exhibited significantly altered levels following radical resection of primary ER+ breast cancers in post-menopausal women. These specific miRNAs may be involved in tumorigenesis and could potentially be used to monitor whether all cancer cells have been removed at surgery and/or, subsequently, whether the patients develop recurrence.

overall_design: 48 serum samples were prospectively collected from 24 patients with early stage breast cancer before and after surgery at Odense University Hospital. Serum was prepared within one hour of sample collection after centrifugation (2000 x g; 10 min at 20 ºC) and immediately stored at -80 ºC.

first: Pernille

last: Zeuthen

first: Harald

last: Binder

first: Ann

middle: S

last: Knoop

first: Henrik

middle: J

last: Ditzel


title: Gene expression profiles in the bovine corpus luteum (CL) of the estrous cycle and pregnancy: Possible roles of chemokines in regulating CL function during pregnancy

status: Public on Aug 10 2014

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: To determine functional differences between the corpus luteum (CL) of the estrous cycle and pregnancy in cows, gene expression profiles between the CL of the estrous cycle and pregnancy were investigated. A 15 K bovine oligo DNA microarray detected 138, 265 and 455 differentially expressed genes (>2-fold; P<0.05) in the bovine CL of 20-25, 40-45, and 150-160 days of pregnancy compared with 10-12 days of the estrous cycle. The different gene expression profiles may contribute to functional differences between the CL of pregnancy and the CL of the estrous cycle in cows. Chemokines including eotaxin and lymphotactin may regulate CL function during pregnancy.

overall_design: Bovine ovaries containing corpora lutea (CLs) were obtained from Japanese-Black cows in the institute ranch within 10-30 min of exsanguination. Tissue samples were collected from cows on 10-12 days of the estrous cycle (cyclic), 20-25, 40-45, and 150-160 days of the gestation (n=4 animals/stage). The day of artificial insemination was designated as day 1.

first: Ryosuke

last: Sakumoto


title: The long noncoding RNA SPRY4-IT1 increases the proliferation of human breast cancer cells by upregulating ZNF703 expression

status: Public on Oct 22 2014

city: Nanjing

first: Yongguo

last: Shi

state: Jiangsu

address: Nanjing xiaguan district jiangjiayuan 121

country: China

institute: The Second Affiliated Hospital of Nanjing Medical University

summary: Background: Long noncoding RNAs (lncRNAs) have emerged recently as a new class of genes regulating cellular processes, such as cell growth and apoptosis. The SPRY4 intronic transcript 1 (SPRY4-IT1) is a 708-bp lncRNA on chromosome 5 with a potential functional role in tumorigenesis. The clinical significance of SPRY4-IT1 and the effect of SPRY4-IT1 on cancer progression are unclear.  Methods: Quantitative reverse transcriptase PCR (qRT-PCR) was performed to investigate the expression of SPRY4-IT1 in 48 breast cancer tissues and four breast cancer cell lines. Gain and loss of function approaches were used to investigate the biological role of SPRY4-IT1 in vitro. Microarray bioinformatics analysis was performed to identify the putative targets of SPRY4-IT1, which were further verified by rescue experiments, as well as by western blotting and qRT-PCR.  Results: SPRY4-IT1 expression was significantly upregulated in 48 breast cancer tumor tissues compared to normal tissues. Additionally, increased SPRY4-IT1 expression was associated with larger tumor size and an advanced pathological stage in breast cancer patients. Knockdown of SPRY4-IT1 significantly suppressed proliferation and caused apoptosis of breast cancer cells in vitro. Furthermore, we discovered ZNF703 was a direct target of SPRY4-IT1 and was downregulated by SPRY4-IT1 knockdown. Moreover, we demonstrated for the first time that ZNF703 is a genetic driver in ER (-) breast carcinoma cells.  Conclusions: SPRY4-IT1 is a novel prognostic biomarker and a potential therapeutic candidate for breast cancer.

overall_design: Five samples are analyzed, including three control groups and two small interfering RNA groups

first: Keming

last: Wang


title: Comparative Genomic Hybridizaions of 3D7∆PfSir2a and NF54 compared to reference strain 3D7

status: Public on Oct 02 2014

city: Notre Dame

first: Michael

last: Ferdig

address: 280 Galvin Life Science

department: Biological Sciences

institute: University of Notre Dame

type: Genome variation profiling by genome tiling array

summary:
Antigenic variation in Plasmodium falciparum is achieved by transcriptional switching amongst polymorphic var genes, enforced by epigenetic modification of chromatin. Histone-modifying ‘sirtuin’ enzymes PfSir2a and PfSir2b have been implicated in this process. We examined the effect of genetic disruption of sirtuins on var gene expression.
Comparative Genomic Hybridization profile indicate that loss of PfSir2a in 3D7 resulted in strikingly rearranged chromosomes.

sample_organism:
Plasmodium falciparum
Plasmodium falciparum NF54
Plasmodium falciparum 3D7

overall_design: 3D7 common reference; Samples: PfSir2a and NF54


title: Transcriptomic analyses indicate that ligule initiation recapitulates gene expression patterns that occur at lateral branching

status: Public on Sep 12 2014

city: Ithaca

last: Scanlon

state: NY

address: Emerson Hall, Room 140

institute: Cornell University

summary: Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize leaf is an ideal system to study plant morphogenesis as it is subdivided into a proximal sheath and a distal blade, each with distinct developmental patterning. Specialised ligule and auricle structures form at the blade-sheath boundary. The auricles act as a hinge, allowing the leaf blade to project at an angle from the stem, while the ligule comprises an epidermally-derived fringe. Recessive liguleless1 mutants lack ligules and auricles, and have upright leaves. We utilized laser-microdissection RNAseq to identify genes that are differentially expressed along discrete cell/tissue-specific domains along the proximal-distal axis of wild-type leaf primordia undergoing ligule initiation, and compared transcript accumulation in wild type and liguleless1 mutant leaf primordia. We identified transcripts that are specifically upregulated at the blade-sheath boundary. A surprising number of these ligule genes are also implicated to function during leaf initiation or lateral branching, and intersect multiple hormonal signalling pathways. We propose that genetic modules utilised in leaf and/or branch initiation are redeployed to regulate ligule outgrowth from leaf primordia.

overall_design: In this study, we analysed the transcriptome associated with ligule formation using laser microdissection RNA-sequencing (LM-RNAseq). We quantified transcript accumulation in the PLB and adjacent pre-blade and pre-sheath regions of wild-type leaf primordia in order to identify candidate genes involved in proximal-distal patterning at the blade-sheath boundary. We also compared transcript accumulation in lg1-R mutants and wild-type siblings to identity genes acting downstream of LG1.

first: Robyn

last: Johnston

first: Anne

middle: W

last: Sylvester

first: Qi

last: Sun

first: Sarah

last: Hake


title: affy_brachy_2011_11-Transcriptomics analysis of DON and Fusarium graminearum response in Brachypodium distachyon

status: Public on Sep 06 2014

city: evry

first: huguet

last: stephanie

address: rue gaston cremieux

country: France

institute: labo

summary:
affy_brachy_2011_11 - affy_brachy_2011_11 - Fusarium graminearum is the causal agent of Fusarium head blight (FHB) of small-grain cereals, including wheat. Besides direct grain losses, this disease is of major concern because of the production by the pathogen of mycotoxins which are hazardous to animals, thus making the grain unfit for food or feed. Major mycotoxins produced by the fungus are trichothecens, including deoxynivalenol (DON). In our laboratory, we use Brachypodium distachyon as a model plant for cereals because of its amenability (short life cycle, numerous genomic and genetic resources, ...). We have recently shown that F. graminearum does induce head blight symptoms on this species and that DON is produced on infected spikes. We have also evidenced that a F. graminearum strain unable to produce DON exhibits reduced virulence on B. distachyon spikes, as previously shown on wheat. The aim of this project is to analyse and compare the plant response to DON producing and non-producing strains of F. graminearum. This analysis will allow to decipher the mechanisms of detoxification set up by the plant and also more specific responses due to the impact of the mycotoxin on plant metabolism and physiology. -Three conditions on B. distachyon spikes:
1-Mock inoculation (Tween 20 0,01%)
2-Inoculation by a F. graminearum wild-type strain
3-Inoculation by a F. graminearum mutant strain, unable to produce DON Spikes were point inoculated with 3ul of either Tween 20 0.01%, wild-type strain or mutant strain (300 spores) and incubated for 96 hours. Six inoculated spikes were collected and pooled for each condition and biological replicate. Three independent biological replicates were conducted.

overall_design: 9 arrays - Brachypodium; normal vs disease comparison,time course

first: Stephanie

last: Huguet

first: Marie

last: Dufresne

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Profiling of the embryonic Atlantic halibut (Hippoglossus hippoglossus L.) transcriptome reveals maternal transcripts as potential markers of embryo quality

status: Public on Sep 04 2014

city: Oslo

first: Knut Erik

last: Tollefsen

address: Gaustadallèen 21

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

summary: Commercial Atlantic halibut (Hippoglossus hippoglossus) farming is restricted by variable oocyte quality, slow growth, and early maturation of male fish. Maternally transferred components regulate early developmental processes; therefore, they have an effect on the future development of an embryo. We profiled components of the transcriptome involved in immune defence as well as germline and muscle development during early developmental stages: 8-cell embryos, germ ring stage, 10-somite stage, and hatched embryos using a 10k oligonucleotide array and quantitative real-time PCR to specifically identify transcripts useful as molecular markers of embryo quality.

overall_design: 4 developmental stages, Two conditions of egg quality, 3 replicates each

first: Maren

last: Mommens

first: Jorge

middle: M

last: de Oliveira Fernandes

first: Knut

middle: E

first: Ian

middle: A

first: Igor

last: Babiak


title: Expression data from Irinotecan resistant LoVo cells comapred to parental LoVo cells

status: Public on Jul 18 2014

first: Hae Yong

last: Yoo

address: 50 Ilwon-Dong, Gangnam-Gu

institute: Sungkyunkwan University

summary:
Irinotecan, an analogue of camptothecin, is frequently used in combination with various anticancer drugs or as a single agent in treatment of colorectal cancer. But drug resistance of tumor is still a major obstacle to overcome for the success of cancer treatment.
In this study, We established chronic irinotecan resistant cell line for new marker to increase the sensitivity to irinotecan and investigated gene expression profiles of the irinotecan-resistant colorectal cancer cell line.

overall_design: To create stable CRC cell line chronically resistant to Irinotecan, LoVo cell was exposed to an initial Irinotecan concentration of 0.1 μmol/L in RPMI 1640 supplemented with 10% FBS. When the growth of the cultured cells reaches at 80% confluency,  cells were passaged twice at same drug concentration to ensure adaptation and then concentration of Irinotecan was sequentially increased in the same manner to 8 μmol/L and then we investigated the gene expressions between parental colorectal cancer cell line, LoVo and Irinotecan resistant LoVo cell lines

first: Seung

last: Choi

first: Hae

middle: Y


title: Molecular Basis of Caste Determination in Polistes metricus

city: Ames

first: Ali

last: Berens

state: IA

address: 251 Bessey Hall

department: Ecology, Evolution, and Organismal Biology

institute: Iowa State University

summary: We investigated environmental determinants of caste differences in paper wasps, specifically the effects of differential nutrition. We found that nutritional restriction only partially biased wasp gene expression patterns toward being worker caste-like, which highlights the complex and multifactorial nature of environmental effects on the gene expression patterns underlying plastic phenotypes

overall_design: PRJNA242774; We sequenced mRNA from 16 individual 5th instar larval Polistes metricus heads from 4 groups: worker-reared (n=4), foundress-reared (n=4), restricted nutrition (n=4), and ad libitum (n=4).

first: James

last: Hunt

first: Amy

last: Toth


title: Hinchcliff 165 microarray dataset

status: Public on Jul 25 2014

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

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

overall_design: Refer to individual Series


title: Expression data from embryonic stem cells (ESCs) and ESC-like cells

status: Public on Jun 23 2014

first: Jeong Mook

last: Lim

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

institute: Seoul National University

summary:
The transplantation of ESCs into living recipients causes teratoma formation which accompanies with several biological reactions in both the transplanted cells and recipient. Co-injection of ESCs with somatic cells that influence donor-recipient homogeneity can affect transcriptional profile of transplanted ESCs.
We investigated global gene expression of parental ESCs and ESC-like cells derived from teratomas which were formed by different injection conditions to find transcriptional differences according to donor-recipient homogeneity and somatic cell co-injection.

overall_design: Parental ESCs or teratoma-derived ESC-like cells from different treatments were retrieved for RNA extraction and hybridization on Affymetrix microarrays.

first: Jeong

first: Jae-Wook

last: Jeong

middle: P

last: Gong

first: Boyun

last: Kim


title: Transcriptomics modifications in inner stem tissues of the flax lignified bast fiber mutant1 (lbf1)

status: Public on Sep 11 2014

city: Villeneuve d'Ascq

first: Chantreau

last: Maxime

state: Nord

address: Université de lille 1

institute: Université de Lille 1

summary: Comparison of whole genome transcriptomics between stem inner tissues from flax lignified bast fiber mutant1 (lbf1) and wild-type

overall_design: RNA was extracted from inner stem tissues of 3 wt and 6 lbf1 mutant flax plants harvested at vegetative stage and used to evaluate differences in transcript accumulation potentially associated with the mutant phenotype

first: Maxime

last: Chantreau

first: Sébastien

last: Grec


title: Affymetrix SNP array data for homozygosity mapping of segregating anhidrosis

status: Public on Sep 05 2014

city: Uppsala

first: Joakim

last: Klar

state: SVERIGE

address: Box 815

country: Sweden

institute: Uppsala University

summary:
A consanguineous family segregating anhidrosis (recessive, familial)
Shared homozygous regions were identified by comparing SNP genotyping results from four affected family members

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

first: Niklas

last: Dahl


title: Global transcriptional profile of Salmonella enterica serovar Cerro 87 wild-type and its dpt genes deletion mutants at different growth state

status: Public on Jul 09 2014

city: Shanghai

first: Bo

last: Cao

address: 1954 Huashan Road

institute: Shanghai Jiaotong University

summary: To explore the molecular mechanism of the DNA phosphorothioate modification-dependent restriction system,  the transcriptomes of Salmonella enterica serovar Cerro 87 wild-type and its modification or restriction genes deletion mutants were compared by microarray analysis.

platform_organism: Salmonella enterica subsp. enterica serovar Cerro

overall_design: Global gene expression in three strains, Salmonella enterica serovar Cerro 87 wild-type and its modification or restriction genes deletion mutants, were measured at three different growth state, respectively. Three independent experiments were performed at each condition.


title: Transcriptomics modifications in inner/outer stem tissues of the flax lignified bast fiber mutant1 (lbf1)


title: Circulating Tumor Cell Clusters are Oligoclonal Precursors of Breast Cancer Metastasis

status: Public on Jul 11 2014

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Clusters of circulating tumor cells (CTC-clusters) are present in the blood of patients with cancer but their contribution to metastasis is not well defined. Here, we first use mouse models to demonstrate that breast cancer cells injected intravascularly as clusters are more prone to survive and colonize the lungs than single cells. Primary mammary tumors comprised of tagged cells give rise to oligoclonal CTC-clusters, with 50-fold increased metastatic potential, compared with single CTCs. Using intravital imaging and in vivo flow cytometry, CTC-clusters are visualized in the tumor circulation, and they demonstrate rapid clearance in peripheral vessels. In patients with breast cancer, presence of CTC-clusters is correlated with decreased progression-free survival. RNA sequencing identifies the cell junction protein plakoglobin as most differentially expressed between clusters and single human breast CTCs. Expression of plakoglobin is required for efficient CTC-cluster formation and breast cancer metastasis in mice, while its expression is associated with diminished metastasis-free survival in breast cancer patients. Together, these observations suggest that plakoglobin-enriched primary tumor cells break off into the vasculature as CTC-clusters, with greatly enhanced metastasis propensity.

overall_design: RNA-seq from 29 samples (15 pools of single CTCs and 14 CTC-clusters) isolated from 10 breast cancer patients

first: Nicola

last: Aceto

first: Aditya

last: Bardia

first: Joel

last: Spencer

first: Min

last: Yu

first: Maria

middle: C

last: Donaldson

first: Adam

last: Pely

first: Amanda

last: Engstrom

first: Huili

last: Zhu

first: Brian

last: Brannigan

first: Ravi

last: Kapur

first: Shannon

last: Stott

first: Toshi

last: Shioda

first: Sridhar

last: Ramaswamy

first: David

last: Ting

first: Charles

last: Lin

first: Mehmet

last: Toner

first: Daniel

last: Haber

first: Shyamala

last: Maheswaran


title: Ribosome profiling upon inhibition of eIF4A

status: Public on Sep 13 2014

city: Emeryville

first: Claudia

middle: Ani

last: Rubio

address: 5300 Chiron Way

department: Oncology

institute: Novartis Institutes for Biomedical Research

summary: Ribosome profiling of MDA-MB-231 cells treated with Silvestrol to monitor transcriptome wide, eIF4A-dependent changes in translation efficiency

overall_design: Translation efficiency (TE) of mRNAs dervied from ribosome footprints was monitored in the presence or absence of 25 nM Silvestrol, an inhibitor of eukaryotic translation initiation factor 4A (eIF4A).  Transcripts with reduced TE in the presence of Silvestrol were compare to transcripts with reduced TE in the presence of INK128, a catalytic mTOR inhbitor.

first: Benjamin

last: Weisburd

first: Matthew

last: Holderfield

first: Carolina

last: Arias

first: Eric

last: Fang

first: Joseph

last: DeRisi

first: Abdallah

last: Fanidi


title: Genetic Diversity Influences the Response of the Brain to Developmental Lead Exposure.

status: Public on Apr 10 2014

city: Philadelphia

middle: William

last: Anderson

state: PA

address: 1020 Locust Street

department: Pathology, Anatomy & Cell Biology

institute: Thomas Jefferson University

summary: In this study we analyzed the effects of lead-exposure up hippocampal gene expression in males and females exposed to 0ppm, 250ppm and 750ppm lead during two different developmental periods, perinatal (in utero through to weaning at PND21) and postnatal (PND0-PND45), across three strains (Fischer, Long Evans and Sprague Dawley).  All tissue was taken at PND 55.  We used affymetrix Rat Gene 1.0ST arrays to obtain global gene expression data from each animal, with a group size of 4 for all conditions (Total number of Arrays = 119)

overall_design: Gene expression was profiled in the hippocampus of rats at no lead exposure (0ppm), 250ppm and 750 ppm lead exposure levels during perinatal and postnatal developmental periods of both males and females of three strains of rat (Fischer, Long Evans and Sprague Dawley).

first: Jay

last: Schneider

first: Keyur

last: Talsania


title: Gene Expression data from mouse bone marrow derived macrophages treated with different inflammatory stimuli

status: Public on Mar 24 2014

city: Midlothian

first: Sobia

last: Raza

address: Easter Bush Campus

department: The University of Edinburgh

country: United Kingdom

institute: The Roslin Institute

summary:
The activation profiles of macrophages under different immune and inflammatory conditions have generated great interest. LPS, in particular, is a commonly used in vitro model of infection and inflammation studies in macrophages. We have used gene expression microarrays to define the effects of each of three variables; LPS dose, LPS vs. interferons beta and gamma, and genetic background on the transcriptional response of mouse bone marrow-derived macrophages
Macrophages derived from the C57BL/6 strain of mouse were challenged with increasing doses of LPS over a 24 hour time-course (0.5ng/ml, 5ng/ml, or 50ng/ml LPS). BALB/c derived macrophages were treated with any of 5ng/ml LPS, 10U/ml of recombinant mouse interferon-beta, or 10U/ml interferon-gamma, over a 24 hour timecourse. Sampling times were 0 hours (pre-treatment) and 1, 2, 4, 8, and 24 hours post-treatment in each case.

overall_design: 64 samples in total were analysed. These incorporated 6 different timecourse studies. A combination of statistical filtering using the Empirical Bayes function in Bioconductor package (R statistical software), and co-expression analysis using the network analysis tool BioLayout Express 3D, was used to compare the timecourse studies.

first: Tom

last: Freeman

last: Hume


title: Non-invasive Analysis of the Airway Transcriptome Discriminates Clinical Phenotypes of Asthma

status: Public on Apr 07 2014

city: New Haven

first: Geoffrey

middle: L.

last: Chupp

address: 300 Cedar St, S441

department: Department of Internal Medicine

institute: Section of Pulmonary, Critical Care and Sleep Medicine

summary: Evaluation of the airway transcriptome may reveal patterns of gene expression that are associated with clinical phenotypes of asthma. To define transcriptomic endotypes of asthma (TEA) we analyzed gene expression in induced sputum that correlate with phenotypes of disease.  Gene expression was measured in sputum of subjects with asthma using Affymetrix HuGene ST 1.0 microarrays.  Unsupervised clustering analysis of genes identified TEA clusters.  Clinical characteristics were compared.

overall_design: Gene expression was measured in sputum of subjects with asthma using Affymetrix HuGene ST 1.0 microarrays.  Unsupervised clustering analysis of genes in pathways selected from the Kyoto Encyclopedia of Genes and Genomes (KEGG) identified TEA clusters.  Clinical characteristics were compared and logistic regression analysis of matched blood samples defined an expression profile to determine the TEA cluster assignment in a cohort of children with asthma for validation.

first: Xiting

last: Yan

first: Jose

last: Gomez-Villalobos

first: Maria

last: Koenigs

first: Carole

last: Holm

first: Xiaoxuan

last: He

first: Hongyu

last: Zhao

first: Shrikant

last: Mane

first: Laren

last: Cohn

middle: L


title: Transcriptomics modifications in outer stem tissues of the flax lignified bast fiber mutant1 (lbf1)

first: Chantreau

last: Maxime

summary: Comparison of whole genome transcriptomics between stem outer tissues from flax lignified bast fiber mutant1 (lbf1) and wild-type

overall_design: RNA was extracted from outer stem tissues of 3 wt and 6 lbf1 mutant flax plants harvested at vegetative stage and used to evaluate differences intranscript accumulation potentially associated with the mutant phenotype

first: Maxime

last: Chantreau

first: Sébastien

last: Grec


title: Hematogenous metastasis of ovarian cancer: Re-thinking mode of spread

status: Public on Jul 14 2014

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: Ovarian cancer has a clear predilection for metastasis to the omentum, but the underlying mechanisms involved in ovarian cancer spread are not well understood. Here, we used a parabiosis model that demonstrates preferential hematogenous metastasis of ovarian cancer to the omentum. Our studies revealed that the ErbB3-neuregulin1 (NRG1) axis is a dominant pathway responsible for hematogenous omental metastasis. Elevated levels of ErbB3 in ovarian cancer cells and NRG1 in the omentum allowed for tumor cell localization and growth in the omentum. Depletion of ErbB3 in ovarian cancer substantially impaired omental metastasis. Our results highlight hematogenous metastasis as a previously under-recognized mode of ovarian cancer metastasis. These findings have implications for designing new strategies aimed at preventing and treating ovarian cancer metastasis.

overall_design: Two groups of samples are included: 1.SKOV3-ip1 2.SKOV3-OM3. Gene expression profiles of SKOV3-OM3 cells were compared to that of parental SKOV3 ip1 cells.

first: Sunila

last: Pradeep

first: Anil

last: Sood

first: Ju-Seog

last: Lee


title: Tissue-Resident Natural Killer (NK) Cells Are Cell Lineages Distinct From Thymic and Conventional Splenic NK Cells

status: Public on Apr 26 2014

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis


title: Expression analysis of Pseudozyma antarctica T-34 and Ustilago maydis on different carbon source

status: Public on Mar 21 2014

city: Tsukuba

first: Hideaki

last: Koike

state: Ibaraki

address: Higashi 1-1-1

institute: National Institute of Advanced Industrial Science and Technology

summary:
Investigation of whole genome gene expression level in Pseudozyma antarctica T-34, compared to Ustilago maydis UM521.
To clarify the transcriptomic characteristics of Pseudozyma antarctica under the conditions of high MEL production, a DNA microarray of both the strains, Pseudozyma antarctica T-34 and Ustilago maydis UM521 was prepared and analyzed the transcriptomes.

sample_organism:
Mycosarcoma maydis
Moesziomyces antarcticus T-34

overall_design: A DNA chip study using mRNA from the cultures of Pseudozyma antarctica T-34 and Ustilago maydis UM521 demonstrated the gene expression level of each strain.

first: Tomotake

last: Morita


title: Mycophenolate Treatment in Systemic Sclerosis

first: Tammara

last: Wood

summary: Skin gene expression signatures, including intrinsic subset, are associated with improvement during Mycophenolate mofetil (MMF) treatment.

overall_design: Longitudinal SSc patient biopsies and controls were integrated into 83 sample dataset totaling 165 arrays for gene expression and analysis

first: Monique

last: Hinchcliff

first: Michael

last: Whitfield


title: Changes of microRNA expression levels in HBV-infected human primary hepatocytes

status: Public on Mar 15 2014

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Human primary hepatocytes isolated from chimeric mice were infected with HBV for 7 days. The comprehensive changes of miRNA levels were determined by miRNA array.

overall_design: MicroRNA expression levels were compared in between control and HBV-replicating primary hepatocytes by 2K microRNA microarrays

first: Motoyuki

last: Otsuka

first: Chikako

last: Shibata


title: Warm sensor protein TRPM2 is required for brain development via SP5 in hyperthermia

status: Public on May 03 2018

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression. The goals of this study are to compare the different transcripts between TRPM2 knockout and WT E16 cerebral brain tissue when the maternal hyperthermia was induced.

overall_design: Methods:  Total RNA was extracted from E16 cortical tissue of TRPM2 KO and WT mice which were induced in hyperthermia at E14-E16. Then RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics. Significantly differentially expressed genes were identified when we compared Normalized Reads Count between groups with p < 0.05 and |Log2FoldChange| > 1.

first: Yanxin

last: Li


title: Transcriptome Sequencing Analysis Reveals the Regulation of the Hypopharyngeal Glands in the Honey Bee, Apis mellifera carnica Pollmann

status: Public on May 20 2014

city: Yangzhou

first: Zhenguo

last: Liu

address: 88 South University Ave.

institute: Yangzhou University

summary: Transcriptome sequencing has become the main methodology for analyzing the relationship between genes and characteristics of interests, particularly those associated with diseases and economic traits. Because of its functional superiority, commercial royal jelly (RJ) and its production are major areas of focus in the field of apiculture. Multiple lines of evidence have demonstrated that many factors affect RJ output by activating or inhibiting various target genes and signaling pathways to augment their efficient replication. The coding sequences made available by the Honey Bee Genome Sequencing Consortium have permitted a pathway-based approach for investigating the development of the hypopharyngeal glands (HGs). In the present study, 3573941, 3562730, 3551541, 3524453, and 3615558 clean reads were obtained from the HGs of five full-sister honey bee samples using Solexa RNA sequencing technology. These reads were then assembled into 18378, 17785, 17065, 17105, and 17995 unigenes, respectively, and aligned to the DFCI Honey Bee Gene Index database. The differentially expressed genes (DEGs) data were also correlated with detailed morphological data for HGs acini. The results identify areas that warrant further study, including those that can be used to improve honey bee breeding techniques and help ensure stable yields of RJ with high quality traits.

overall_design: The 5 samples at given time (d3, d6, d9, d12, d16 after adult worker bees emergence from the comb) are in the critical stage of the RJ secretion and HGs developments indicated (triggered) the further caste differentiation (worker bees and queen) and task switch (nurse bees and foragers). 30 pooled heads of each samples were

first: Ting

last: Ji

first: Ling

last: Yin

first: Jie

last: Shen

first: Fang

first: Guohong

last: Chen


title: An epigenetically distinct breast cancer cell subpopulation promotes collective invasion

status: Public on Jun 19 2014

city: Dallas

first: Xiaoyu

last: Wang

state: Texas

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

summary: A distinct highly invasive subpopulation was identified in breast cancer cell lines.  The molecular characteristics of these cells was investigated, revealing a set of genes whose high expression confers the ability to invade.

overall_design: Total RNA  isolated from the invasive subpopulation from 2 cells lines was  compared to total RNA isolated from 2 noninvasive populations.

first: Gray

last: Pearson


title: Changes of mRNA expression levels in HBV-infected human primary hepatocytes and those cells treated with bionanocapsules containing microRNA-93.

summary:
Human primary hepatocytes isolated from chimeric mice were infected with HBV for 7 days. The comprehensive changes of mRNA levels were determined by mRNA array.
Also, microRNA93 was delivered into those cells using bionanocapsules to determine the effects of rescue expression of miR93 in HBV replicating cells, because we found that miR93 expression level was downregulated in HBV-infected hepatocytes.

overall_design: mRNA expression levels were compared in among control cells, HBV-infected cells, miR93 delivered cells, and HBV-infected cells with miR93 delivered, by 25K mRNA arrays.


title: Wolbachia infection modifies the profile, shuttling and structure of microRNAs in a mosquito cell line

status: Public on Feb 22 2014

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

summary: We characterized the miRNA composition of the nucleus and the cytoplasm of uninfected cells and compared it with the one of cells infected with the endosymbiotic bacterium Wolbachia strain wMelPop-CLA. We found an overall increase of small RNAs between 18 and 28 nucleotides in both cellular compartments in Wolbachia-infected cells and identified specific miRNAs induced and/or suppressed by the Wolbachia infection. We discuss the mechanisms that the cell may use to shuttle miRNAs between the cytoplasm and the nucleus. In addition, we identified piRNAs that changed their abundance in response to Wolbachia infection. The miRNAs and piRNAs identified in this study provide promising leads for investigations into the host-endosymbiont interactions and for better understanding of how Wolbachia manipulates the host miRNA machinery in order to facilitate its persistent replication in infected cells.

overall_design: Examination of small RNA profile in cytoplasmic and nuclear fractions of Aag 2 and Pop cells (Aedes aegypti)

first: Sassan

last: Asgari


title: A rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages

status: Public on Feb 14 2014

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

summary: The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNASeq on 320 samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats. We catalogue the expression profiles of 40,064 genes, 65,167 transcripts, 31,909 alternatively spliced transcript variants and 2,367 non-coding genes/non-coding RNAs (ncRNAs) annotated in AceView. We find that organ-enriched, differentially expressed genes reflect the known organ-specific biological activities. A large number of transcripts show organ-specific, age-dependent or sex-specific differential expression patterns. We create a web-based, open-access rat BodyMap database of expression profiles with crosslinks to other widely used databases, anticipating that it will serve as a primary resource for biomedical research using the rat model.

overall_design: We constructed a comprehensive RNA-Seq data set for studying the dynamics of the rat transcriptome using 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old). Four biological replicates were used for each of the 80 sample groups.

first: Charles

first: James

last: Fuscoe


title: 3D7 PfHda2 Knockdown vs. Wildtype

status: Public on Feb 11 2014

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: The asexual forms of the malaria parasite Plasmodium falciparum are uniquely adapted for chronic persistence in human red blood cells, continuously evading the immune system using an epigenetically regulated process. However, parasite survival on a population level also requires transmission of sexual parasite forms to subsequent human hosts. Here, we reveal that the essential nuclear gene, P. falciparum histone deacetylase 2 (PfHda2), silences specific subsets of genes involved in antigenic variation or conversion to sexual stages.

overall_design: Two parallel timecourses resulting in a total of 22 samples (11 wildtype, 11 PfHda2 knockdown) were hybridized against a Cy3-labeled reference pool of 3D7 mixed stage parasites on a two-color array.

first: Bradley

middle: I

last: Coleman

first: Kristen

last: Skillman

first: Rays

middle: H

last: Jiang

first: Lauren

last: Childs

first: Lindsey

last: Altenhofen

first: Markus

last: Ganter

first: Yvette

last: Leung

first: Ilana

last: Goldowitz

first: Björn

middle: F

last: Kafsack

first: Matthias

last: Marti

last: Llinás

first: Caroline

middle: O

last: Buckee

first: Manoj

middle: T

last: Duraisingh


title: Global Bidirectional Transcription of the Epstein-Barr Virus Genome During Reactivation

status: Public on Dec 24 2013

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

summary: Using strand specific RNA-seq to assess the EBV transcriptome during reactivation of Akata cells, we found extensive bidirectional transcription extending across nearly the entire genome.

overall_design: Illumina strand-specific RNA-seq of BCR-activated Akata cells at 9 time points

first: Tina

last: O'Grady

first: Subing

last: Cao

first: Michael

middle: J

last: Strong

first: Monica

last: Concha

first: Xia

last: Wang

first: Sandra

middle: S

last: BonDurant

first: Marie

last: Adams

first: Melody

last: Baddoo

first: Sudesh

last: Srivastav

first: Zhen

last: Lin

first: Claire

last: Fewell

first: Qinyan

last: Yin


title: The effect of a novel form of macrophage colony-stimulating factor (CSF1-Fc) on gene expression in the liver.

status: Public on Dec 31 2013

city: Roslin

first: Kristin

last: Sauter

address: Easter Bush, Midlothian

institute: Roslin Institute/The University of Edinburgh

summary: Treatment of mice with daily injections of CSF1-Fc produce a 50% increase in the size of the liver within 5 days. There was extensive proliferation of hepatocytes, similar to that seen following partial hepatectomy.

overall_design: Comparative gene expression profiles of the treated and control livers, alongside macrophages  grown in CSF1, indicate extensive infiltration by macrophages in response to CSF1-Fc, and demonstrate that infiltrating macrophages produced several candidate mediators of hepatocyte proliferation.

first: Deborah

last: Gow

middle: A

first: David

last: Hume


title: Genome-wide transcriptional changes in the Clostridium perfringens-afflicted chicken intestine in an avian necrotic enteritis (NE) disease model

status: Public on Sep 26 2013

city: Beltsville

first: Duk Kyung

last: Kim

state: MD

address: Bldg. 1043, BARC-East

institute: USDA, ARS

summary: This study utilized comparative global gene expression microarray analysis to evaluate the effects of NE on intestinal immunity of chicken.

overall_design: Two-condition experiment, NE-afflicted chickens vs. Non-infected control chickens. Biological replicates: 2 control replicates, 2 NE-afflicted replicates with dye-switching.

first: Duk

first: Hyun

last: Lillehoj


title: Molecular Signatures in Skin Associated with Clinical Improvement During Mycophenolate Treatment in Systemic Sclerosis

status: Public on Apr 09 2013

city: Lebanon

first: Tammara

last: Wood

address: WTRB 674

institute: Dartmouth Medical School

summary: Skin gene expression signatures, including intrinsic subset, are associated with skin score/MRSS improvement during mycophenolate mofetil (MMF) treatment.

overall_design: Gene expression and intrinsic subset assignment were measured in SSc patients amd  controls at baseline, and from biopsies of MMF-treated patients.

first: Monique

last: Hinchcliff

last: Huang

last: Mahoney

first: Swati

last: Bhattacharyya

first: Zenshiro

last: Tamaki

first: Jungwha

last: Lee

first: Mary

last: Carns

first: Sofia

last: Podlusky

first: Arlene

last: Sirajuddin

first: Sanjiv

last: Shah

first: Rowland

middle: W

last: Chang

first: Viktor

last: Martyanov

first: Robert

last: Lafyatis

first: John

last: Varga

last: Whitfield


title: Liver gene expression patterns in pigs as indicators of serum plasma levels and meat quality atributes

status: Public on Jan 01 2014

city: Lleida

first: Romi

middle: N

last: Pena

state: Lleida

address: 191 Alcalde Rovira Roure Ave

department: Animal Production

country: Spain

institute: University  of Lleida

summary: In pigs, most of the lipogenic activity takes place in liver and the adipose tissue. Moreover, liver is responsible for the production and release of lipoproteins, which transports lipids from the liver to target tissues such as adipose and muscle. In the context of animal production, the amount and composition of lipoprotein have an implication in the accumulation of fat in adipose deposits but also in muscle in the form or intramuscular fat. These two events have consequences in the quality of the carcasses and meat. We have measured the level of liver gene expression in 104 commercial Duroc pigs belonging to two groups with extreme phenotypes for traits strongly related with lipid deposition and composition. This has allowed us to compare the physiological and metabolic implications of selecting for each of these extreme groups. This information has been complemented with genome-wide genotyping data in order to describe the implication of the liver transcriptome in the production traits which encompass the production and marketing of the products with consumer and industry-relevant added-value characteristics.

overall_design: 104 liver samples form pigs belonging to two groups of animals: HIGH group (n=53) had higher carcass, plasma and muscle fat content; LOW group (n=51) had lower carcass, plasma and muscle fat content

first: R

last: Quintanilla

first: M

last: Amills

first: N

last: Aznárez

first: A

last: Cánovas


title: OpaR Controls a Network of Downstream Transcription Factors in Vibrio parahaemolyticus BB22

city: Blacksburg

first: Roderick

middle: V

last: Jensen

address: Washington street

department: Biological Sciences

institute: Virginia Polytechnic Institute and State University

summary: Vibrio parahaemolyticus an emerging pathogen that is a causative agent of foodborne gastroenteritis when raw or undercooked seafood is consumed.   Previous microarray data using a Vibrio parahaemolyticus RIMD2210633 chip has shown the master quorum-sensing regulator OpaR controls virulence, type III and type VI secretion systems, and flagellar and capsule production genes.  In a parallel study, RNA-Seq was used to comparatively study the transcriptome changes of wild type Vibrio parahaemolyticus BB22 and a ΔopaR strain directly. Differences in mRNA expression were analyzed using next generation Illumina sequencing and bioinformatics techniques to align and count reads.  A comparison with the previous microarray data showed good correlation between the shared genes.  The RNA-Seq offered an insight into control of genes specific to the Vibrio parahaemolyticus BB22 strain as well as a new look at the sRNAs that are expressed.  Eleven transcriptional regulators with greater than 4 fold regulation in the previous microarray study and 2 fold regulation in the RNA-Seq analysis, were chosen to validate the data using qRT-PCR and further characterized with electrophoretic mobility shift assays (EMSAs) to determine if they are direct targets of OpaR.   The transcription factors chosen play key roles in virulence, surface motility, cell to cell interactions, and cell surface characteristics.  One small RNA was identified in the RNA-Seq data to be quorum-sensing controlled and unidentified by other programs.  The RNA-Seq data has aided in understanding and elucidating the hierarchy of quorum-sensing control of OpaR in Vibrio parahaemolyticus.

overall_design: The wild type Vibrio parahaemolyticus BB22 strain LM5312 and an opaR deletion strain LM5674 were analyzed for mRNA expression using RNA-Seq.

first: Alison

last: Burke

first: Leah

middle: C

last: Guthrie

first: Thero

last: Modise

first: Guy

last: Cormier

first: Linda

last: McCarter

first: Ann

middle: M

last: Stevens


title: Human islets exposed to cytokines IL-1β and IFN-γ

status: Public on Dec 19 2013

city: Brussels

first: Miguel

last: Lopes

address: Campus de la Plaine Boulevard du Triomphe

department: Computer Science Department

country: Belgium

institute: Universite Libre de Bruxelles

summary:
In the context of T1 Diabetes, pro-inflammatory cytokines IL-1β and IFN-γ are known to contribute to β-cell apoptosis;
The measurement of mRNA expression following β-cell exposure to these cytokines gives a picture of the changes in gene expression characterizing the path to β-cell dysfunction and death.

overall_design: Human islets were isolated and exposed (or not) to IL-1β and IFN-γ. The samples were collected at various time points for profiling with Affymetrix arrays. These measurements were performed three times.

first: Burak

last: Kutlu


title: Global gene expression analysis of CDCP1, KDM3B, and SDC1 knockdown in human marrow stromal cells

status: Public on Dec 10 2013

city: Seattle

first: mineo

last: iwata

state: WA

address: 1100 Fairview Ave N

department: Transplantation Biology

institute: Fred Hutchinson Cancer Research Center

summary: To elucidate functions of CDCP1, KDM3B and SDC1 molecules in HS5 human marrow stromal cells, global gene expression profiles were obtained and analyzed after knocking down the gene transcripts by using siRNA technology.

overall_design: Global gene expression profiles were obtained from HS5 marrow stromal cells after knocking  down mRNA of CDCP1, KDM3B or SDC1 by using siRNA technology.

first: Mineo

last: Iwata

first: Beverly

last: Torok-Storb


title: Inflammatory Expression Profiles in Monocyte to Macrophage Differentiation amongst Patients with Systemic Lupus Erythematosus and Healthy Controls with and without an Atherosclerosis Phenotype

status: Public on Apr 17 2012

city: Chicago

first: Chiang-Ching

last: Huang

state: IL

address: 680 N. Lake Shore Dr., Suite 1400

institute: Northwestern University

summary: To examine mononuclear cell gene expression profiles in patients with and without SLE and subsets with and without atherosclerosis

overall_design: Monocytes were obtained from 20 patients with SLE and 16 healthy controls and were in vitro differentiated into macrophages.  Subjects also underwent laboratory and imaging studies of the coronary arteries, carotid arteries, and aorta to evaluate for subclinical atherosclerosis.

first: Rosalind

last: Ramsey-Goldman

first: Benjamin

last: Korman


title: Identification of Novel NRF2-Regulated Genes by ChIPSeq

status: Public on Jun 18 2012

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cellular oxidative and electrophilic stress triggers a protective response in mammals regulated by NRF2 (nuclear factor (erythroid-derived) 2-like; NFE2L2) binding to DNA-regulatory sequences near stress responsive genes. Studies using Nrf2-deficient mice suggest that hundreds of genes may be regulated by NRF2. To identify human NRF2-regulated genes, we conducted ChIP-sequencing experiments in lymphoid cells treated with the dietary isothiocyanate, sulforaphane (SFN) and carried out follow-up biological experiments on candidates. We found 242 high-confidence, NRF2-bound genomic regions and 96% of these regions contained NRF2-regulatory sequence motifs. The majority of binding sites were near potential novel members of the NRF2 pathway. Validation of selected candidate genes using parallel ChIP techniques and in NRF2-silenced cell lines indicated that the expression of about two thirds of the candidates are likely to be directly NRF2-dependent including retinoid X receptor alpha (RXRA). NRF2 regulation of RXRAhas implications for response to retinoid treatments and adipogenesis. In mouse 3T3-L1 cells SFN treatment affected Rxra expression early in adipogenesis and knockdown of Nrf2 delayed Rxra expression, both leading to impaired adipogenesis.

overall_design: ChIP-Seq analysis of NRF2 binding sites in human lymphoblastoid cells treated with sulforaphane or vehicle

first: Brian

last: Chorley

first: Michelle

middle: R

last: Campbell

first: Douglas

last: Bell


title: Plasticity of the ripening process among berry classes

status: Public on Aug 07 2013

city: Corvallis

first: Laurent

middle: Gerard

last: Deluc

state: OR

address: 4017 ALS Building

department: Horticulture

institute: Oregon State University

summary:
Investigation of gene expression differences between three tissues of developmentally different berry classes before, at the onset of ripening, and at maturity
The berry classes analyzed in these studies were at prevéraison stage, at midvéraison and 5 week postmidvéraison.

overall_design: A 63-array study on gene expression variability among developmentally berry classes (PV, GS, PS, RS, GSH, PSH, RSH) sampled at three developmental stages (prevéraison for PV, midvéraison for GS, PS, and RS and maturityfor GSH, PSH, and RSH ) in skin, seed, and pulp tissues. Each data point was performed in triplicate

first: Satyanarayana

last: Gouthu

first: Caprice

last: Rosato


title: CGH analyses for the Chinese indigenous pig breeds and commercial pig breeds

status: Public on May 15 2013

first: Huimin

last: Kang

address: Beijing

institute: China Agriculture University

summary:
Since CNVs play a vital role in genomic studies, it is an imperative need to develop a comprehensive, more accurate and higher resolution porcine CNV map with practical significance in follow-up CNV functional analyses
To detect CNV of pigs, we performed high density aCGH data of diverse pig breeds in the framework of the pig draft genome sequence (Sscrofa10.2)

overall_design: 9 Chinese indigenous pig, 2 commercial pigs, 1 wild pig were detected using one pig of Duroc as reference.

first: Jianfeng

last: Liu

first: Jiying

first: Jicai

last: Jiang


title: eQTL linkages in wine yeasts to decipher regulatory networks in wine fermentation

status: Public on Oct 21 2013

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

institute: INRA

summary:
We performed here the transcriptomic profile of 44 segregants from a cross between S288c and 59A (a spore of EC1118 strain). The analysis was performed in wine fermentation condition in stationary phase during nitrogen starvation and in alcoholic stress.
These data, associated with an individual genotyping by Affymetrix array allow us to highlight genetic variations involved in perturbation of regulatory network and fermentative behavior.

overall_design: 56 transcriptomic profiles were performed with Agilent mono-color array. 6 hybridizations were performed for each parental strains: 3 technical replicates for 2 biological replicated samples (59As1 and 59As5; S288Cs1 and S288Cs5). One hybridization was performed for each of the 44 segregants. Using mono-color array, the logarithm base 2 of intensity was directly used after normalization.

first: Christian

last: Brion


title: Whole genome bisulfite sequencing of idm1, rdd, ros1 mutants and Col-0 WT

status: Public on Jun 17 2012

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

type: Methylation profiling by high throughput sequencing

summary: Using whole genome bisulfite sequencing to provide single-base resolution of DNA methylation status in ros1, idm1, and rdd mutants and identify hypermethylated regions comparing to wild type Arabidopsis plants.

overall_design: Examination of 3 different mutants' methylome. 8 samples (3 mutants, 1 WT, each has two biological replicates)

first: Weiqiang

last: Qian

first: Daisuke

last: Miki

first: Kai

last: Tang

first: Renyi


title: microRNA expression profile of hypopharyngeal squamous cell carcinoma

city: Chiba city

first: Naohiko

last: Seki

state: Chiba

address: Inohana1-8-1, Chuo-ku

institute: Chiba University

summary: To identify differentially expressed microRNAs in tumor tissues, human hyopophryngeal squamos cell carcinoma tissues were subjected to miRCURY LNA microRNA Array.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: A total of 11 pairs of primary hypopharyngeal squamous cell carcinoma samples and adjacent normal mucosa were obtained from patients who underwent tumor resection at Chiba University Hospital (Chiba, Japan). The Ethics Committee of Chiba University approved our study, and informed consent was obtained from all patients for use of their tissue samples and clinical data. The tissue samples were immersed in RNAlater and stored at -20°C until use.


title: Genomic Signatures of Metastasis in Prostate Cancer

status: Public on Dec 01 2013

city: Bronx

first: Alex

last: Pearlman

state: NY

address: 1300 Morris Park Avenue

department: Pediatrics and Genetics

institute: Albert Einstein College of Medicine

summary:
Background:

Metastases result in 90% of all cancer deaths.  Prostate cancer primary tumors evolve to become metastatic through selective alterations, such as amplification and deletion of genomic DNA.

Methods:

Genomic DNA copy number alterations were used to develop a gene signature that measured the metastatic potential of a prostate cancer primary tumor.  We studied the genomic landscape of these alterations in 294 primary tumors and 49 metastases from 5 independent cohorts.  Receiver-operating characteristic cross-validation and Kaplan-Meier survival analysis were performed to assess the accuracy of our predictive model.  The signature was measured in a panel of 337 cancer cell lines from 29 different tissue origins.

Results:

We identified 399 copy number alterations around genes that were over-represented in metastases and predictive of whether a primary tumor will metastasize.  Cross-validation analysis resulted in a predictive accuracy of 80.5% and log rank analysis of the metastatic potential score was significantly related to the endpoint of metastasis-free survival (p=0.014).  The metastatic signature was observed in cell lines originating from lung, breast, colon, thyroid, rectum, pancreas and melanoma. The signature was comprised in part of genes of known or putative metastatic role — 8 solute carrier genes, 6 Cadherin family genes and 5 potassium channel genes — that function in metabolism, cell-to-cell adhesion and escape from anoikis/apoptosis.

Conclusions:

Somatic Copy number alterations are an independent predictor of metastatic potential.  The data indicate a prognostic utility for using primary tumor genomics to assist in clinical decision making and developing therapeutics for prostate and likely other cancers.

overall_design: genomic DNA from 29 prostate cancer tumors with matched normals run on Affymetrix 6.0 SNP arrays.

first: Alexander

first: Christopher

first: Eric

last: Brooks

last: Genshaft

first: Shahin

last: Shajahan

first: Michael

last: Ittmann

first: G

last: Bova

first: Jonathan

last: Melamed

first: Ilona

last: Holcomb

first: Robert

last: Schneider

first: Yongzhao

last: Shao

first: Harry

last: Ostrer


title: Affymetrix SNP array data for Non-Smoking Female Lung Cancer in Taiwan

status: Public on Dec 31 2012

city: Taipei

first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Genome-Wide Screening of Genomic Alterations and  Transcriptional Modulation in Non-Smoking Female Lung Cancer in Taiwan

overall_design: Sixty-one pairs of cancer and normal lung tissue specimens from non-smoking females were collected at National Taiwan University Hospital and Taichung Veterans General Hospital.   The selection criteria of clinical specimens depend on pathology report, physical examination and cigarette-smoking history.  Surgical lung tissue specimens were immediately snap-frozen in liquid N2 and stored at -80 °C.  Surgical specimens would be further processed for RNA and DNA extraction.  Only those samples passed quality controls were processed for gene expression profiling analysis and single nucleotide polymorphism (SNP) analysis respectively.

first: Liang-Chuan

last: Lai

middle: Y

last: Chuang


title: Diet-induced Obesity Disturbs Epigenetic Responses to Ionizing Radiation in Mouse

status: Public on Nov 09 2013

city: Fontenay-aux-Roses

first: Guillaume

last: Vares

institute: IRSN

summary: Both exposure to ionizing radiation and obesity have been associated with various pathologies including cancer. There is a crucial need in better understanding the interactions between ionizing radiation effects (especially at low doses) and other risk factors, such as obesity. In order to evaluate radiation responses in obese animals, C3H and C57BL/6 mice fed a control low fat or a high fat (HF) diet were exposed to fractionated doses of X-rays (4×0.75 Gy). Bone marrow micronucleus assays did not suggest a modulation of radiation-induced genotoxicity by HF diet. Both HF diet and irradiation resulted in increased oxidative damage, H2AX levels and proliferation in C57BL/6 mouse liver. Using methylation-specific PCR, we observed that the promoters of p16 and Dapk genes were methylated in the livers of C57BL/6 mice fed a HF diet (irradiated and non-irradiated); Mgmt promoter was methylated in irradiated and/or HF diet-fed mice. In addition, methylation PCR arrays identified Ep300 and Socs1 (whose promoters exhibited higher methylation levels in non-irradiated HF diet-fed mice) as potential targets for further studies. We then compared microRNA regulations after radiation exposure in the livers of C57BL/6 mice fed a normal or an HF diet, using microRNA arrays. Interestingly, radiation-triggered microRNA regulations observed in normal mice were not observed in obese mice. All together, our results suggested the existence of dietary effects on radiation responses (especially epigenetic regulations) in mice, possibly in relationship with obesity-induced chronic oxidative stress.

overall_design: C57BL/6J mice were fed a normal or a high-fat diet and exposed to 4 x 0.75 Gy X-rays. miRNA expression was measured in the livers of 3 mice for each experimental group.

first: Bing

last: Wang

first: Hiroko

last: Ishii

first: Mitsuru

last: Nenoi

first: Tetsuo

last: Nakajima


title: Impact of PDR8 allelic variation on yeast transcriptome profile in wine fermentation condition.

first: Bruno

last: Blondin

summary:
An eQTL analysis show that mutations in PDR8 gene in 59A strain versus S288c could trigger expressions variations of QDR2. In order to confirm this result and highlight other gene expression variations associated to PDR8 allelic variation, we performed an allele switch of PDR8 in 59A background (59A PDR8-S288c) and compared the transcriptomic profile of this strain to 59A. The analysis was performed in wine alcoholic fermentation conditions in stationary phase during nitrogen starvation and in alcoholic stress.
PDR8 allelic variation: 9 non synonymous SNP (S288c->59A)   9(K->T), 17(S->L), 79(P->S), 198(G->D), 263(H->R), 267(T->S), 371(L->F), 550(A->G), 601(I->V).

overall_design: 6 transcriptomic profiles were performed with Agilent mono-color array: 3 hybridizations were performed for each strain corresponding to 3 biological replicated samples. Using mono-color array, the intensity was used after normalization to calculate logarithm base 2 of expression ratios.

first: Christian

last: Brion


title: SNP genotyping analyses for the Chinese indigenous pig breeds and commercial pig breeds

status: Public on May 09 2013

city: Beijing

first: Huimin

last: Kang

summary:
Genome-wide SNP genotyping array can genotyped SNP highthroughly.
It can be used in many aspects, such as phylogeny relationships, genome-wide association studies, copy number identification.

overall_design: 9 Chinese indigenous pig, 4 commercial pigs and 1 wild pig were genotyped by PorcineSNP60 array (Illumina) for exploring the phylogeny relationships among them.

first: Jianfeng

last: Liu

first: Jiying

first: Jicai

last: Jiang


title: Expression data from SPHINX (SPaceflight of Huvec: an INtegrated eXperiment)

status: Public on Jan 20 2013

city: Milan

first: Silvia

last: Bradamante

address: Via Golgi 19

country: Italy

institute: CNR-ISTM, Institute of Molecular Science and Technology

summary: Changes in the physical environment modulate cell responses and may lead to the impairment or even failure of tissue function as a result of mechanotransduction processes. It has been suggested that this situation occurs in some age-related diseases and some pathological conditions observed in space, such as cardiovascular deconditioning, bone loss, muscle atrophy, and impaired immune responses. All of these are associated with endothelial dysfunction but the precise mechanism is still unclear.  We used the microarray approach to obtain insights into the mechanism responsible for endothelial dysfunction by taking advantage of the challenging environment of gravitational unloading onboard the International Space Station.

overall_design: The effects of gravitational unloading on HUVEC gene expression were investigated by means of cDNA microarray analyses of six randomly chosen samples (three for each of the two conditions of spaceflight and 1g) using Affymetrix Gene Human 1.0 ST Arrays

last: Versari

first: Giulia

last: Longinotti

first: Livia

last: Barenghi

first: Jeanette

last: Maier


title: Genome-wide analysis of gene expression patterns in mir-122 knockout mice livers

status: Public on Aug 07 2012

first: Ann-Ping

last: Tsou

address: 155, Li-Nong St., Sec.2

department: Inst. Biotechnology in Medicine

institute: National Yang-Ming University

summary: To invesigate the physiology roles of mir-122 in liver, we performed expression profiling of mir-122 knockout mice and the control B6/129 mice.

overall_design: Total RNA was extracted from four mir-122 knockout mice and three control mice of 2 months of age. Gene expression was quantified by robust multi-array analysis (RMA) using the Genomic Suite software from Partek.

first: Wei-Chih

last: Tsai

first: Chu-Sui

last: Hsu

first: Shu-Jen

last: Chen

first: Yi

last: Huang

first: Hua-Chien


title: Stable gene expression of serial skin biopsies defines patient subsets in diffuse cutaneous systemic sclerosis

status: Public on Mar 23 2012

first: Tammara

last: Wood

state: NH

department: Biomedical Data Science

institute: Dartmouth Medical School

summary: Systemic sclerosis (SSc) shows complex clinical manifestations including progressive skin and internal organ fibrosis. SSc can be divided into 'intrinsic subsets' by gene expression suggesting patient-specific heterogeneity in pathogenesis or temporal evolution of disease.  Here we validate these subsets using an independent patient population, and test whether the genes vary over time with patients changing subsets as disease progresses, or if the genes are a stable feature of the patients within each subset. Skin biopsies were analyzed from 13 dSSc patients enrolled in an open label study of rituximab, 9 dSSc patients not treated with rituximab, and 9 healthy controls. These data recapitulate the patient 'intrinsic subsets' described previously with gene expression associated with cell proliferation, inflammatory processes, and a normal-like group.  Serial skin biopsies showed consistent and non-progressing gene expression. We were unable to detect significant differences in gene expression before and after rituximab treatment, consistent with an apparent lack of clinical response. Serial biopsies from each patient stayed within the same gene expression subset regardless of treatment regimen or the time point at which they were taken. This demonstrates the intrinsic subsets are an inherent, reproducible and stable feature of SSc that is independent of disease duration.

first: S

last: Pendergrass

first: M

last: Whitfield


title: The human pancreatic islet transcriptome: impact of pro-inflammatory cytokines

status: Public on Mar 09 2012

first: Guy

last: Bottu

address: U.L.B. CP618, Route de Lennik 808

department: Faculty of Medecine

institute: Free University of Brussels

summary: We have used RNA-seq to identify transcripts, including splice variants, expressed in human islets of Langerhans under control condition or following exposure to the pro-inflammatory cytokines interleukin-1β (IL-1β) and interferon-γ (IFN-γ). A total of 29,776 transcripts were identified as expressed in human islets. Expression of around 20% of these transcripts was modified by pro-inflammatory cytokines, including apoptosis- and inflammation-related genes. Chemokines were among the transcripts most modified by cytokines. Interestingly, 35% of the genes expressed in human islets undergo alternative splicing as annotated in RefSeq, and cytokines caused substantial changes in spliced transcripts. Nova1, previously considered a brain-specific regulator of mRNA splicing, is expressed in islets. 25/41 of the candidate genes for type 1 diabetes are expressed in islets, and cytokines modified expression of several of these transcripts.

overall_design: 5 human islet of Langerhans preparations examined under 2 conditions (control and cytokine treatment)

first: Décio

middle: L

last: Eizirik

first: Miriam

last: Cnop


title: Transcriptional program induced by SCL/TAL1 in the megakaryopoietic differentiation from hESCs

status: Public on Jan 30 2014

city: Granada

first: Pedro

middle: Jose

last: Real

state: Granada

address: Avda. Ilustracion 114

department: Molecular Oncology

institute: GENyO

summary: To deepen the understanding of the molecular mechanisms that regulate megakaryocytic differentiation mediated by SCL, We performed gene expression profiling (GEP) using oligonucleotide microarrays of control (EV) and SCL-overexpressing cells that were undifferentiated or at day 14 of EB differentiation.

overall_design: We studied the SCL-overexpression-associated transcriptomic changes during megakaryocytic differentiation from hESCs at 14 days.  Two independent experiments were performed.


title: Comparison between cell lines from 9 different cancer tissue (NCI-60) (Affymetrix U133 Plus 2.0)

status: Public on Sep 29 2011

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

summary: Comparison between cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, Renal) from NCI-60 panel.

overall_design: Cell lines from 9 different cancer tissue of origin types

first: William

last: Reinhold

first: John

last: Weinstein

first: Eric

last: Kaldjian


title: Genome-wide screening of genomic alterations and transcriptional modulation in non-smoking female lung cancer in Taiwan

status: Public on Dec 19 2012

first: Tzu-Pin

last: Lu

type:
Genome variation profiling by SNP array
Expression profiling by array
SNP genotyping by SNP array

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

overall_design: Refer to individual Series

first: Liang-Chuan

last: Lai

last: Chuang


title: Effect of wood block enrichment on gene expression data in rat liver and spleen following treatment with cyclophosphamide for 5 days

status: Public on Jun 29 2013

city: North Chicago

first: Amy

last: Ditewig

address: 1 North Waukegan Road

department: Exploratory Toxicology

institute: AbbVie Inc

summary:
Wood blocks are a suggested form of rodent enrichment, however, if ingested, wood blocks could potentially confound early toxicology results.
We used microarrays to determine if transcriptomically, rats treated with cyclophosphamide and administered wood blocks were different from those treated with cyclophosphamide and not allowed access to wood blocks

overall_design: Rats (n=3/group) were dosed orally with 40 mg/kg/day Cyclophosphamide or vehicle.  In each group half of the rats were allowed access to wood blocks and the other half were not allowed access to wood blocks.  At necropsy the liver and spleen were removed and flash frozen in liquid nitrogen.  The frozen organs were homogenized individually in Qiazol and RNA extraction was performed.  Using a 5ug input, samples were processed for microarray following the Affymetrix procotol.  Samples were hybed to Rat 230 2.0 microarray chips.

first: Wayne

last: Buck


title: Comparison between cell lines from 9 different cancer tissue (NCI-60) (Agilent WG platform)

status: Public on Jun 12 2011

overall_design: Comparison between cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, Renal) from NCI-60 panel

first: Stephanie

last: Fulmer-Smentek

first: Petula

last: D'Andrade

first: Susan

last: Holbeck


title: Comparison between cell lines from 9 different cancer tissue (NCI-60) (Affymetrix HuEx 1.0)

status: Public on Jun 17 2011

summary: Comparison between cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, Renal) from NCI-60 panel

first: Thomas

last: Gingeras


title: Gene expression analysis of Salmonella enterica regulatory mutants

status: Public on Apr 08 2011

city: Rockville

last: Braisted

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

summary: The study aims to determine the effects of mutants and deletions of several known regulators on S. enterica gene expression.

overall_design: Samples were hybridized on aminosilane coated slides with 70-mer oligos.  Samples were hybridized with at least one flip dye experiment. Cells were grown in media LB or LPM and RNA harvest at mid log or stationary phase.

first: Marcus

middle: B

last: Jones

first: Bryan

last: Frank

first: Afshan

last: Kidwai

first: Fred

last: Heffron

first: Scott

last: Peterson.


title: Expression Quantitative Trait Loci and their relationship with lipid deposition in gluteus medius muscle of Duroc pigs

status: Public on Dec 16 2010

city: lleida

first: angela

last: canovas

state: lleida

address: 191, rovira roure

institute: irta

summary: In the last 20 years, there has been significant research towards defining the genetic basis of lipid metabolism and meat quality related traits in pigs. Nowadays, the study of the transcriptome and its regulatory mechanisms allows going far beyond in the genetic dissection of these complex traits. In present study, a genome-wide eQTL scan aiming to detect pig genome regions regulating levels of skeletal muscle mRNA expression has been performed. This study has been conducted on a commercial Duroc population where a number of QTL for muscle fat deposition and fatty acid composition had been detected. GeneChip Porcine Genome® arrays (Affymetrix) were used to determine the gene expression levels of gluteus medius samples from 105 Duroc pigs belonging to two groups with divergent phenotypes for fatness traits. This experimental design aimed to favour detection of eQTL affecting genes related to lipid metabolism and meat quality traits. The whole genome scan with a panel of 110 microsatellites allowed us detecting 613 genome-wide significant eQTL unequally distributed across the pig genome, SSC5 and SSC3 harbouring the highest number of eQTL. Moreover, 11 genome regions with eQTL affecting the expression levels of a high number of genes (eQTL hot spots) have been described. After mapping target probes and discarding low quality probes, a total of 59 cis- and 396 trans-acting eQTL were retained for further analyses. The functional classification showed that lipid-related GO terms were not the most enriched by the list of eQTL-regulated genes. However, a number of regulated genes functionally related to lipid metabolism and fat deposition traits were identified, and their functional relationship with these phenotypes were further investigated. With this purpose, eQTL results were integrated with 1) QTL linkage maps and 2) correlation data between phenotypes and gene expression levels. As a result, a comprehensive list of 29 positional and functional candidate genes was elaborated. These results represent a valuable contribution to the comprehension of genetic regulation of skeletal muscle individual gene expression in swine species, and a first step towards disentangling gene networks and molecular mechanisms involved in lipid metabolism and meat quality traits.

overall_design: 105 gluteus medius samples from 105 animals belonging to two groups of 53 and 52 animals each: HIGH group had higher carcass, plasma and muscle fat content; LOW group had lower carcass, plasma and muscle fat content

first: A

last: Cánovas

first: P

last: Pena

first: D

last: Gallardo

first: M

last: Amills

first: R

last: Quintanilla


title: Gene expression analysis of Salmonella enterica regulatory mutants.

first: Fatma

last: Onmus-Leone

address: 9704 Medical Center Dr.

institute: JCVI

overall_design: Samples were hybridized on aminosilane coated slides with 70-mer oligos.  Each sample have biological replicates. Cells were grown in media LB or LPM and RNA harvest at log, mid log or stationary phase. Salmonella enterica strain 14028 is used as reference throughout the study.

last: Peterson


title: Genome-wide screening of transcriptional modulation in non-smoking female lung cancer in Taiwan

status: Public on Jan 30 2011

first: Tzu-Pin

last: Lu

summary: Although smoking is the major risk factor for lung cancer, only 7% of female lung cancer patients in Taiwan have a history of cigarette smoking, extremely lower than those in Caucasian females.  This report is a comprehensive analysis of the molecular signature of non-smoking female lung cancer in Taiwan.

overall_design: RNA was extracted from paired tumor and normal tissues for gene expression analysis.

first: Liang-Chuan

last: Lai

first: Eric

last: Chuang


title: Comparison between cell lines from 9 different cancer tissue (NCI-60) (U133 platform)

status: Public on Mar 26 2007

city: Bethesda

first: Uma

last: Shankavaram

address: 9000 Rockville Pike

department: NCI

institute: NIH

summary:
Comparison between cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, Renal) from NCI-60 panel

Keywords: cell_type_comparison_design; disease state; cell line; tissue type

first: John

last: Weinstein

first: Ari

last: Kahn

last: Kaldjian


title: Comparison between cell lines from 9 different cancer tissue (NCI-60) (U95 platform)

status: Public on Aug 06 2007

overall_design: cell lines from 9 different cancer tissue of origin types


title: Intraspecific variation in the Populus balsamifera drought transcriptome

status: Public on Dec 31 2010

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

country: Canada

institute: University of Toronto

summary: Drought is a major limitation to the growth and productivity of trees in the ecologically and economically important genus Populus. The ability of Populus trees to contend with drought is a function of the responsiveness of their genome to this environmental insult, involving reconfiguration of the transcriptome to appropriately remodel growth, development and metabolism. The Populus drought transcriptome is shaped by interspecific genotypic variation, but the extent to which intraspecific variation shapes the drought transcriptome has not yet been examined. Here we test hypotheses aimed at examining the extent of intraspecific variation in the drought transcriptome. Transcriptome remodeling in response to water-deficit conditions was examined in six different Populus balsamifera L. genotypes using Affymetrix GeneChip technology. There were significant differences in the transcriptomes of the genotypes in response to water-deficit conditions; however, a common species-level response could also be identified across all individuals. Genotypes that had more similar drought-responsive transcriptomes also had fewer genotypic differences, as determined by microarray-derived single feature polymorphism (SFP) analysis, suggesting that responses may be conserved across individuals that share a greater degree of genotypic similarity. This work highlights the fact that a core species-level response can be defined; however, the underpinning genotype-derived complexities of the drought response in Populus must be taken into consideration when defining both species- and genus-level responses.

overall_design: 72 arrays total. 6 genotypes, 2 time points. 2 water regimes. 3 biological replicates per treatment

first: Erin

last: Hamanishi

first: Barb

last: Thomas

first: Shawn

middle: D

last: Mansfield

first: Aine

last: Plant


title: Transcript abundance comparison between uninfected DCs and DCs housing L. amazonensis

status: Public on Jun 15 2010

city: Paris

last: Prina

address: 25 rue du Dr Roux

department: Parasitology and Mycology

institute: Institut Pasteur

summary: To determine the modulation of gene expression of mouse BMDCs in the presence of living intracellular Leishmania amazonensis amastigotes

overall_design: Dendritic cells were generated in vitro from bone marrow progenitors. Leishmania amazonensis amastigotes were purified from mouse cutaneous lesions and were added to DC cultures. After 24h, and following a sorting procedure, only BMDCs housing living amastigotes were selected for total RNA extraction based on the expression of MHC class II (host cell) and DsRed2 (parasites) molecules.

first: Herve

last: Lecoeur

first: Hugo

last: Varet

first: Jean-Yves

last: Coppee

first: Gerald

last: Spaeth

first: Genevieve

last: Milon