title: The role of the MfsR repressor on the transcriptome of the integrative and conjugative element ICEclc  in Pseudomonas putida UWC1

city: Lausanne

first: Jan

middle: Roelof

last: van der Meer

address: Bâtiment Biophore, Quartier UNIL-Sorge

department: Department of Fundamental Microbiology

institute: University of Lausanne

summary: These transcriptomic data are used in two distinct but subsequent and complementary studies:(i) the role of the mfsR gene on the expression of the mfsABC operon as well as on its own promoter, (ii) the role of the mfsR operon on the activation of the core genes of ICEclc.

overall_design: ICEclc-specific gene expression in Pseudomonas putida UWC1 was measured during exponential phase and the subsequent stationary phase (sole carbon and energy sources : 10mM 3-chlorobenzoate). 6 genotypes were tested: (i) wild type P. putida UWC1 ICEclc (strain n°2737) ; (ii) P. putida UWC1 ICEclc-KmR19033 (strain n°2961) ; (iii) P. putida UWC1 ICEclc∆'mfsR (strain n°4322) ; (iv) P. putida UWC1 ICEclc∆'orf17984 (strain n°4372) ; (v) P. putida UWC1 ICEclc∆'tciR (strain n°4321) ; (vi) P. putida UWC1 ICEclc∆mfsR-∆'orf17984 (strain n°3543). For each strain, in each phase, 3 or 4 replicates were used.

first: Nicolas

last: Pradervand

middle: R


title: Patterns of genome-wide VDR locations

status: Public on Nov 14 2014

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The genome-wide analysis of the binding sites of the transcription factor vitamin D receptor (VDR) is essential for a global appreciation the physiological impact of the nuclear hormone 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3).  Genome-wide analysis of lipopolysaccharide (LPS)-polarized THP-1 human monocytic leukemia cells via chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq) resulted in 1,318 high-confidence VDR binding sites, of which 789 and 364 occurred uniquely with and without 1,25(OH)2D3 stimulation, while only 165 were common. We re-analyzed five public VDR ChIP-seq datasets with identical peak calling settings (MACS, version 2) and found in total 23,409 non-overlapping VDR binding sites, 75% of which are unique within the six analyzed cellular models. LPS-differentiated THP-1 cells have 22% more genomic VDR locations than undifferentiated cells and both cell types display more overlap in their VDR locations than the other investigated cell types. In general, the intersection of VDR binding profiles of ligand-stimulated cells is higher than those of unstimulated cells. De novo binding site searches and DR3-type binding site screening using HOMER of the six VDR ChIP-seq datasets suggest that DR3 sites are strongly associated with the ligand-responsiveness of VDR occupation. Importantly, all VDR ChIP-seq datasets display the same relationship between the VDR occupancy and the percentage of DR3-type sequences below the peak summits.  The comparative analysis of six VDR ChIP-seq datasets demonstrated that the mechanistic basis for the action of the VDR is independent of the cell type. Only the minority of genome-wide VDR binding sites contains a DR3-type sequence. Moreover, the total number of identified VDR binding sites in each ligand-stimulated cell line inversely correlates with the percentage of peak summits with DR3 sites.

overall_design:
Systematic reanalysis of 5 published VDR ChIP-seq datasets together with a new dataset from 24 h LPS-treated THP-1 cells at the unstimulated state and after 80 min ligand (10 nM 1α,25(OH)2D3 (1,25D, calcitriol)) treatment.

See GSM1280896 and GSM1280896 Sample records for data processing information. GSE53041_README.txt has additional details.

first: Pauli

last: Tuoremäki

last: Väisänen

first: Carsten

last: Carlberg


title: Peg3 mutational effects on reproduction and placenta-specific gene families

status: Public on Sep 11 2014

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences

department: Biological Sciences

country: USA

institute: Louisiana State University

summary: Peg3 (paternally expressed gene 3) is an imprinted gene encoding a DNA-binding protein.  This gene plays important roles in controlling fetal growth rates and nurturing behaviors.  In the current study, a new mutant mouse model has been generated to further characterize the functions of this DNA-binding protein.  Besides known phenotypes, this new mutant model also revealed potential roles of Peg3 in mammalian reproduction.  Female heterozygotes produce a much smaller number of mature oocytes than the wild-type littermates, resulting in reduced litter sizes.  According to genome-wide expression analyses, several placenta-specific gene families are de-repressed in the brain of Peg3 heterozygous embryos, including prolactin, cathepsin and carcinoembryonic antigen cell adhesion molecule (Ceacam) families.  The observed de-repression is more pronounced in females than in males.  The de-repression of several members of these gene families is observed even in the adult brain, suggesting potential defects in epigenetic setting of the placenta-specific gene families in the Peg3 mutants.  Overall, these results indicate that Peg3 likely controls the transcription of several placenta-specific gene families, and further suggest that this predicted transcriptional control by Peg3 might be mediated through unknown epigenetic mechanisms.

overall_design: Mouse Breeding Two different types of heterozygotes were prepared for breeding experiment: male and female heterozygotes carrying the paternally (+/-p) and maternally (-m/+) transmitted targeted allele.  These 4 heterozygotes were bred with their littermates: for Breeding 1, female wild-type littermates x male heterozygotes (+/-P); Breeding 2, female heterozygotes (+/-P) x male wild-type littermates; Breeding 3, female wild-type littermates x male heterozygotes (-m/+); for Breeding 4, female heterozygotes (-m/+) x male wild-type littermates.  Genome-wide expression analysis  A litter of 14.5-dpc fetuses were harvested from a timed mating between a male heterozygote (-m/+) and wild-type female littermate.  Three tissues were obtained from each fetus: embryo head, placenta and amnionic sac.  Total 16 samples were used for this series of genome-wide expression analyses: 8 embryo heads and placenta representing two biological replicates of each of the four following combinations: male wild-type, male heterozygote, female wild-type, and female heterozygote.

first: Wesley

middle: D

last: Frey

first: Hongzhi

last: He

first: Hana

first: Muhammad

middle: B

last: Ekram

first: Arundhati

last: Bakshi

first: Mohammad

last: Faisal

first: Bambarendage

middle: U

last: Perera

first: An

last: Ye

first: Ryoichi

last: Teruyama


title: Gene-level analysis of 1231 samples originating from 134 Caucasian individuals

status: Public on Aug 29 2014

city: London

first: Mina

last: Ryten

address: Queen Square

department: Department of Molecular Neuroscience

country: United Kingdom

institute: UCL Institute of Neurology

summary:
This data set was generated by the UK Brain Expression Consortium and consists of gene expression data generated from post-mortem human brain samples, dissected from 10 brain regions and originating from a large cohort of neurologically and neuropathologically normal individuals.
The UK Brain Expression Consortium has generated gene expression data on a large cohort of neurologically and neuropathologically normal individuals in order to better understand gene expression differences across the human brain.

overall_design: 1231 samples are analysed in total and these samples originate from 134 Caucasian individuals. From each individual, up to ten brain regions were sampled and analysed.

first: Daniah

last: Trabzuni

first: Robert

last: Walker

first: Colin

last: Smith

first: Adaikalavan

last: Ramasamy

first: Sebastian

last: Guelfi

first: Michael

middle: E

last: Weale

first: John

last: Hardy


title: Differential expression profile of chicken embryo fibroblast DF-1 cells infected with cell-adapted Infectious Bursal Disease Virus

status: Public on Oct 01 2014

city: Hong Kong

first: Raymond

last: Hui

address: 5N01, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam

department: School of Biological Science

country: Hong Kong

institute: The University of Hong Kong

type: Expression profiling by high throughput sequencing

summary: RNA-Seq was used to unveil the transcriptional profile of DF-1 cells at the early stage of cell-adapted Infectious Bursal Disease Virus (caIBDV) infection. Total RNAs were extracted from virus-infected cells at 0, 6 and 12 hpi. RNA-Seq datasets of respective samples mapped to 56.5 - 57.6% of isoforms in the reference genome Galgal4.73. At 6 hpi, 23 isoforms underwent an elevated expression, while 128 isoforms were up-regulated and 5 were down-regulated at 12 hpi in the virus-infected group. Besides, 10 isoforms were exclusively expressed in the virus-infected cells. Though no significant change was detected in cytokine and interferon expression levels at the first 12 hours of infection, modulations of the upstream regulators were observed. In addition to the reported regulatory factors including EIF2AK2, MX, OAS*A, GBP7 and IFIT, IBDV infection also triggered a IFIT5-IRF1/3-RSAD5 pathway in the DF-1 cells which potentially restricted the viral replication cycle in the early infection stage. Over-expression of LIPA and CH25H, together with the suppression of STARD4, LSS and AACS genes implied a modulation of membrane fluidity and lipid raft arrangement in the infected cells. Alternative splicing of the EFR3 homolog A gene was also through to be involved in the lipid membrane regulation, and these cumulative responses projected an inhibition of viral endocytosis. Recognition of viral RNA genomes and intermediates was presumably enhanced by the elevated levels of IFIH1, DHX58 and TRIM25 genes which possess properties on detecting viral dsRNA. On the other hand, the caIBDV arrested the host's apoptotic process by inducing the expression of apoptosis inhibitors including NFKBIA/Z, TNFAIP2/3 and ITA at the first 12 hours of infection. In conclusion, the differential expression landscape demonstrated with RNA-Seq provides a comprehensive picture on the molecular interactions between host cells and virus at the early stage of infection.

overall_design: Two sample groups (infected and mock-infected) at three time points (0, 6, 12 hpi) were analysed.

middle: K

first: Frederick

middle: C

last: Leung


title: Baseline expression of lymphatic and inflammatory genes in CD14+ blood monocytes from healthy donors

status: Public on Apr 22 2016

city: Springfield

first: Sophia

last: Ran

state: IL

address: 801 N. Rutledge St.

department: MMICB

institute: Southern Illinois University - School of Medicine

summary: Blood was donated by four healthy volunteers with no known illness or malignancies. Mononuclear cells were separated from the blood by density gradient and CD14+ cells were isolated using anti-CD14 IgG-conjugated magnetic beads and magnetic separation (Miltenyi Biotec).  We used an in-house array to analyze the gene expression of a total of 270 targets including 67 cytokines, 57 cytokine receptors, 18 chemokines, 11 chemokines receptors, 10 known TLR4 downstream targets, 64 other inflammation-related proteins, 12 genes expressed primarily in lymphatic endothelial cells, and 32 endothelial cell associated proteins. The results show a baseline expression in CD14+ PBMC in healthy individuals which can be used to detect changes in CD14+ PBMC population via transcript expression in individuals with illnesses and malignancies such as breast cancer.

overall_design: Transcript of CD14+ peripheral blood monocytic cells (PBMC) was analyzed by RT-qPCR gene expression profiling. CD14+ PBMC were isolated from four donors. For each specimen total RNA was isolated, cDNA synthesized, and 269 targets were analyzed by RT-qPCR.

first: Caitlin

last: Griggs

first: Kelly

last: Hall

first: Lisa

last: Volk-Draper


title: Gene profiling studies in postnatal Mfrprd6 mutant eyes reveal differential expression of Prss56, a trypsin-like serine protease, and genes involved in visual and phototransduction pathways.

status: Public on Oct 24 2014

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

summary: Mutations in the membrane frizzled-related gene (Mfrp) are linked to posterior microphthalmia, retinitis pigmentosa and nanophthalmia in humans. In homozygous Mfrprd6 mice, a splice site mutation causes a slow photoreceptor degeneration characterized by shortening and disorganization of outer segments with eventual photoreceptor loss.  To better understand the function of MFRP in the retina, microarray analysis was carried out in mutant and control mice at postnatal day14 (P14), prior to the loss of photoreceptors.  Analysis of the data revealed differentially expressed RPE and neuroretina transcripts.  Although the analysis of the microarray data from Mfrprd6 mutant mice compared to age-matched wild-type controls identified some transcripts with relative fold change > 5.0, most of the differentially expressed genes showed a relative fold change between1.5 - 2.0.  Global gene expression analysis using Ingenuity Pathway Analysis software identified decreased levels of transcripts in phototransduction and visual pathways in Mfrprd6 mutants. Select candidate transcripts were validated by quantitative real-time PCR analyses. The expression of RPE-specific visual transduction protein, RPE65, was significantly decreased in Mfrprd6 mutants. As an indirect consequence of the primary RPE cell defect due to the Mfrprd6 mutation, retinal specific transcripts Rgr, Pde6a, GuCa1b, and Rgs9 were also significantly decreased. We also confirmed the significantly elevated levels of Prss56, a gene previously associated with myopia and open angle glaucoma.  In the Mfrprd6 mutant, a progressive increase in Prss56 mRNA levels from 14- to 70-fold was observed from P7 to P21, respectively. In situ hybridization and glutamine synthetase staining of mutant eyes indirectly identified Müller glia in the inner nuclear layer of retina as the cell type expressing the Prss56 transcript.

overall_design: This experiment had one model term, a combination of strain and time, which consisted of four levels (B6_P0, B6_P14, Rd6_P0 and Rd6_P14). Three biological replicates were used per term level. A total of 12 Affymetrix Mouse 430v2 Arrays were used in gene expression analysis.

first: Ramani

last: Soundarararajan

first: Jungyeon

last: Won

first: Wanda

last: Hicks

first: Jürgen

last: Naggert

first: Mark

middle: P

last: Krebs

first: Patsy

middle: M

last: Nishina


title: Expression data from  RLT-PSC, human pancreatic stellate cell lineage

status: Public on Aug 10 2014

city: Budapest

first: Gabor

last: Firneisz

address: Szentkiralyi St. 46

department: 2nd Department of Medicine

country: Hungary

institute: Semmelweis University

summary: Gene expression patterns in human PSCs exposed to chronic hyperglycemia with and without subsequent 48h TGF-β1 treatment or to TGF-B1 treatment alone. Treatments were compared to control human PSCs cultured in normal glucose concentration

overall_design: Total RNA was extracted from human PSCs of RLT-PSC line exposed to chronic hyperglycemia with or without subsequent TGF-β1 treatment and in PSCs exposed to 48h TGF-β1 treatment. Each treatment was compared to control human PSCs cultured in normal glucose concentration. Samples from all treatment arms were hybridized on Affymetrix PrimeView Human Gene Expression Array

first: Katalin

last: Kiss

first: Sándor

last: Spisák

first: Barna

last: Wichmann

first: Ilona

last: Kovalszky

first: Gábor


title: Synergism between Hedgehog-GLI and EGFR signaling in Hedgehog-responsive human medulloblastoma (Daoy) cells

status: Public on Jul 31 2014

city: Berlin

first: Christoph

last: Wierling

address: Ihnestr. 73

department: Department Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Aberrant activation of Hedgehog (HH) signaling has been identified as a key etiologic factor of many human malignancies. Signal strength, target gene specificity, and oncogenic activity of HH signaling profoundly depend on interactions with other pathways such as epidermal growth factor receptor-mediated signaling which has been shown to cooperate with HH/GLI in basal cell carcinoma and pancreatic cancer.   We demonstrate that the human medulloblastoma cell line Daoy possesses a fully inducible endogenous HH pathway. Treatment of Daoy cells with Sonic Hedgehog or Smoothened agonist induced expression of GLI1 protein and prevented processing of GLI3 to its repressor form. To study interactions between HH- and EGF-induced signaling in greater detail, time-resolved measurements were carried out and analyzed on the transcriptomic as well as proteomic level. Daoy cells responded to the co-treatment by downregulating GLI1, PTCH, and HHIP on the transcript level which was also seen when Amphiregulin (AREG) was used instead of EGF. The finding that EGFR signaling silences proteins acting as negative regulators of HH signaling is firstly described here as a novel crosstalk mechanism. Furthermore, combined EGFR/HH signaling maintains high GLI1 protein levels contrasting its downregulation on the transcript level. On the other hand, high level synergism was observed with respect to a strong and significant upregulation of numerous canonical EGF-targets with putative tumor-promoting properties such as MMP7, VEGFA, and IL-8. In conclusion, synergistic effects between EGFR and HH signaling can selectively induce a switch from a canonical HH/GLI profile to a modulated specific target gene profile pointing to more wide-spread, yet context-dependent, interactions between HH/GLI and growth factor receptor signaling in human malignancies.

overall_design: To study interactions between HH- and EGF-induced signaling, time-resolved measurements were carried out over a period of 24 h at 14 different time points after stimulation by EGF with and without additional stimulation by SHH. Furthermore, as a control, cells without any stimulation by EGF and SHH (control) and cells in the presents of SHH were analyzed. Overall, three biological replicates of 60 different treatment/timepoints were analyzed yielding 180 different samples.

first: Frank

last: Götschel

first: Hendrik

last: Hache

first: Daniela

last: Berg

first: Markus

last: Eberl

first: Fritz

last: Aberger

first: Wilfried

last: Nietfeld

first: Ulrike

last: Korf


title: Transcriptome analysis of porcine immune organs following porcine cytomegalovirus infection

status: Public on Jul 12 2014

city: Ya’an

first: Xiao

last: Liu

state: Sichuan Province

address: 46# Xinkang Road

department: College of Veterinary Medicine

country: China

institute: Sichuan Agricultural University

summary: Porcine cytomegalovirus (PCMV) is a member of the genus Cytomegalovirus, subfamily Betaherpesvirinae, and family Herpesvirus. PCMV is a major immunosuppressive virus that mainly suppress the immune function of T lymphocytes and macrophages. PCMV is widely distributed all over the world, but there are not significantly different serotypes found. Moreover, the molecular mechanisms of host anti-PCMV infection and the molecular immunosuppressive mechanisms of PCMV is still not well charaterized. To understand the PCMV potential impact on the function of immune organs, we performed microarray assay to analyze the transcriptome of porcine immune organs after PCMV infection. We identified 5582 differential expression genes by PCMV infection in microarray.   There are 2161 upregulated genes and 3421 down-regulated by PCMV infection genes compare to the uninfected control group. We confirmed 13 differentially expressed immune-related genes by quantitative real-time RT-PCR (qPCR).      Gene ontology, gene interaction networks and KEGG pathway analysis uncovered the differentially expressed genes interaction regulatory network. These findings indicated that PCMV regulates multiple functional pathways, including immune system process, cellular process, metabolic process, networks of cytokine-cytokine receptor interaction, TGF-beta signaling pathway, lymphocytes receptor signaling pathway and TNF signaling pathway.  Our study is the first comprehensive attempt to explore the host transcriptional response to PCMV infection in porcine immune systems. It provided new insights into the immunosuppressive molecular mechanisms and pathogenesis of PCMV. This previously unrecognized endogenous antiviral mechanism has implications for development of host-directed strategies to the prevention and treatment of immunosuppressive viral diseases.

overall_design: 2 samples were analysed. PCMV infected porcine immune organs; control porcine organs. piglets were divided into two groups of five pigs each, and maintained under controlled temperature and humidity. Each pig in the first group was inoculated with 5 ml of 109 PFU/ml PCMV SC strain by intramuscular and intranasal injection, and the other five pigs were injected with 5 ml of RPMI-1640 nutrient solution (Thermo Fisher Scientific, Waltham, UK) as the control. The sera, lymph nodes, spleens, and thymuses of the infected and control pigs were collected at 14 dpi


title: Exon-level analysis of 1231 samples originating from 134 Caucasian individuals

first: Mina

last: Ryten

first: Daniah

last: Trabzuni

first: Robert

last: Walker

first: Colin

last: Smith

first: Adaikalavan

last: Ramasamy

first: Sebastian

last: Guelfi

first: Michael

last: Weale

first: John

last: Hardy


title: The miRNAome of O. viverrini induced cholangiocarcinoma by microarray:

status: Public on Jul 17 2014

city: Washington

first: Jeffrey

last: Bethony

state: DC

address: 2300 Eye St. NW.

department: Microbiology, Immunology, and Tropical Medicine

institute: George Washington University

summary: Cholangiocarcinoma is the second most common primary hepatic malignancy worldwide, with intrahepatic cholangiocarcinoma (ICC) a particularly significant public health problem in Southeast Asia, due to its strong association with the food-borne parasite Opisthorchis viverrini (OV). This manuscript represents the first comprehensive miRNA expression profiling by microarray of the three most common histological grades of OV-induced ICC: moderately differentiated, papillary, and well differentiated tumor tissue. No cohort of miRNAs emerged as commonly dysregulated among these histological grades of OV-induced ICC. Instead, each histological grade of ICC tissue showed a distinct miRNA profile. Moderately differentiated tumor tissue showed both the greatest number and the highest magnitude of miRNA dysregulation, followed by papillary ICC tumor tissue, and differentiated ICC tumor tissue. When ICC tumor tissue was compared to adjacent non-tumor tissue, a remarkable similarity in miRNA dysregulation was observed between these samples, indicative of intrahepatic metastasis. These findings indicate the possibility of determining the histological grade of ICC by profiling miRNA dysregulation, which not only would greatly enhance the molecular diagnosis of ICC, but could even lead to the personalized the treatment for ICC by the early classification of histological grade.

overall_design: A total of 46 unique liver tissue samples were analyzed on Agilent human miRNA microarray (miRBase Release 16.0). Of the 46 samples, 13 are from non-cancer healthy patients with gastric bypass surgery. The rest of 33 samples are CCA tumor tissue samples and their paired adjacent normal/necrotic tissue: 12 from well differentiated CCA, 17 from papillary CCA, 4 from moderately differentiated CCA.

first: Jordan

middle: L

last: Plieskatt

first: Yan

last: Feng

first: Jin

last: Peng

first: Ponlapat

last: Yonglitthipagon

first: Gabriel

last: Rinaldi

first: Samantha

last: Easley

first: Norman

last: Lee

first: Therawatch

last: Laha

first: Banchob

last: Sripa

first: Paul

middle: J

last: Brindley

first: Jason

last: Mulvenna


title: Differentiation of human neural precursor cells from pluripotent stem cells

status: Public on Jul 04 2014

city: San Diego

first: Ronald

last: Coleman

state: California

address: 3215 Merryfield Row

department: Chemical Physiology

institute: The Scripps Research Institute

summary:
Pluripotent stem cells were differentiated using a 4 factor differentiation method to neural precursor cells (NPCs)
The objective of this study is to find similar gene expression patterns in hNPCs derived from different cell lines through a single technique.

overall_design: 10 Samples were analyzed in this study. This included 5 hNPC lines 4 hPSC lines and one sample of human dermal fibroblasts.


title: The transcriptomes for primary panicle in four near-isogenic lines combined of different allele of two major grain length loci GS3 and qGL3 in rice

status: Public on Jul 22 2014

city: Qingdao

first: Xiaojun

last: Zhang

state: Shandong

address: Changcheng road No. 700

institute: QAU

summary: To investigate the genetic relationship between two major grain length loci GS3 and qGL3, we developed the near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3), NIL-qgl3 (gs3/qgl3), NIL-GS3/qgl3 (GS3/qgl3) in the background of 93-11 (gs3/qGL3) by crossing  and MAS approach.

overall_design: Four samples was analyzed: three near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3), NIL-qgl3 (gs3/qgl3), NIL-GS3/qgl3 (GS3/qgl3) and their background of 93-11. Every sample had three independed duplications. And the primary panicle with 3-6 cm length from the three NILs and 93-11 were used for RNA preparation and hybrid with Rice Genome OneArray Microarray (Phalanx Biotech Group).

first: Ji

last: Huang

first: Xiuying

last: Gao

first: Hongxia

last: Lan

first: Jianfei

last: Wang

first: Hongsheng


title: DHT-AR, E2-AR and R5020-AR target gene profiles in LNCaP

status: Public on Jun 19 2014

city: Itabashi-ku

first: Takao

last: Susa

state: Tokyo

department: Department of Biochemistry

country: Japan

institute: Teikyo University School of Medicine

summary: We previously encountered regulatory processes where dihydrotestosterone (DHT) exerted its inhibitory effect on parathyroid hormone-related protein (PTHrP) gene repression through the estrogen receptor (ER)α, but not the androgen receptor (AR) in breast cancer MCF-7 cells. Here, we investigated whether such an aberrant ligand-nuclear receptor (NR) interaction is present in prostate cancer LNCaP cells. First, we confirmed that LNCaP cells expressed a functional AR and at negligible levels of ERα, and progesterone receptors. Both suppression of PTHrP and activation of the PSA genes were observed after treatment of E2, DHT and R5020. Consistent with the previous notion that the AR in LNCaP cells lost the ligand specificity due to a mutation AR (Thr-Ala877), our study using siRNA targeting each NR revealed that the AR, but not the other NRs, monopolized the role as the mediator of shared hormone-dependent regulation. These results were invariably associated with nuclear translocation of this mutant AR. Microarray of the genes regulated by either DHT, E2 or R5020 downstream of the AR (Thr-Ala877) revealed that more than half genes overlapped in LNCaP cells. Noticeably, AR (wild-type, wt) and AR (Thr-Ala877) were equally responsible for the E2-AR interactions. Fluorescent microscopic experiments demonstrated that both EGFP-AR (wt) and EGFP-AR (Thr-Ala877) were exclusively localized within the nucleus after E2 or DHT treatment. Further, a promoter assay revealed that breast cancer MCF-7 and Rv22 cells also exhibited such an aberrant E2-AR (wt) signaling. We postulate entangled interactions between the AR (wt) and E2 in a certain hormone-sensitive cancer cells.

overall_design: Total RNAs from the LNCaP cells transfected with control siRNA (siCT) or siRNA for AR (siAR) transfected LNCaP cells before 24 hr followed by exposed to 10-7M of DHT, E2 or R5020 exposure for another 24 h, respectively, were used.

first: Tomoki

last: Okazaki


title: Transcriptional responses of Middle East respiratory syndrome coronavirus (MERS-CoV) in marmosets

status: Public on Jun 10 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: The absence of a robust disease model currently hinders the evaluation of countermeasures for Middle East respiratory syndrome coronavirus (MERS-CoV). While a rhesus macaque model of MERS-CoV that results in mild-to-moderate disease has been utilized to describe the pathogenesis of this virus and for the evaluation of therapeutics, the inability to produce uniform disease with substantial virus replication complicates analysis in countermeasure studies. In an attempt to identify a more robust disease model, DPP4 sequences of various non-human primates were aligned. Modeling of the interactions between the receptor binding domain of MERS-CoV and its cognate receptor DPP4 predicted a "good fit" with complete conservation of all of the critical residues. To determine the feasibility of the marmoset as a MERS-CoV disease model, common marmosets were inoculated with MERS-CoV via combined intratracheal, intranasal, oral and ocular routes. Marmosets developed signs of moderate to severe illness with progressive serious to severe pneumonia. Progressive gross lesions were evident in animals necropsied at 3, 4 and 6 days post inoculation and two animals were euthanized during the study due to disease severity. This is the first description of a moderate-to-severe, with potentially lethality, disease model of MERS-CoV and as such will have utility for vaccine and other countermeasure efficacy evaluations in addition to further pathogenesis studies.

overall_design: Lung tissue samples were isolated and sequenced at 3, 4 and 6 days post inoculation. Two animals were euthanized during the study due to disease severity.

first: Angie

last: Rassmussen

first: Xinxia

last: Peng

first: Darryl

last: Falzarano

first: Heinz

last: Feldman

first: Matt

last: Thomas

first: Richard

last: Green

middle: G


title: Transcriptome of Dinoroseobacter shibae under changeing light regimes

status: Public on Jul 01 2014

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: D. shibae was cultivated under changing light regimes and samples for transcriptome and metabolome were taken.

sample_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design: Two independent cultivations in a Chemostat have been performed. Each reactor was run for 3 light/dark-cycles of 12h/12h. Sampling started from the second cycle and continued to the third cycle.

first: Nelli

last: Bill

first: Kerstin

last: Schmidt-Hohagen

last: Jarek

first: Sabin

last: Bhuju

first: Irene

last: Wagner-Döbler

first: Dietmar

last: Schomburg


title: Anopheles gambiae G3 small RNA sequence: Adult Female Body

status: Public on Aug 13 2014

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

summary: We provide a broad overview of sequence diversity in An. gambiae mature microRNAs, including annotation of novel microRNAs identified in this study.

overall_design: Non-coding RNA profiling by high throughput sequencing, in duplicate, using Illumina GAIIx.

first: Inna

last: Biryukova

last: Ye

first: Elena

last: Levashina


title: The long non-coding RNA lnc277 mediates a repressive gene signature in Ewing's sarcoma and is required for oncogenesis

status: Public on Nov 01 2014

city: Palo Alto

first: Dedeepya

last: Vaka

address: 265 Campus Drive

department: Pediatrics

institute: Stanford

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

overall_design: Refer to individual Series


title: Expression data from vessels of differing embryonic origin

status: Public on Aug 26 2014

city: Nashville

first: David

last: Bader

address: Pierce

institute: Vanderbilt

summary:
Vascular smooth muscle cells (VSMCs) are derived from distinct embryonic origins. Vessels originating from differing smooth muscle cell populations have distinct vascular and pathological properties of calcification, atherosclerosis, and structural defects such as aneurysm and coarctation. We hypothesized that domains within a vessel vary in phenotype based on embryonic origin.
We used microarrays to detail the expression differences in vasculature of different embryonic origin.

overall_design: Mouse tissues were selected from different vascular compartments for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify embryonic origin-specific expression profiles.

first: Elise

last: Pfaltzgraff


title: Immune response to MVA85A or placebo in BCG-vaccinated South African infants at days 0 and 28 post-vaccination

status: Public on Jun 11 2014

city: Oxford

first: Magali

last: Matsumiya

address: Roosevelt Drive

department: Jenner Institute

institute: University of Oxford

summary: Background: Tuberculosis (TB) remains a global health problem, with vaccination likely to be a necessary part of a successful control strategy. Results of the first Phase 2b efficacy trial of a candidate vaccine, MVA85A, evaluated in BCG-vaccinated infants were published last year. Although no improvement in efficacy above BCG alone was seen, cryopreserved samples from this trial provide an opportunity to study the immune response to vaccination in this population.   Methods: We investigated blood samples taken before vaccination (baseline) and one and 28 days post-vaccination with MVA85A or placebo (Candin). The IFN-γ ELISpot assay was performed at baseline and on day 28 to quantify the adaptive response to Ag85A peptides. Gene expression analysis was performed at all three timepoints to identify early gene signatures predictive of the magnitude of the subsequent adaptive T cell response using the significance analysis of microarrays (SAM) statistical package and gene set enrichment analysis.  Results: One day post-MVA85A, there is an induction of inflammatory pathways compared to placebo samples. Modules associated with myeloid cells and inflammation pre- and one day post-MVA85A correlate with a higher IFN-γ ELISpot response post-vaccination. By contrast, previous work done in UK adults shows early inflammation in this population is not associated with a strong T cell response but that induction of regulatory pathways inversely correlates with the magnitude of the T cell response. This may be indicative of important mechanistic differences in how T cell responses develop in these two populations following vaccination with MVA85A.  Conclusion: The results suggest the capacity of MVA85A to induce a strong innate response is key to the initiation of an adaptive immune response in South African infants but induction of regulatory pathways may be more important in UK adults. Understanding differences in immune response to vaccination between populations is likely to be an important aspect of developing successful vaccines and vaccination strategies.   Trial registration: ClinicalTrials.gov number NCT00953927

overall_design: PBMC collected pre or 28 days post vaccinated, stimulated with either Ag85A peptides (20 samples) or media alone (60).


title: Novel markers of gonadectomy-induced adrenocortical neoplasia in the mouse and ferret

city: St. Louis

first: Maximiliaan

last: Schillebeeckx

state: MO

address: 4444 Forest Parkway

department: Genetics

institute: Washington University in St. Louis

summary: Gonadectomy (GDX) induces sex steroid-producing adrenocortical tumors in certain mouse strains and in the domestic ferret. Complementary approaches, including DNA methylation mapping and microarray expression profiling, were used to identify novel genetic and epigenetic markers of GDX-induced adrenocortical neoplasia in female DBA/2J mice. Markers were validated by quantitative RT-PCR, laser capture microdissection, in situ hybridization, and immunohistochemistry. Two genes with hypomethylated promoters, Igfbp6 and Foxs1, were upregulated in post-GDX adrenocortical neoplasms. The neoplastic cells also exhibited hypomethylation of the fetal adrenal enhancer of Sf1, an epigenetic signature that typifies descendants of fetal adrenal rather than gonadal cells. Expression profiling demonstrated upregulation of gonadal-like genes, including Spinlw1, Insl3, and Foxl2, in GDX-induced adrenocortical tumors of the mouse. One of these markers, FOXL2, was detected in adrenocortical tumor specimens from gonadectomized ferrets. These new markers may prove useful for studies of steroidogenic cell development and for diagnostic testing.

overall_design: Total RNA extracted from whole adrenal glands of gonadectomized and non-gonadectomized mice.

middle: A

last: Wilson


title: Molecular Profiles Associated with Calcineurin Inhibitor Toxicity Post-Kidney Transplant: Input to Chronic Allograft Dysfunction

status: Public on Jun 01 2014

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary:
The molecular basis of calcineurin inhibitor toxicity (CNIT) in kidney transplantation (KT) and its contribution to chronic allograft dysfunction (CAD) with interstitial fibrosis (IF) and tubular atrophy (TA) were evaluated.
Molecular signatures characterizing CNIT samples were identified.  The recognized CNIT gene signature was most common in patients with decreased graft function and histological evidence of IF/TA.

overall_design: To test CNIT contribution to CAD progression, kidney biopsies from transplant recipients with histological diagnosis of CNIT (n=14), acute rejection (ACR, n=13), and CAD with IF/TA (n=10), including 18 Normal allografts, were analyzed using gene expression microarrays.

first: Valeria

last: Mas

middle: I

first: Daniel

last: Maluf


title: RNA-seq alignment to individualized genomes

first: Steven

last: Munger

summary: The source of most errors in RNA sequencing (RNA-seq) read alignment is in the repetitive structure of the genome and not with the alignment algorithm. Genetic variation away from the reference sequence exacerbates this problem causing reads to be assigned to the wrong location. We developed a method, implemented as the software package Seqnature, to construct the imputed genomes of individuals (individualized genomes) of experimental model organisms including inbred mouse strains and genetically unique outbred animals. Alignment to individualized genomes increases read mapping accuracy and improves transcript abundance estimates. In an application to expression QTL mapping, this approach corrected erroneous linkages and unmasked thousands of hidden associations. Individualized genomes accounting for genetic variation will be useful for human short-read sequencing and other sequencing applications including ChIP-seq.

overall_design: Illumina 100bp single-end liver RNA-seq from 277 male and female Diversity Outbred 26-week old mice raised on standard chow or high fat diet. In addition, Illumina 100bp single-end liver RNA-seq from 128 male 26-week old male mice (20 weeks for NZO strain) from each of the DO founder strains raised on standard chow or high fat diet (8 males per strain by diet group). Each sample was sequenced in 2-4x technical replicates across multiple flowcells. Samples were randomly assigned lanes and multiplexed at 12-24x.

first: Gary

last: Churchill

first: Elissa

last: Chesler

first: Narayanan

last: Raghupathy

first: Kwangbom

last: Choi

first: Allen

last: Simons

last: Gatti

first: Douglas

last: Hinerfeld

first: Karen

last: Svenson

first: Mark

last: Keller

first: Alan

last: Attie

first: Matthew

last: Hibbs

first: Joel

middle: H

last: Graber


title: Gene expression profiling in an induced pluripotent stem cell model of the developing human telencephalon: effect of heat shock and its potential impact on the development of neuropsychiatric disorders

city: Bronx

first: Herb

last: Lachman

state: NY

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

summary: Schizophrenia (SZ) and autism spectrum disorders (ASD) are highly heritable neuropsychiatric/neurodevelopmental disorders, although environmental factors, such as maternal immune activation (MIA), play a role as well. Inflammatory cytokines appear to mediate the effects of MIA on neurogenesis and behavior in animal models. However, drugs and cytokines that trigger MIA can also induce a febrile reaction, which could have independent effects on neurogenesis through heat shock (HS)-regulated cellular stress pathways. However, this has not been well-studied. As a first step towards addressing the role of fever in MIA, we used a recently described model of human brain development in which induced pluripotent stem cells (iPSCs) differentiate into 3-dimensional neuronal aggregates that resemble a first trimester telencephalon. RNA-seq was carried out on aggregates that were heat shocked at 39oC for 24 hours, along with their control partners maintained at 37oC.  Overall, 186 genes showed significant differences in expression following HS (p<0.05), including known HS-inducible genes, as expected, as well as those coding for NGFR and a number of SZ and ASD candidates, including SMARCA2, DPP10, ARNT2, AHI1 and ZNF804A. The degree to which the expression of these genes decrease or increase during HS is similar to that found in copy loss and copy gain CNVs, although the effects of HS are likely to be more transient.

overall_design: RNA-seq was carried out on neuronal aggregates as described by Mariani et al. with slight modification (PMID:22761314). For the heat shock experiment, a group of 49 day old aggregates was placed in an incubator set at 39C for 24 hours, while control sets of aggregates were maintained at 37C. The incubator conditions were otherwise unchanged. After detaching the aggregates, total cellular RNA was isolated using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol. Lastly, RNAseq profiles of HS and Control were compared

first: Herbert

first: Deyou

last: Zheng


title: Differential analysis of neural crest and mesodermally derived VSMC in the aorta

first: David

last: Bader

first: Patricia

last: Labosky

first: Cristi

last: Galindo


title: Array comparative hybridization (array-CGH) for detection of gene dose alterations in VACTERL association [4x180k Array v.025990]

city: Stockholm

first: Johanna

last: Winberg

address: CMM L8:02, Karolinska University Hospital

department: Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

type: Genome variation profiling by genome tiling array

summary: The aim of the study was to screen for pathogenic gene dose alterations in patients and fetal cases with VACTERL association using a 180K oligonucleotide microarray.

overall_design: The experiment was performed by hybridization of genomic DNA from patients, labelled with Cy3 fluorophore, with a mix of DNA from healthy sex-matched controls labelled with Cy5 fluorophore (fetal case FC17 was analysed with sex-mismatch for the control DNA). 36 patients/fetal cases were analyzed using a Oxford Gene Technology (OGT) 180K oligonucleotide platform with whole genome coverage (27 patients were analyzed on version 025990 and 9 patients on version 031035). The raw microarray image files were initially analyzed using the Feature Extraction software from Agilent Technologies. Further data analysis was performed using the CytoSure Interpret software from OGT.

first: Peter

last: Gustavsson

first: Nikos

last: Papadogiannakis

first: Ellika

last: Sahlin

first: Frideborg

last: Bradley

first: Edvard

last: Nordenskjöld

first: Pär-Johan

last: Svensson

first: Göran

last: Annerén

first: Erik

last: Iwarsson

first: Ann

last: Nordgren

first: Agneta


title: Immune response to MVA85A or placebo in BCG-vaccinated South African infants at day 1 post-vaccination

first: Magali

last: Matsumiya

overall_design: Whole blood collected 1 day post-vaccination with MVA85A or Candin placebo (82 samples)


title: Array comparative hybridization (array-CGH) for detection of gene dose alterations in VACTERL association [4x180k Array v.031035]


title: Array comparative hybridization (array-CGH) for detection of gene dose alterations in VACTERL association


title: Genome-wide prediction of genes targeted by titrated levels of miR-17~92

city: Louisville

first: Hong

last: Jiang

address: 505 S Hancock St

institute: University of Louisville

summary:
The miR-17-92 cluster targets mRNAs involved in distinct pathways which either promote or inhibit tumor progression. However, the cellular and molecular mechanisms underlying miR-17~92 cluster mediated pro- or anti- tumorigenic effects has not been studied. In this study, we found that inhibition of colon cancer progression is dictated by quantitatively controlling expression of the miR-17~92 cluster.
To identify molecular mechanisms giving rise to the different growth/metastasis patterns, we profiled gene expression in miR-Ctrl, miR-17~92Med and miR-17~92Hi cells using Affymetrix Murine GeneST Arrays.

overall_design: Total RNA from miR-Ctrl, miR-17~92Med and miR-17~92Hi cells (3 subclones of each group) was isolated and subsequently processed for microarray hybridization using Affymetrix.

first: Huang-Ge

last: Zhang


title: Identification of microRNAs specific for high producer CHO cell lines

status: Public on Aug 04 2014

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

summary: Mature microRNA levels were analyzed in 4 producing CHO cell lines expressing 2 structurally different recombinant proteins at low and high level as well as in 1 non-producing CHO cell line. The goal was to identify microRNAs that are involved in heterologous protein formation and secretion.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 5 recombinant CHO cell lines. 3 biological replicates each. All samples were hybridized against a common reference (pool of all total RNA samples).

first: Andreas

last: Maccani

first: Christian

last: Leitner

first: Willibald

last: Steinfellner

first: Alexandra

last: Graf

first: Nadine

last: Tatto

first: Michael

last: Karbiener

first: Marcel

last: Scheideler

first: Johannes

last: Grillari

first: Diethard

last: Mattanovich

first: Renate

last: Kunert

first: Nicole

last: Borth

first: Reingard

last: Grabherr

first: Wolfgang

last: Ernst


title: Gene expression data of livers from C57BL/6 fed a normal diet or high-fat-diet

status: Public on May 09 2014

city: Shanghai

first: Yan

last: Lu

address: 197, Ruijin No.2 Road

department: Department of Endocrine and Metabolic Diseases

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

summary: Obesity is tightly associated with an increased risk of nonalcoholic fatty liver disease (NAFLD). However, the molecular mechanisms of obesity-induced fatty liver remain largely unknown.In order to identify genes that are potentially involved in dysfunctional hepatic lipid homeostasis in obesity, we performed a clustering analysis of Affymetrix arrays,which revealed that a number of mRNAs were dys-regulated in the livers of mice fed a high-fat diet (HFD), compared with mice fed a normal chow diet (ND).

overall_design: To identify genes that are potentially involved in dysfunctional hepatic lipid homeostasis in obesity, male C57BL/6 mice aged 8 weeks were fed a normal diet (ND) or high-fat-diet (HFD) containing 60 Kcal% of fat for 12 weeks. Then mice were sacrificed and total RNAs were isoloated from hepatic tissues. Affymetrix array hybridisation and scanning were performed using Mouse Genome 430 2.0 chips.Total RNA samples obtained from six mice per group (ND and HFD) and pooled by each of the two were used for microarray analysis.

first: Xing

last: Liu


title: Genome-wide Genotyping of Acute Myeloid Leukemia with Translocation t(9;11)(p22;q23) Reveals Novel Recurrent Genomic Alterations

status: Public on May 22 2014

city: Ulm

last: Kuehn

address: Albert-Einstein-Allee 23

institute: University Hospital of Ulm

summary: To identify cooperating lesions in de novo and therapy-related acute myeloid leukemia (t-AML) with translocation t(9;11)(p22;q23) we performed high-resolution SNP-array profiling on 40 leukemia samples [de novo: n=22; t-AML: n=16; unknown: n=2]. A mean of 1.73 copy number alterations (CNAs)/case were identified with no differences between de novo and t-AML cases. We identified a novel minimally deleted region (MDR) at 7q36.1-q36.2 partly overlapping with a MDR previously identified in core-binding factor AML; MLL3 was the only gene affected in both regions. In addition, a recurrent gain was found at 13q21.33-q22.1 harboring the potential oncogene KLF5. Sequence/expression analysis of selected candidate genes revealed deregulated EVI1 at high frequency (50%). Copy-neutral loss-of-heterozygosity (CN-LOH) was absent in the paired cohort Further analysis of the candidate genes might provide novel insights into the pathogenesis of t(9;11) AML

overall_design: SNP genotyping was performed on 40 de novo and therapy-related MLL-MLLT3-rearranged acute myeloid leukemia samples; Germline control DNA from remission bone marrow or peripheral blood was available for paired analysis in 15 patients. Data were processed using reference alignment, dChipSNP and circular binary segmentation.

middle: W

last: Kühn

first: Lars

last: Bullinger

first: Stefan

last: Gröschel

first: Jan

last: Krönke

first: Jennifer

last: Edelmann

first: Frank

last: Rücker

first: Karina

last: Eiwen

first: Peter

last: Paschka

first: Verena

last: Gaidzik

first: Karlheinz

last: Holzmann

first: Richard

middle: F

last: Schlenk

first: Hartmut

last: Döhner

first: Konstanze


title: Global assessment of Antrodia cinnamomea induced microRNA and mRNA transcriptomic alterations in hepatocarcinoma cells

status: Public on May 10 2014

city: Taipei

first: mike

last: thang

state: Taipei

address: 128 Academia Road, Section 2, Nankang

department: Genome Research Center

country: Taiwan

institute: Academia Sinica

type: Non-coding RNA profiling by high throughput sequencing

summary: Antrodia cinnamomea (Ac), a traditional medicine and an endemic fungus in Taiwan, has been used in cancer research. Recent research has revealed decreased cell proliferation after treatment of Ac on tumor. In this study, we profiled the 2 hours and 4 hours genome-wide miRNA and mRNA transcriptome by next-generation sequencing techniques to report the early apoptotic effect on Ac fruiting body extract treated human hepatocarcinoma cells, SK-HEP-1, instead of prolonged treatment. Results showed that miRNAs were globally downregulated during the first 2-4 hours in, and solely in, AcFBE-treated SK cells. The inhibition of miRNAs imposed no discrimination against any particular miRNA species, but oncogenic miR-21, miR-191 and two oncogenic clusters miR-17-92 and miR-106b-25 were among the most significantly inhibited miRNAs. In addition to miRNA expression, mRNA transcriptome data indicated the association of apoptosis mechanism with AcFBE treatment. Western blotting indicated a decrease in key proteins Drosha and Dicer required for miRNA biogenesis, and an increase of XRN2 involved in miRNA degradation. Our results suggest that miRNAs appeared to be the prime targets of Ac in disrupting multiple miRNA regulatory pathways and global disruption of miRNA transcriptome resulting in activation of extrinsic and intrinsic (mitochondrial) pathways.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human liver SK-Hep-1 cells with or without Antrodia cinnamomea treatment at 2 hours and 4 hours were sequenced by SOLiD 3 and SOLiD 5500xl to obtain miRNA profiles; mRNA profiles also were profiled by SOLID 3. Mouse liver BNL CL.2 cells with or without Antrodia cinnamomea treatment at 2 hours and 4 hours were sequenced by SOLiD 3 to obtain miRNA profiles.

first: Yen

first: Wai

last: Thang


title: Meiotic Consequences of Genetic Extension of Unsynapsed Autosomal Chromatin

city: Prague 4

first: David

last: Homolka

address: Videnska 1083

department: Department of Mouse Molecular Genetics

institute: Institute Of Molecular Genetics

summary: We investigated the influence of extension of autosomal asynapsis on expression profiles during spermatogenesis. We used the mouse autosomal translocation T(16;17)43H (abbreviated T43H) and t12 haplotype, a natural variant of Chr 17 encompassing four adjacent non-overlapping inversions proximal to the T43H translocation breakpoint, as a model. The presence of t12 haplotype in trans to the T43H translocation resulted in stringent spermatogenic block and in more complete silencing of genes surrounding the T43H translocation break. Strikingly, silencing of the unsynapsed autosomal chromatin preceded the inactivation of the sex chromosomes (MSCI) and was apparent already in the population of pre-mid pachytene spermatocytes and testes of 15 days old males.

overall_design: Populations of pre-mid-pachytene spermatocytes were isolated from Ttf+/+T43H and t12+/+T43 males in three biological replicates. Their expression was compared to two biological replicates of the populations of pre-mid pachytene spermatocytes and mid-late pachytene spermatocytes obtained from C57BL/10J fertile males. Independently, testicular RNA was isolated from 15 days old Ttf+/+T43H and  t12+/+T43 males in three biological replicates and the expression was compared to the testicular expression of two 15 days old C57BL/6J males.


title: The effects of fluoride on the gene expression of enamel forming ameloblasrs

status: Public on May 02 2014

city: San Francisco

first: Yan

last: Zhang

state: CA

address: 513 Parnassus Avenue

department: Orofacial Sciences

institute: UCSF

summary:
We compared the overall gene expression pattern between secretory ameloblasts and maturation ameloblasts, and found out there were 244 genes differentially exppressed in the maturation ameloblasts as compared to secretory ameloblasts.
Upon treatment, the genes coregulated with MMP-20 were  downregulated in maturation ameloblasts, though the difference was not significant.

overall_design: Stage specific secretory ameloblasts (SAB) and maturation ameloblasts (MAB) were laser microdissected from mandibular incisors of control and 50 ppm F treated mice.

first: Pamela

last: Denbesten


title: Global indiscriminate methylation in cell-specific gene promoters following reprogramming into human induced pluripotent stem cells

status: Public on May 01 2014

city: Jerusalem

first: Jonathan

last: Nissenbaum

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary:
Genome wide DNA methylation profiling of somatic and pluripotent cells from different lineages (mesoderm, endoderm and parthenogenetic germ cells) The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 1 Human ES cell line, 2 beta cells, 2 beta-iPS cells, 1 fibroblast, 2 fibroblast-iPS cells, 2 parthenogenetic cells and 3 parthenogenetic-iPS cells.
Molecular reprogramming of somatic cells into human induced pluripotent stem cells (iPSCs) is accompanied by extensive changes in gene expression patterns and epigenetic marks. To better understand the link between gene expression and DNA methylation, we have profiled human somatic cells from different embryonic cell types (endoderm, mesoderm and parthenogenetic germ cells) and the iPSCs generated from them. We show that reprogramming is accompanied by extensive DNA methylation in CpG-poor promoters, sparing CpG-rich promoters. Intriguingly, methylation in CpG-poor promoters occurred not only in downregulated genes, but also in genes that are not expressed in the parental somatic cells or their respective iPSCs. These genes are predominantly tissue-specific genes of other cell types from different lineages. Our results suggest a role of DNA methylation in the silencing of the somatic cell identity by global non-specific methylation of tissue-specific genes from all lineages, regardless of their expression in the parental somatic cells.

overall_design: Genomic DNA from each sample was bisulfite converted, DNA was applied to BeadChips (Illumina). 13 samples included, Human ES cell as control.

first: Ori

last: Bar-Nur

first: Eyal

last: Ben-David

first: Nissim

last: Benvenisty


title: Effects of vitamin D supplementation on alveolar macrophage gene expression

status: Public on Apr 08 2014

city: Iowa City

first: Thomas

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

summary:
The objective of the overall study was to determine the effects of  oral vitamin D supplementation on alveolar macrophages from human subjects. In this substudy, subjects treated with vitamin D (intervention group) in paired analysis had small, but significant effects on immune-related differential gene expression pre versus post supplementation.
In this study, we obtained alveolar macrophages by bronchoalveolar lavage of subjects before and after a 3 month vitamin D trial.  RNA for the array was obtained shortly after bronchoscopy.

overall_design: Randomized Controlled Trial: This is a substudy of paired samples of subjects treated with vitamin D.   Each sample was studied once.  22 individuals were studied.

first: Alicia

last: Gerke

first: Martha

last: Monick


title: Linezolid Exerts Greater Bacterial Clearance but No Modification of Host Lung Gene Expression Profiling: a Mouse MRSA Pneumonia Model

status: Public on Apr 10 2014

city: Chicago

first: Jiwang

last: Chen

address: 840 S Wood Street

institute: University of Illinois at Chicago

summary: Using the stringent criteria (fold change ≥ 1.5 up or down, P < 0.01, FDR < 0.05) to filter significantly differentially expressed genes, we did not identify any genes whose expression levels were significantly different between the PBS and PBS+LZD groups or between the LAC and LAC+LZD at Day 1 or Day 3 post MRSA infection. However, a remarkable difference was demonstrated (Figure 5A) between PBS and LAC groups at either Day 1 or Day 3 post MRSA infection.

overall_design: Four independent mouse lung tissue samples at Day 1 and Day 3 post MRSA infection with and without Linezolid therapy were randomly selected from each group for microarray analysis.

first: Gang

last: Feng

first: Yang

last: Song

first: Juliane

last: Wardenburg

first: Simon

last: Lin

first: Ichiro

last: Inoshima

first: Michael

last: Otto

last: Wunderink


title: Prospective Evaluation of Whole Genome MicroRNA Expression Profiling in Childhood Acute Lymphoblastic Leukemia

status: Public on Apr 05 2014

city: Izmir

first: Burak

last: Durmaz

address: Bornova

department: Medical Genetics

country: Turkey

institute: Ege University

summary:
Dysregulation of microRNA (miRNA) expression contributes to the pathogenesis of several clinical conditions.
The aim of this study is to evaluate the associations between miRNAs and childhood acute lymphoblastic leukemia (ALL) to discover their clinical and therapeutic implications. Forty-three children with ALL and 14 age-matched healthy controls were included in the study. MicroRNA microarray expression profiling was used for peripheral blood and bone marrow samples. Aberrant miRNA expressions associated with the diagnosis and outcome were prospectively evaluated. Confirmation analysis was performed by real time RT-PCR. miR-128, miR-146a, miR-155, miR-181a, miR-195 were significantly dysregulated in ALL patients at day 0. Following a six-month treatment period, the change in miRNA levels was determined by real time RT-PCR and expression of miR-146a, miR-155, miR-181a, miR-195 significantly decreased.

first: Ozgur

last: Cogulu


title: Transcriptional regionalization of the fruit fly's airway epithelium

status: Public on Apr 01 2014

city: Cologne

first: Julia

last: Hoffmann

address: Joseph-Stelzmann-Str. 9b

department: Partridge

institute: MPI for Biology of Ageing

summary: Although airway epithelia are primarily devoted to gas exchange, they have to fulfil a number of different tasks including organ maintenance and the epithelial immune response to fight airborne pathogens. These different tasks are at least partially accomplished by specialized cell types in the epithelium. In addition, a proximal to distal gradient mirroring the transition from airflow conduction to real gas exchange, is also operative. We analysed the airway system of larval Drosophila melanogaster with respect to region-specific expression in the proximal to distal axis. The larval airway system is made of epithelial cells only. Previously, it had been anticipated that these cells are very similar in their functional and transcript properties. We found differential expression between primary trunks of the airways and more distal ones comprising secondary and tertiary ones. Among these genes are especially those involved in signal transduction. A more detailed analysis was performed using DNA-microarray analyses to identify cohorts of genes that are either predominantly expressed in the primary or in the secondary/tertiary parts of the airways. Genes, including a putative mucin and the neuropeptide FMRFamide are predominantly found in primary branches, whereas the wnt- and the TGF-beta signalling pathways appear to be overrepresented in the secondary/tertiary ones. This differential expression is indicative for a proximal to distal transcriptional regionalization presumably reflecting functional differences in these parts of the fly’s airway system.

overall_design: Trachea of wildtype L3 larvae were dissected and primary branches were processed seperately from secondary and tertiary branches. 3 biological replicates were included per group.

first: Muhammad

middle: N

last: Faisal

last: Roeder


title: Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome

status: Public on Mar 11 2014

city: Irvine

first: Maria Concepcion

last: Munoz Diez

address: 321 Steinhaus Hall

department: Ecology and Evolutionary Biology

institute: UC-Irvine

summary: Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remains poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24:22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome

overall_design: We compared TE abundances and siRNA profiles among B73 (maize inbred line) and two additional maize landraces, Palomero Toluqueño (PT) and Olote Colorado (OAXA) using HTS

first: Concepcion

last: Diez


title: Expression data from gastric cancer and pancreatic cancer

status: Public on Apr 15 2014

city: Kawasaki

first: Shihori

last: Tanabe

state: Kanagawa

address: 3-25-26, Tonomachi, Kawasaki-ku

department: Division of Risk Assessment

institute: National Institute of Health Sciences

summary:
Cancer cells have wide variety of gene expression profile. The objective of the study is to reveal the cancer-associated gene expression profile.
Microarray analysis was used to investigate gene expression of cancer cells.

overall_design: Both gastric and pancreatic cancer tissues were surgically resected and total RNA was purified from these tissues by a conventional method.

first: Kazuhiko

last: Aoyagi

first: Hiroki

last: Sasaki

first: Hiroshi

last: Yokozaki


title: Papillary thyroid cancer cell lines treated with Y15

status: Public on Mar 06 2014

city: Buffalo

first: Biao

last: Liu

address: Elm and Carlton streets

department: Center for Personalized Medicine

institute: Roswell Park Cancer Institute

summary: 3 papillary thyroid cancer cell lines were compared, treated with Y15 to untreated.

overall_design: 1 million cells of each papillary thyroid cell line (TPC1, K1, BCPAP) were plated, treated 24 hours later with 10uM Y15, and collected 24 hours later by trypsinization.

first: Vita

last: Golubovskaya

first: Shalana

last: O'Brien

first: Song

first: David

last: Ostrov

first: William

last: Cance


title: Transcriptomic profiles of wild brown trout chronically exposed to metals using RNA-seq in a Illumina GAII platform

city: Exeter

first: Ronny

last: van Aerle

state: Devon

address: Stocker Road

department: Biosciences, College of Life and Environmental Sciences

institute: University of Exeter

summary: To investigate mechanisms of metal tolerance in the gill, gut, kidney and liver of brown trout inhabiting the river Hayle (highly metal contaminated) compared with a control population from the river Teign.

overall_design: mRNA samples were sequenced (Illumina GAII) from a pooled embryonic sample and 12 multiplexed samples of different tissues from the the Hayle and Teign populations (pooled from 5 and 10 individuals respectively) and used to generate a transcriptome assembly. Expression profiling was then conducted for the gill, gut, kidney and liver samples.  Expression profiling results are presented in this Series.

first: Tamsyn

last: Uren Webster

first: Nic

middle: R

last: Bury

first: Eduarda

last: Santos


title: Identification of hypoxia target genes in human CB CD34+ cells

status: Public on Mar 01 2014

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

country: Netherlands

institute: UMCG

summary: Although it has been shown that HIF1 and 2 fulfill essential roles within the hematopoietic system and in the regulation of HSC fate, little is currently known about the specific mechanisms that are involved. We identified transcriptome changes induced by hypoxia, constitutively active HIF1(P402/564) and HIF2(P405/531) in human cord blood CD34+ cells. Thus, we were able to identify common hypoxia-HIF1-HIF2 gene signatures, but we also identified specific target genes that were exclusively regulated by HIF1, HIF2 or hypoxia.

overall_design: CB CD34+ cells were isolated by Miltenyi miniMACS column. Cells were prestimulated in HPGM with 100 ng/ml KITL, FLT3L and TPO for 3 days after which cells were placed either at normoxia or hypoxia (1% O2 for an additional 24 hrs). 5 independent CB CD34+ batches were used and isolated RNA was combined and used for Illumina beadhchip arrays HT12 v4

first: J

first: A

middle: T

last: Wierenga


title: Identification of hypoxia, HIF1 and HIF2 target genes in human CB CD34+ cells

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

overall_design: Refer to individual Series


title: Identification of HIF1 and HIF2 target genes in human CB CD34+ cells

overall_design: CB CD34+ cells were isolated by Miltenyi miniMACS column. Cells were prestimulated in HPGM with 100 ng/ml KITL, FLT3L and TPO for 48 hrs. Cells were transduced with control pRRL-IRS2-EGFP lentiviral vectors or vectors expressing HIF1α(P402A,P564A) or HIF2α(P405A,P531A) in one or two  rounds of 12 hrs each. 24 hrs later transduced cells were sorted after which RNA was isolated. 5 independent CB CD34+ batches were isolated, transduced and sorted, and isolated RNA was combined and used for Illumina beadhchip arrays HT12 v4


title: Identification and Characterization of Maize MicroRNAs Involved in the Very Early Stage of Seed Germination

status: Public on Mar 03 2014

city: Taian

first: Huabang

last: Chen

address: Daizong Street 61

institute: Shandong Agricultural University

summary: In this study, a small RNA library from maize seed 24 hours after imbibition was sequenced by the Solexa technology. A total of 11,338,273 reads were obtained.    1,047,447 total reads representing 431 unique sRNAs matched to known maize miRNAs. Further analysis confirmed the authenticity of 115 known miRNAs belonging to 24 miRNA families and the discovery of 167 novel miRNAs in maize. Both the known and the novel miRNAs were confirmed by sequencing of a second small RNA library constructed the same way as the one used in the first sequencing. We also found 10 miRNAs that had not been reported in maize, but had been reported in other plant species. All novel sequences had not been earlier described in other plant species. In addition, seven miRNA* sequences were also obtained. Putative targets for 106 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in maize imbibed seed.  This study led to the confirmation of the authenticity of 115 known miRNAs and the discovery of 167 novel miRNAs in maize. Identification of novel miRNAs resulted in significant enrichment of the repertoire of maize miRNAs and provided insights into miRNA regulation of genes expressed in imbibed seed.

overall_design: Discovery of novel miRNAs involved in imbibed maize seed by deep sequencing 2 independent small RNA libraries

first: Liwen

last: Wang

first: Huaihua

first: Detao

last: Li


title: Human Peripheral Blood Lymphcoyte(PBL): Simulated Microgravity  vs. Control

city: Harbin

first: Lijun

last: Wei

address: No 92 Western Dazhi street

institute: Harbin Institute of Technology

summary: Transcriptional profiling of human peripheral blood  lymphocyte comparing simulated microgravity for 72 hours with untreated control.

overall_design: Two-condition experiment, simulated microgravity vs.untreated control. Biological replicates: 1 control, 1 treated, independently grown and harvested.


title: Genome-wide analysis of gene expression in MDA-MB-231 breast cancer cells in response to conditional miRNA mediated BSP knockdown.

status: Public on Feb 28 2014

city: Heidelberg

first: Martin

last: Berger

address: INF 581

institute: DKFZ

summary: Our goal was to identify the genes, which are modulated following conditional BSP knockdown for 3 and 6 days. Thus, to elucidate the BSP relevance and to broaden the knowledge on the affected signalling pathways.

overall_design: Cell pellets were collected after 3 and 6 days of cultivating the cells in media with or without doxycycline. There were duplicated total RNA samples for each time interval and each condition.The mRNA expression of the in vitro miRNA treated cells was compared to the respective +dox control.

first: Marineta

last: Kovacheva


title: Liver mRNA microarray study for mice treated with various diets

status: Public on Feb 24 2014

city: Seattle

first: Julia

last: Cui

state: Washington

address: 4225 Roosevelt Way NE Suite # 100

institute: University of Washington

summary: The goal of this study was to investigate the effects of vairous diets on the expression of genes involved in intermediary metabolism in liver. Adult wild type male mice (3 for each group) were fed with the corresponding diet for two weeks, and then liver samples were collected. Total RNA was isolated by the RNAzol B reagent, and pellet was disolved in DEPC-treated water. Total RNA was isolated using RNA Bee reagent (Tel-Test Inc., Friendswood, TX) per the manufacturers protocol. RNA concentrations were quantified using a NanoDrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE) at a wavelength of 260 nm. The integrity of the total RNA samples was evaluated by formaldehyde-agarose gel electrophoresis, and confirmed by visualization of 18S and 28S rRNA bands. The gene expression was determined by Affymetrix Mouse 430 2.0 Gene Expression Microarray. Nine different diets were used: Diet 1. TD.84224. EFA Deficient diet; Diet 2. TD 97070. High fat diet: Diet 3. TD.88137. Adjusted Calories Diet (42% from fat) (Western Diet); Diet 4. TD.02028. Atherogenic Rodent Diet; Diet 5. TD.89247. 60% Fructose Diet; Diet 6. TD.94048. AIN-93M Purified Diet, Diet 7. Current rodent diet used in LAR; Diet 8. DHA-supplemented diet; Diet 9. Diet-restriction: 75% of the diet consumed by ad lib feeding. Mice (n=3/diet) were fed one of these diets (Harlan Laboratories) for 3 weeks. All mice were euthanized in the morning (8:00–10:00 A.M.) and blood and tissue samples were collected. All procedures were approved in accordance with Institutional Animal Care and Use Committee guidelines.

overall_design: A total of 27 samples were analyzed, n=3 per diet, control: AIN-93 Purified Diet

middle: Y


title: Transcriptome of Dinoroseobacter shibae in co-culture with the dinoflagellate Prorocentrum minimum

status: Public on Feb 01 2014

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

platform_organism: Dinoroseobacter shibae DFL 12 = DSM 16493


title: The long noncoding RNA expression profile of hepatocellular carcinoma identified by microarray analysis

status: Public on Feb 21 2014

city: Beijing

first: Hanjiang

last: Fu

address: 27 Taiping Road

department: Department of Biochemistry and Molecular Biology

institute: Beijing Institute of Radiation Medicine

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

summary: To explore the potential involvement of lncRNAs in hepatocellular carcinoma (HCC) oncogenesis, we conducted lncRNA and mRNA profiling in 3 pairs of human HCC and adjacent normal tissue (NT) by microarray. With abundant probes accounting for 33,045 lncRNAs and 30,215 coding transcripts in our microarray, the number of lncRNAs and coding transcripts that could be detected here is 10,149 and 14,944, respectively. From the data, thousands of lncRNAs and mRNAs were found to bedifferentially expressed (Fold Change≥2.0) in HCC tissues compared with NT and identified 624 lncRNAs and 1050 mRNAs were differentially expressed in all three HCC tissues.Bioinformatic analysis (gene ontology, pathway and network analysis) was performed for further study of these differentially expressed mRNAs.By qRT-PCR analysis in nineteen pairs HCC and adjacent normal tissues, we found that eightl ncRNAs were aberrantly expressed in HCC compared with corresponding NT, which is consistent with microarray data. Additionally, change trends of seven lncRNAs were basically identical to their nearby coding genes.

overall_design: In this study, to explore the potential involvement of lncRNAs in hepatocellular carcinoma (HCC) oncogenesis, we conducted lncRNA and mRNA profiling in 3 pairs of human HCC and adjacent normal tissue (NT) by microarray.

first: Juanjuan

last: Zhu


title: Parent vs. Induced drug tolerant cells Microarray Analysis

status: Public on Feb 06 2014

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

institute: Medical University Graz

summary: WM164 BRAF mutant Melanoma cells were treated with 500nM PLX4032 for 16 days and their gene expression was compared to parent cells kept in DMSO.

overall_design: WM164 treated and untreated cells were kept in triplicate and the mRNA from individual samples were isolated independently for analysis.

first: Dinoop

last: Menon

first: Helmut

last: Schaider


title: Light-dark changes in the transcriptome of Dinoroseobacter shibae in co-culture with the dinoflagellate Prorocentrum minimum

summary: Comparison of the transcriptome of D. shibae 5 h in the light versus 5 h in the dark after 12 days in co-culture with the dinoflagellate P. minimum.

overall_design: Two biological replicates of each condition are compared.

first: Hui

first: Michael

last: Jarek

first: Sabin

last: Bhuju

first: Irene

last: Wagner-Döbler


title: Transcription factor activator protein 2C (TFAP2C) regulates luminal differentiation in mammary development and carcinogenesis

first: Thomas

middle: B

last: Bair

summary: Molecular subtypes of breast cancer are characterized by patterns of gene expression, which can be used to predict response to therapy and overall clinical outcome. The luminal breast cancer subtypes are defined by the expression of ER-alpha (ERa) and a set of ERa-associated genes. The transcription factor activator protein 2C (TFAP2C, AP-2C, AP-2g) transcription factor plays a critical role in regulating cell growth and differentiation during ectodermal development and has been implicated in the regulation of ERa and other luminal-associated genes in breast cancer. While TFAP2C has been established as a prognostic factor in human breast cancer, the role of TFAP2C in development of the luminal epithelial cells in the normal mammary gland and in breast cancer have remained elusive. Herein, we demonstrate a critical role of TFAP2C in maintaining the luminal differentiation phenotype during normal mammary development and in luminal breast carcinoma cell lines.

overall_design: Total RNA from MCF7 cells with and without knockdown of TFAP2c. 3 biological replicates, with 2 technical replicates each, were performed for each sample type.

first: Anthony

last: Cyr

first: Mikhail

middle: V

last: Kulak

first: Jung

last: Park

first: Maria

last: Bogachek

first: Philip

last: Spanheimer

first: George

last: Woodfield

first: Weizhou

last: Zhang

first: Frederick

middle: E

last: Domann

first: Ronald

last: Weigel


title: Transcriptome-wide effects of sexual selection on the fate of new mutations

city: Nouzilly

first: Julie

last: Collet

address: Centre INRAE

institute: INRAE

summary: Sexual selection on males is predicted to have widespread effects on genetic variation as a consequence of the pleiotropic allelic effects on sexual and non-sexual traits. We manipulated the opportunity for sexual selection on males during 27 generations of mutation accumulation in inbred lines of Drosophila serrata, and used a microarray platform to investigate the effect of sexual selection on the expression of 2689 genes. While gene expression signal was, on average, higher in the absence of sexual selection, this difference was small (0.1%). In contrast, sexual selection impacted substantially on the mutational variance in gene expression. Over all genes, mutational variance in gene expression was, on average, 42% higher when sexual selection operated than when it was absent. Our results indicate that sexual selection on males can generate widespread effects across the genome. An increase in mutational variance without a corresponding change in mean suggested that most expression traits were unlikely to be under direct sexual selection. Instead, the mutational variance in gene expression traits is consistent with divergence generated by widespread pleiotropic associations with traits affecting male mating success.

overall_design: We measured gene expression of male Drosophila serrata from 41 mutation accumulation lines (whole-body) that were sexually selected. Data from two replicates for each line are presented.

first: Mark

last: Blows

first: Katrina

last: McGuigan


title: Characterization of circulating microRNA expression in patients with a ventricular septal defect

status: Public on Feb 10 2014

first: Dong

last: Li

state: Shandong Province

address: No 2, Yingshengdonglu

department: Department of Public Health

institute: Taishan Medical College

summary: 36 differentially expressed miRNAs were found in the patients with VSD and the VSD-free controls. Compared with VSD-free controls, expression of 15 miRNAs were up-regulated and 21 miRNAs were down-regulated in the VSD group

overall_design: MiRNA microarray analysis and reverse transcription-polymerase chain reaction (RT-PCR) were employed to determine the miRNA expression profile from 3 patients with VSD and 3 VSD-free controls

first: Long

last: Ji

first: Zhongtang

last: Zhao


title: A high-resolution Amphimedon queenslandica transriptomic timecourse

status: Public on Jan 24 2014

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

institute: Technion - Israel Institute of Technology

summary: Transcriptomic data for 59 single embryos and larvae samples of the sponge Amphimedon queenslandica

first: Leon

last: Anavy

first: Michal

last: Levin

first: Sally

last: Khair

first: Nagayasu

last: Nakanishi

first: Selene

last: Fernandez-Valverde

first: Bernard

last: Degnan


title: Cistrome profiles of Retinoids x Receptor alpha (RXRα) , Retinoic Acid Receptor alpha (RARα), and Retinoic Acid Receptor beta (RARβ) in livers of mice treated by control and retionic acid-containing diet

status: Public on Jan 23 2014

city: Sacramento

first: Yuqi

last: He

address: Rm3400, Research III, UC Davis Medical Center, 4645 2nd Ave

institute: UC Davis Medical Center

summary: Comparison between ChIP-Seq data of RARα and RARβ, between RAR and RXR, as well as between control and retinoic acid-treatment for each investigated nuclear receptors.

overall_design: Mouse were treated by control diet and RA-diet for 1 days. After treatment, livers were used to do ChIP using antibodies of RXRα, RARα, and RARβ. An aliquote of total chromatin without pull-down process by any antibodies was used as input control. A single-end read of 35bp sequencing was performed on each of ChIPed DNA and input.   Sequencing data of RARα and RARβ were compared to each other. In addtional, each of RARα and RARβ data were compared with RXRα data. For each nuclear receptor,  ChIP-Seq data prior or after RA-treatment were also compared with each other.

first: Yu-Jui

last: Wan

first: Qi

last: Zhan

first: Yanliu

last: Lu

first: Huixin

last: Liu


title: GSK3B shRNA in Panc-1 xenografts

status: Public on Jan 09 2014

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

summary: The Panc-1 human pancreatic cancer line (ATCC) was constructed to stably express control or GSK3B shRNA. Control or GSK3B shRNA expressing Panc-1 cells were implanted subcutaneously into the flanks of 3-5 week old, female, athymic nude mice. Tumors were grown to at least 250mm3. Tumor tissue was microdissected for further analysis.   We compared control shRNA (n=4) to GSK3B shRNA (n=3) Panc-1 xenografts. The array data with simple statistical calculations are also provided in a supplementary Excel workbook, with probe-set annotation that we used at the time (users may want newer annotation).

overall_design: We compared xenografts of Panc-1 (Human pancreatic carcinoma cell line, grown in mice) stably expressing GSK3B shRNA (n=3) to similar xenografts with control shRNA (n=4).  Xenografts were grown in the flanks of female, athymic nude mice until they reached at least 250mm3. Tumor tissue was microdissected for further analysis. mRNA abundance assays were performed using Affymetrix HG_U133_plus_2 arrays, with 54675 probe-sets.

first: Meredith

last: Morgan

first: Mahaveer

middle: S

last: Bhojani

first: Aaron

last: Spalding

first: Edgar

last: Ben-Josef


title: Diversity of HrpL-regulons across Pseudomonas syringae isolates

status: Public on Jan 01 2014

city: Chapel Hill

first: Emma

last: Johnson

state: North Carolina

address: 250 Bell Tower Dr

institute: University of North Carolina - Chapel Hill

summary: We implemented transcriptional analysis methods using cDNA and high-throughput sequencing data to identify HrpL-regulated genes for six strains of Pseudomonas syringae

overall_design: Each Pseudomonas syringae strains was transformed with either pBAD::EV or pBAD containing native hrpL sequence. Strains were grown in MM media supplemented with arabinose and collected 1, 3, and 5 hours post arabinose treatment. RNA was extracted for each time point and mixed at a 1/3 ratio. After removal of rRNA, double stranded cDNA was generated and library prepared accordeing to Illumina protocols.

first: Tatiana

last: Mucyn

first: Abigail

last: Lind

first: Surge

last: Biswas

first: Scott

last: Yoursatone

first: Marc

last: Nishimura

first: Jason

last: Cumbie

first: Sarah

last: Grant

first: Jeff

last: Chang

first: Corbin

middle: D

last: Jones

first: Jeffrey

last: Dangl


title: Detection of antibiotic resistance genes in human gut microbiota

status: Public on Jan 16 2014

first: Yongfei

last: Hu

address: NO.1 West Beichen Road, Chaoyang District

department: CAS key Laboratory of Pathogenic Microbiology and Immunology

institute: Institute of Microbiology, Chinese Academy of Sciences

summary:
We used a DNA microarray chip covering 369 resistance types to investigate the relation of antibiotic resistance gene diversity with humans’ age. Metagenomic DNA from fecal samples of 123 healthy volunteers of four different age groups, i.e. pre-school Children (CH), School Children (SC), High School Students (HSS) and Adults (AD) were used for hybridization. The results showed that 80 different gene types were recovered from the 123 individuals gut microbiota, among which 25 were present in CH, 37 in SC, 58 in HSS and 72 in AD. Further analysis indicated that antibiotic resistance genes in groups of CH, SC and AD can be independently clustered, and those ones in group HSS are more divergent.
The detailed analysis of antibiotic resistance genes in human gut is further described in the paper DNA microarray analysis reveals the antibiotic resistance gene diversity in human gut microbiota is age-related submitted to Sentific Reports

overall_design: The antibiotic resistance gene microarray is custom-designed (Roche NimbleGen), based on a single chip containing 3 internal replicated probe sets of 12 probes per resistance gene, covering the whole 315K 12-plex platform spots.

last: Lu


title: Gene Expression analysis of hESC B2M knock-out

first: Laura

last: Riolobos

address: 1959 NE Pacific St

summary: The clinical use of human pluripotent stem cells and their derivatives is limited by the rejection of transplanted cells due to differences in their HLA genes. This has led to the proposed use of histocompatible, patient-specific stem cells, however the preparation of many different stem cell lines for clinical use is a daunting task.  Here we develop two distinct genetic engineering approaches that address this problem.  First, we use a combination of gene targeting and mitotic recombination to derive HLA-homozygous embryonic stem cell (ESC) subclones from an HLA-heterozygous parental line.  A small bank of HLA-homozygous stem cells with common haplotypes would match a significant proportion of the population.  Second, we derive HLA class I-negative cells by targeted disruption of both alleles of the B2M gene in ESCs.  Mixed leukocyte reactions and peptide-specific HLA-restricted CD8+ T cell responses were reduced in class I-negative cells that had undergone differentiation in embryoid bodies.  These B2M-/- ESCs could act as universal donor cells in applications where the transplanted cells do not express HLA class II genes.  Both approaches used adeno-associated virus (AAV) vectors for efficient gene targeting in the absence of potentially genotoxic nucleases, and produced pluripotent, transgene-free cell lines.

overall_design: Total RNA, 4 samples were analyzed as follows: 2 replicates for the hESC H1 wt ( rep1 and rep2) and 2 independent clones of hESC B2M knock-out

first: Roli

middle: K

last: Hirata

first: Cameron

last: Turtle

first: Pei-Rong

last: Wang

first: German

last: Gornalusse

first: Maja

last: Zavajlevski

first: Stanley

last: Ridell

first: David

last: Russell


title: Candida albicans TRKO rbf1Δ/hfl1Δ/dpb4Δ vs WT transcriptome data

status: Public on Jan 15 2014

city: Washington

first: Dongmei

last: Li

state: DC

address: 3900 Reservoir Rd Med dent SE318

department: Microbiology

summary: To determine potential roles of three transcript factors (Rbf1p, Hfl1p and Dpb4p) in cell metabolic activities and other cellular bioprocesses, we have performed genomic microarray in each gene knockout strain and transcription profiles were compared  to its parental strain SN250

overall_design: The total RNAs were extracted from exponential growth of null mutants  and SN250, then used to synthesize cDNA for microarray assays in Aglient array that contains 6101 genes in duplicate

first: Nuo

last: Sun

first: Richard

last: Calderone


title: Transcriptome of Dinoroseobacter shibae in co-culture with the dinoflagellate Prorocentrum minimum [RNA-seq]

first: Jürgen

last: Tomasch

summary: Transcriptome of D. shibae 5 h in the light and dark after 12 days in co-culture with the dinoflagellate P. minimum.

overall_design: Two biological replicates.

first: Hui

first: Michael

last: Jarek

first: Sabin

last: Bhuju

first: Irene

last: Wagner-Döbler


title: Effect of photoperiod on feline adipose transcriptome profiles as assessed by RNA sequencing

city: Urbana

first: Kelly

middle: Scott

last: Swanson

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

summary:
Purpose: Photoperiod is known to cause physiological changes in seasonal mammals, including body weight, physical activity, and reproductive status. Because cats are seasonal breeders, we recently tested the effects of day length on resting metabolic rate, voluntary physical activity, and food intake.  In that study, resting metabolic rate, physical activity, and food intake to maintain body weight were greater in cats exposed to long days vs. short days.  Because photoperiod has also been demonstrated to affect adipose tissue gene expression in several species, including dairy cows, sheep, and Siberian hamsters, the objective of this study was to determine the effects of day length on the adipose transcriptome profile of cats as assessed by RNA-seq.
Methods: Ten healthy adult neutered male domestic shorthair cats were used in a randomized crossover design study.  During two 12-wk periods, cats were exposed to either short days (8 hr light:16 hr dark) or long days (16 hr light:8 hr dark). Cats were fed a commercial diet to maintain baseline body weight.  Subcutaneous adipose biopsies were collected at wk 12 of each period for RNA isolation and Illumina sequencing.
Results: A total of 578 million sequences (28.9 million/sample) were generated by Illumina sequencing.  Using a raw p value of P<0.005, 170 mRNA transcripts were differentially expressed between short day- and long day-housed cats.  Of the 170 transcripts highlighted, 25 annotated transcripts were up-regulated, while 116 annotated transcripts were down-regulated by long days.  Another 29 un-annotated transcripts (name and function not known) were also different between groups.  In general, adipose tissue of long day-housed cats had greater expression of genes involved with cholesterol trafficking, fatty acid synthesis and immune function, and lower expression of genes involved with cell cycle and growth, cell development and structure, and protein processing, when compared to short day-housed cats.

overall_design: Subcutaneous adipose tissue mRNA profiles of healthy adult neutered male cats exposed to short days (8 hr light: 16 hr dark) or long days (16 hr light: 8 hr dark) using Illumina sequencing.


title: Serum Follistatin-Like Protein 1 Is a Biomarker for Macrophage Activation Syndrome and May Predict Disease Course in Systemic Juvenile Idiopathic Arthritis

city: Cincinnati

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

summary:
Objective. Follistatin-like protein 1 (FSTL-1) is a secreted glycoprotein that is over-expressed in certain inflammatory diseases.  Our objective in this study was to correlate FSTL-1 levels with measures of clinical disease activity in systemic juvenile idiopathic arthritis (sJIA), including macrophage activation syndrome (MAS).
Methods. FSTL-1 serum levels were measured by ELISA in 28 patients with sJIA, including 7 patients who developed MAS, as well as in 30 normal controls.  Levels were correlated with erythrocyte sedimentation rate (ESR), ferritin and sIL-2Rα expression.  Differential gene expression based on FSTL-1 levels was analyzed in peripheral blood mononuclear cells (PBMCs).
Results. FSTL-1 serum levels were elevated at time of presentation (pre-treatment) of sJIA (mean 200.7 ng/ml) and decreased to normal (mean 133.7 ng/ml) over 24 months (p<0.01). FSTL-1 levels were markedly elevated during acute MAS (mean 279.8 ng/ml) and decreased to normal (mean 120.3 ng/ml) following treatment (p<0.001).  FSTL-1 levels correlated with serum markers of inflammation, including sIL-2Rα and ferritin, in patients with MAS.  PBMCs from patients with FSTL-1 levels >200 ng/ml showed an increase in expression of genes related to innate immunity and erythropoiesis, and decrease in NK cell function.  Patients with the highest FSTL-1 levels at disease onset (>300 ng/ml) ultimately required cyclosporine treatment.
Conclusion. In patients with sJIA, serum FSTL-1 is a biomarker for MAS and FSTL-1 levels at presentation may predict subsequent disease course.  Patients with FSTL-1 levels >200 ng/ml had altered gene expression patterns suggestive of subclinical MAS and may represent a subgroup of sJIA with more severe disease.

overall_design:
FSTL-1 serum levels were measured by ELISA in 28 patients with sJIA, including 7 patients who developed MAS, as well as in 30 normal controls.  Levels were correlated with erythrocyte sedimentation rate (ESR), ferritin and sIL-2Rα expression.  Differential gene expression based on FSTL-1 levels was analyzed in peripheral blood mononuclear cells (PBMCs).
Only 11 patients were run on microarray.

first: Mark

last: Gorelik

first: Ndate

last: Fall

first: Mekibib

last: Altaye

middle: G

first: Susan

last: Thompson

first: Alexei

last: Grom

first: Raphael

last: Hirsch


title: Effect of selection on residual feed intake on gene expression in porcine skeletal muscle (115 kg body weight)

city: Saint-Gilles

first: Annie

last: Vincent

address: domaine de la prise

institute: INRA

summary: Transcriptional profiling in liver of 24 pigs of 115 kg body weight from lines divergently selected for residual feed intake (RFI): low-RFI pigs fed ad libitum (RFIneg), high-RFI pigs fed ad libitum (RFIpl) and high-RFI pigs restricted at RFIneg feeding level (RFIplR) to investigate the impact of feeding independently of selection.

overall_design: Three experimental conditions: low-RFI (RFIneg), high-RFI (RFIpl) and restricted high-RFI (RFIplR). 8 pigs per condition except for RFIneg (7 pigs). One replicate per array.

first: Isabelle

last: Louveau


title: Transcriptome analysis of deletion of adenylate cyclase in T. reesei upon growth on cellulose in light and darkness

status: Public on Jan 08 2014

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

institute: University of Vienna

summary:
The aim of this study was to evaluate changes in the transcriptome due to the lack of adenylate cyclase in light or darkness. As the cAMP pathway represents an output pathway of heterotrimeric G-protein signaling
ACY1 is likely to be important for regulation of enzymes in response to different nutrient conditions. Also, a light dependent effect was found earlier.

overall_design: Strains of this study were grown on Mandels Andreotti Minimal Medium with 1 % w/v microcrystalline cellulose as sole carbon source in constant light or constant darkness for 72 hours; 2 biological replicates were included

first: Andre

last: Schuster


title: Functional Roles of Hdac1/2 in lung development

status: Public on Dec 31 2013

city: Philadelphia

first: Yi

last: Wang

address: 3400 Civic Center Boulevard, Bldg 421

institute: University of Pennsylvania

summary: Hdac1/2 are important epigenetic factors, yet their functional roles in specific tissues inluding lung is not determined. We used the conditional knockout model of Hdac1/2 to determine their roles in lung development.

overall_design: To explore the genes that are regulated by Hdac1/2 during lung development, we performed microarray analysis of Shhcre control and Hdac1/2DKO lungs at E11.5 embryos.

first: Ying

last: Tian

middle: P

last: Morley

first: Francesco

middle: J

last: DeMayo

first: Brigid

middle: L

last: Hogan

first: Eric

last: Olson

first: Edward

last: Morrisey