title: Expression data from mouse embryonic lung epithelial tip progenitor cells

status: Public on Aug 31 2016

city: Cambridge

first: Emma

middle: Louise

last: Rawlins

address: Tennis Court Road

department: Gurdon Institute

institute: University Of Cambridge

summary:
Epithelial tip progenitor cells are an important epithelial progenitor population in the developing lung. At early stages of development they produce SOX2+ bronchiolar progenitor cells. At later stages of embryonic lung development they produce SOX2- alveolar progenitor cells.
We purified the tip progenitor cells from early (E11.5, bronchiolar progenitor producing) and late (E17.5, alveolar progenitor producing) stages of mouse lung development and used Affymetrix microarrays to compare their gene expression profiles.

overall_design: Lung epithelial tip progenitor cells were microdissected from E11.5 embryos. Or, they were isolated from E17.5 Id2-CreER; Rosa26R-fGFP embryos by flow cytometry.

middle: L


title: Identify factors associated with preserved hepatic insulin sensitivity despite of hepatic steatosis.

status: Public on Dec 23 2016

city: Tokyo

first: Fumika

last: Shigiyama

address: 6-11-1, Omori Nishi, Otaku

department: Internal Medicine

country: Japan

institute: Toho University

summary: Among all the evaluated factors, only adipose tissue insulin sensitivity (assessed by clamped % suppression of serum free fatty acid), serum concentration of high molecular weight adiponectin, and plasma concentration of TCA cycle metabolites such as citric acid and cis-aconitic acid (assessed by metabolome analysis), associated significantly and positively with hepatic insulin sensitivity in NAFLD.

overall_design: We analyzed the data to identify factors associated with preserved hepatic insulin sensitivity despite of hepatic steatosis. The 26 NAFLD patients with intrahepatic lipid content of >5% were divided into three groups according to the level of hepatic insulin sensitivity, as assessed by clamped % suppression of endogenous glucose production. Then, all the evaluated factors were compared between the hepatic insulin sensitive and resistant patients with comparable hepatic steatosis (n=9 vs 8, respectively).

first: Naoki

last: Kumashiro


title: Knockdown of STAiR18, an IL-6/STAT3-induced long noncoding RNA, in INA-6 multiple myeloma cells

status: Public on Jul 17 2016

city: Leipzig

first: Stefanie

last: Binder

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: STAiR18, an mRNA-like STAT3-induced long noncoding RNA shows ubiquitous expression. RNAi-mediated knockdown of STAiR18 led to a dramatic decrease in INA-6 cell vitality. Furthermore, STAiR18 knockdown reduced the STAT3 RNA and protein levels in these cells, suggesting a positive feedback loop between STAT3 and its target ncRNA STAiR18. Microarray analyses of INA-6 cells after STAiR18 or STAT3 knockdown revealed overlapping changes of transcription patterns indicating a close functional interplay between the two molecules. Taken together, STAiR18 represents a novel noncoding RNA that is likely to play an important role for the oncogenic function of the STAT3 pathway.

overall_design: STAT3- and STAiR18-dependent gene expression in human multiple myeloma cell line INA-6 was measured 40 hours after transfection with either a negative control siRNA, an siRNA to STAT3 or an siRNA to STAiR18. Four independent experiments were performed for each siRNA approach, yielding 12 approaches in total.

first: Nadine

last: Hösler

first: Ivonne

last: Zipfel

first: Tilo

last: Buschmann

first: Friedemann

last: Horn


title: Distinct Function for ASCL1 and NEUROD1 in Pulmonary Neuroendocrine Tumors

status: Public on Jul 21 2016

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

country: USA

institute: UT Southwestern Medical Center

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: ncRNA expression-based, individualized outcome prediction for CRC patients

status: Public on Dec 28 2016

city: Houston

first: Simone

last: Anfossi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Therapeutics

institute: UT MD Anderson Cancer Center

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling of ncRNAs in 165 CRC cases.

overall_design: In the study presented here, a well-defined cohort of 165 CRC cases from MD Anderson Cancer Center, followed up more than ten years, was used to acquire expression profiles of ncRNAs.

first: Isidore

last: Rigoutsos

first: George

middle: A

last: Calin

first: Scott

last: Kopetz


title: Whole Genome Bisulfite sequencing for liver DNA methylation analysis of rat exposed to 0.05% Pb

status: Public on Nov 17 2016

city: Shanghai

first: Sun

middle: hong

last: ling

address: No.639  Zhizaoju Raod , Shanghai

department: Institute and Department of Endocrinology and Metabolism

country: China

institute: Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: We generated 4 Gb of high-quality sequencing data (~1 Gb per sample). The NCD+0.05%Pb group had hypermethylation at the whole genome level, compared to NCD. Difference analysis in gene methylation aimed at TSS region indicated that a total of 2733 genes experienced DNA methylation changes, with 2320 hypermethylated genes and 413 hypomethylated genes of the NCD+0.05%Pb group compared with the NCD group.

overall_design: 8-week-old Wistar rats were divide into NCD and NCD+0.05%Pb groups. Rats of the NCD group were treated normal dringking water,rats of NCD+0.05%Pb group were exposed to 0.05% dosages of lead acetate through drinking water.two liver samples were taken out from each group for WGBS,and the DNA methylation level of livers were analyzed and compared between the two groups.

first: Honglin

last: Sun

first: Yingli

last: Lu


title: Distinct Function for ASCL1 and NEUROD1 in Pulmonary Neuroendocrine Tumors (ChIP-seq)

summary: Small cell lung carcinoma (SCLC) and large cell neuroendocrine carcinoma (LCNEC) are high-grade pulmonary neuroendocrine tumors. The neural basic helix-loop-helix (bHLH) transcription factors ASCL1 and NEUROD1 have been shown to play crucial roles in promoting the malignant behavior and survival of human SCLC cell lines. In this study, we find ASCL1 and NEUROD1 identify distinct neuroendocrine tumors, bind distinct genomic loci, and regulate mostly distinct genes. ASCL1 and NEUROD1 are often bound in super-enhancers that are associated with highly expressed genes in their respective SCLC cell lines suggesting different cell lineage of origin for these tumors. ASCL1 targets oncogenic genes such as MYCL1, RET, and NFIB, while NEUROD1 targets the oncogenic gene MYC. Although ASCL1 and NEUROD1 regulate different genes, many of these gene targets commonly contribute to neuroendocrine and cell migration function. ASCL1 in particular also regulates genes in the NOTCH pathway and genes important in cell-cycle dynamics. Finally, we demonstrate ASCL1 but not NEUROD1 is required for SCLC and LCNEC tumor formation in current in vivo genetic mouse models of pulmonary neuroendocrine tumors

overall_design: ChIP-seq analysis performed on three ASCL1high and two NEUROD1high human SCLC cell lines to identify ASCL1 and/or NEUROD1 binding sites in these two types of cells. Also, we performed ChIP-seq for Ascl1 binding sites in mouse neuroendocrine lung tumors obtained from Trp53;Rb1;Rbl2 triple knockout model mice treated with Adeno-CMVCRE intratracheally.

first: Mark

middle: D

last: Borromeo

first: Trisha

middle: K

last: Savage

first: Rahul

last: Kollipara

first: Min

last: He

first: Alexander

last: Augustyn

first: Jihan

last: Osborne

first: Luc

last: Girard

first: John

last: Minna

first: Adi

middle: F

last: Gazdar

first: Melanie

middle: H

last: Cobb


title: A global view of the transcriptional profiling of adipose tissue in Chinese Qinchuan cattle using RNA sequencing

status: Public on Jun 05 2016

city: Yangling

first: Yang

last: Zhou

address: No.22 Xinong Road

institute: Northwest A&F University

summary: We constructed a transcriptional profiling of adipose tissue by RNA sequencing. Samples were collected from Chinese Qinchuan fetal bovine, heifers, bulls, and steers. We unambiguously detected a substantial number of differently expressed genes (DEGs), novel transcript units (NTUs), and splicing variants.The expressional profile of adipose tissue changed considerably from fetuses to adults, whereas smaller differences were detected between the adipose tissues of adult cows (ATACs). As an endocrine organ, DEGs related to inflammatory and immune process were significantly enriched in the ATACs. These genes may play some roles in different regulation mechanisms of adipose tissue in different genders. In addition, adipose tissue abundantly expressed genes concerning the functions of the mitochondria and the ribosomes. These support the adipose tissue as an extremely active tissue for energy and protein metabolism besides the storage of surplus fuel. In this study, about two-thirds of the NTUs did not have coding ability. Both the NTUs with and without coding ability were enriched from 300bp to 1,500bp. The main difference in the number of the two types of NTUs was also concentrated in this range.  In total, about 18.2% of the genes in adipose tissues were alternatively spliced, and half of them were specially expressed in different patterns. Combined with previous studies, we concluded that alternatively splicing events occur variously in different tissues or different patterns of adipose tissue. Taken together, our study provided complete datasets involving the spatial and temporal transcriptome of adipose tissue which suggested the complexity of adipose tissue and our study will provide essential information for further research.

overall_design: Examinations of subcutaneous adipose tissues of fetal bovines, adult heifers, adult bulls, and adult steers

first: Hong

last: Chen


title: RNA-Seq of Saccharomyces cerevisiae cells carrying different YRR1 alleles in response to 4-nitroquinoline-N-oxide (4NQO) and to glycerol as the sole carbon source

status: Public on Mar 01 2016

city: Morgantown

first: Xiaoqing

last: Rong-Mullins

state: West Virginia

address: 53 Campus Dr

institute: West Virginia University

summary: In this study, we constructed three isogenic strains of S96 yrr1Δ background (its native YRR1 gene was knocked out) carrying three different YRR1 alleles, YRR1_S96, YRR1_YJM789 and YRR1_S96-I775E, respectively. We then conducted RNA deep sequencing (RNA-Seq) on the three strains grown in Yeast Peptone Dextrose medium (YPD), YPD + 4NQO and Yeast Peptone glycerol medium (YPglycerol).

overall_design: RNA-Seq was performed in biological duplicates on S96 cells carrying three different YRR1 alleles grown in YPD, YPD + 4NQO, YPglycerol

first: Jennifer

last: Gallagher


title: Identification of novel gene targets and functions of p21-activated kinase 1 during DNA damage by gene expression profiling

status: Public on Jan 01 2016

city: Washington

first: Mona

last: Motwani

state: DC

address: 2300 I St NW

institute: George Washington University

summary:
The purpose of the study was to identify new PAK1 targets in response to ionizing radiation with putative role in the DNA damage response.
We examined the effect of IR on the gene expression patterns in the murine embryonic fibroblasts with or without Pak1 using microarray.

overall_design: Differentially expressed transcripts were identified using Gene Spring GX 10.0.2. The samples used were Wild type, Pak1 knock out, Wild type treated with ionizing radiation and Pak1 knock out treated with ionizing radiation. Triplicates of each sample type were used for analysis.

first: M

first: D

last: Li

first: A

last: Horvath

first: R

last: Kumar


title: Expression data from human Th1 and Th2 cells

status: Public on Aug 01 2016

city: Leicester

first: David

middle: John

last: Cousins

address: NIHR BRC Respiratory, Glenfield Hospital

department: Respiratory Sciences

country: United Kingdom

institute: University of Leicester

summary:
T-helper cells differentiate from naïve precursors into multiple lineages, including Th1, Th2, Th17 and inducible Treg, in humans and mice. The identification of each lineage is currently determined by examination of a small number of genes encoding hallmark cytokines and/or transcription factors in both species
To gain a better understanding of human T-helper cell function we have performed detailed transcriptional profiling of highly polarized Th1 and Th2 cells in both resting and activated states examining gene and miRNA expression

overall_design: Naïve CD4 positive T-cells were isolated from peripheral blood of three different human donors. Cells were differenitated into Th1 and Th2 cells in vitro for 28 days to achieve homogeneous cell lineages. Samples were taken at resting state or activated for 4 hours with PMA/Ionomycin.

middle: J

first: Joanne

last: McDonald


title: Human tongue squamous cell carcinoma cell line SAS-Control vs. SAS-LYRIC knockdown stable clones global gene profiling

status: Public on Feb 28 2016

city: Taipei

first: Yi-Ping

last: Wang

address: No.1, Changde St., Zhongzheng Dist.

department: Department of Dentistry

country: Taiwan

institute: National Taiwan University Hospital

summary: Transcriptional profiling of SAS cells transfected with pLKO.1-LYRIC shRNA-B expression vector (desinaged as B) and control SAS cells (transfected with pLKO.1 vector, designated as CTL). Goal was to determine the effects of LYRIC knockdown on global SAS cells gene expression.

overall_design: Two-condition experiment, SAS cells transfected with pLKO.1-LYRIC shRNA-B expression vector (desinaged as B) v.s. control SAS cells (transfected with pLKO.1 vector, designated as CTL). Biological replicates: 4 control replicates, 4 transfected replicates.


title: Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells

status: Public on Nov 21 2015

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary: Self-renewing tissue-resident macrophages are thought to be exclusively derived from embryonic progenitors. However, whether circulating monocytes can also give rise to such macrophages has not been formally investigated. Here we use a new model of diphtheria toxin-mediated depletion of liver-resident Kupffer cells to generate niche availability and show that circulating monocytes engrafted in the liver, gradually adopt the transcriptional profile of their depleted counterparts and become long-lived self-renewing cells. Underlining the physiological relevance of our findings, circulating monocytes also contribute to the expanding pool of macrophages in the liver shortly after birth, when macrophage niches become available during normal organ growth. Thus, like embryonic precursors, monocytes can and do give rise to self-renewing tissue-resident macrophages if the niche is available to them.

overall_design: Clec4F+ Kupffer cells were isolated and sorted from livers from adult WT mice or KC-DTR or KC-DTR littermate control mice +/- 50ng DT at indicated timepoints. 19 samples (arrays) in total. RNA was isolated, amplified with Nugene pico kit, converted to cDNA and then hybridised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.

first: Charlotte

last: Scott

first: Fang

last: Zheng

first: Patrick

last: De Baetselier

first: Yvan

last: Saeys

first: Sofie

last: De Prijck

first: Saskia

last: Lippens

first: Chloé

last: Abels

first: Steve

last: Schoonooghe

first: Geert

last: Raes

first: Nick

last: Devoogdt

first: Bart

middle: N

last: Lambrecht

first: Alain

last: Beschin

first: Martin

last: Guilliams


title: Effect of summer daylight exposure and genetic background on growth in growth hormone deficient children

status: Public on Nov 30 2015

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

department: Medicine

institute: University of Manchester

summary: The response to growth hormone in humans is dependent on phenotypic, genetic and environmental factors. The present study in children with growth hormone deficiency (GHD) collected worldwide characterised gene-environment interactions on growth response to recombinant human growth hormone (r-hGH). Growth responses in children are linked to latitude, and we found that a correlation of latitude, summer daylight exposure (SDE) was a key environmental factor related to growth response to r-hGH. In turn growth response was determined by an interaction between both SDE and genes known to affect growth response to r-hGH. In addition analysis of associated networks of gene expression implicated a role for circadian clock pathways and specifically the developmental transcription factor NANOG. This work provides the first observation of gene-environment interactions in children treated with r-hGH.

overall_design: Whole blood from patients with growth hormone deficiency (GHD) was used for RNA extraction and hybridization on Affymetrix microarrays. Reduction of globin messenger RNA was undertaken using the Ambion GLOBIN Clear Human Kit (Life Technologies, Paisley, UK). Complementary RNA was generated using the Two-Cycle Eukaryotic Target Labelling Kit (Affymetrix, Santa Clara, CA, USA) and a final quality check performed before hybridization to Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays. Arrays were then scanned on an Affymetrix GeneChip 7G scanner and assessed for quality against internal and hybridization controls. Confounding effects due to variations in cell populations and outliers were examined by cross validation using principal component analysis and iso-map multidimensional scaling (Qlucore Omics Explorer 2.2, Qlucore, Lund, Sweden).


title: Expression data from Drosophila third instar larvae eye imaginal discs

status: Public on Oct 01 2015

city: Burjassot

first: Veronica

last: Munoz-Soriano

state: Valencia

address: C/ Dr. Moliner, 50

department: Genetics

country: Spain

institute: University of Valencia

summary:
The kinase nmo is required for proper ommatidial rotation in the developing Drosophila compound eye. It has been suggested to regulate gene expression by phosphorylating transcription factors.
We used microarray analysis to identify genes which expression is regulated by nmo during ommatidial rotation.

overall_design: armGFP (used as wild type control) and armGFP, nmoP1 mutant eye discs were dissected for RNA extraction and hybridization of Affymetrix microarrays.

first: Verónica

first: Nuria

last: Paricio


title: ChIP-Seq for Yrr1 protein on Saccharomyces cerevisiae cells carrying different YRR1 alleles in response to 4-nitroquinoline-N-oxide (4NQO)

status: Public on Dec 04 2015

first: Xiaoqing

last: Rong-Mullins

summary: In this study, we constructed three isogenic strains of S96 yrr1Δ background (its native YRR1 gene was knocked out) carrying three different YRR1 alleles, YRR1_S96, YRR1_YJM789, YRR1_S96-I775E, respectively. We then conducted chromatin immuno-precipitation followed by high-throughput sequencing (ChIP-Seq) for Yrr1 protein on the three strains grown in Yeast Peptone Dextrose medium (YPD) and YPD + 4NQO.

overall_design: ChIP-Seq for Yrr1 protein was performed in biological triplicates on S96 cells carrying three different YRR1 alleles grown in YPD and YPD + 4NQO. Immune-precipitated DNA were sequenced for all the three cultures and input genomic DNA was sequenced for one culture.

first: Jennifer

last: Gallagher

first: Barbara

last: Dunn

first: Lixia

last: Jiang

first: Michael

middle: P

last: Snyder


title: Transcriptome analysis of single cells from the mouse dentate gyrus [10X]

status: Public on Dec 13 2017

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: RNA sequencing was performed on 5454 single cells from dentate gyrus of CD-1 mice, sampled at postnatal day 12, 16, 24 and 35, with the aim of studying the postnatal dentate gyrus neurogenesis.

overall_design: 1129 single cells from postnatal day 12, 1440 from day 16, 1063 from day 24, and 1822 from day 35.

first: Hannah

last: Hochgerner

first: Amit

last: Zeisel

first: Patrik

last: Ernfors


title: Genome-wide analysis of ATF4 binding in histidinol-treated cells and RNA-Seq experiment to identify genes regulated by ATF4

status: Public on Aug 28 2015

city: Bethesda

first: Stefan

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID


title: Genome-wide analysis of ATF4 binding in histidinol-treated cells

summary: Activating Transcription Factor 4 (ATF4) is a transcription factor induced by the integrated stress response (ISR). This experiment is a genome-wide occupancy profiling of ATF4 in human HAP1 cells. HAP1 is a near-haploid human cell line that was derived from KBM-7 cells isolated from a patient with Chronic Myelogenous Leukemia. We induced ATF4 expression by mimicking amino acid starvation with the drug histidinol. We identified peaks of ATF4 binding using three independent antibodies.

overall_design: Examination of ATF4 binding in HAP1 cells treated with 2 mM histidinol for 24 hours.

first: David

last: Raulet

first: Benjamin

middle: G

last: Gowen

first: Bryan

last: Chim

first: Patrick

last: Burr


title: Ribosome profiling analysis of Dengue Virus

status: Public on Sep 01 2016

city: Durham

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

summary: Dengue virus is an + strand RNA virus. We have carried our infections of human cells with Dengue and analyzed the translation, replication, and localization of the Dengue RNA. This allowed for clear definition of the life cycle of the Dengue virus inside a host cell. We also assessed the host response to Dengue virus, finding that a large fraction of the translational response is due to Interferon function.

overall_design: Translational and transcriptional analysis of the cellular response to Dengue virus infection

middle: W

first: Rafael

last: Campos

first: Kitti

last: Chan

first: Christopher

middle: V

last: Nicchitta

first: Subhash

last: Vasudevan

first: Mariano

last: Garcia-Blanco


title: RNA-Seq experiment to identify genes regulated by ATF4

summary: Activating Transcription Factor 4 (ATF4) is a transcription factor induced by the integrated stress response (ISR). This experiment is a genome-wide profiling of ATF4-dependent RNA expression in human HAP-1 cells. HAP-1 is a near-haploid human cell line that was derived from KBM-7 cells isolated from a patient with Chronic Myelogenous Leukemia. We analyzed WT and ATF4 KO cells. We induced ATF4 expression by mimicking amino acid starvation with the drug histidinol.

overall_design: RNA expression profiles were generated for WT and ATF4 KO HAP1 cells. ATF4 genes were mutated using Cas9 genome editing technology. Amino acid starvation was mimicked by treating WT and ATF4 KO cells with 2 mM histidinol for 24 hours, which increases ATF4 expression.


title: Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 and isogenic pdhS2 (Atu1888) deletion strain

status: Public on Jul 24 2015

city: Bloomington

first: Jason

middle: Eugene

last: Heindl

state: IN

address: 1001 E. 3rd St., Jordan Hall 142

department: Biology

institute: Indiana University

summary: A conserved regulatory pathway directs developmental transitions and asymmetries in Agrobacterium tumefaciens. Core components of this coordination of division and development (CDD) pathway include two integrated phosphorelays. One of these phosphorelays includes at least four histidine sensor kinase homologues, DivJ, PleC, PdhS1, and PdhS2, and at least two response regulators, DivK and PleD. Previously we demonstrated that PdhS2 reciprocally regulates biofilm formation and swimming motility. In the current study we further dissect the architecture of the CDD pathway in A. tumefaciens with respect to PdhS2. We show that PdhS2-dependent effects on attachment and motility require the response regulator, DivK, but do not require PdhS2 autokinase or phosphotransfer activities. We also demonstrate that PdhS2 regulation of biofilm formation is dependent upon multiple diguanylate cyclases, including PleD, DgcA, and DgcB, implying that PdhS2 regulation of this process intersects with pathways regulating levels of the second messenger cyclic-di-GMP. Finally, we show that upon cell division a GFP fusion to PdhS2 dynamically localizes to the new pole of the bacterium suggesting that PdhS2 controls processes in the daughter cell compartment of predivisional cells. These observations suggest that PdhS2 negatively regulates DivK, and possibly PleD, activity to control developmental processes in the daughter cell compartment of predivisional cells, as well as in newly released motile daughter cells.

overall_design: Three biological replicates, independent RNA preparations, one dye swap.

first: Clay

last: Fuqua


title: Enhancer divergence and cis-regulatory evolution in the human and chimpanzee neural crest

status: Public on Sep 11 2015

city: Stanford

first: Tomek

last: Swigut

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

summary: Here we derive human and chimpanzee cranial neural crest cells (CNCCs) and profile histone modifications, transcription factors, chromatin accessibility and gene expression to systematically and quantitatively annotate evolutionary divergence of craniofacial cis-regulatory landscapes.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K27me3), chromatin modifiers (p300), transcription factors (NR2F1, TFAP2A), chromatin accessibility (ATACseq) and gene expression (RNAseq) were assayed in CNCCs derived from iPSCs/ESCs from 2 chimpanzee and 3 human individuals.

first: Sara

last: Prescott

first: Joanna

last: Wysocka

first: Tomasz


title: Differential miRNA expression in Cells and Matrix Vesicles in Vascular Smooth Muscle Cells from Rats with Kidney Disease

status: Public on Jun 12 2015

city: Indianapolis

first: Neal

middle: X

last: Chen

address: 950 W. Walnut Street

summary: Vascular calcification is a complex process and has been associated with aging, diabetes, chronic kidney disease (CKD).  Although there have been several studies studying the role of miRNAs (miRs) in bone osteogenesis, little is known about the role of miRs in vascular calcification and their role in the pathogenesis of vascular abnormalities. Matrix vesicles (MV) are known to play an important role in initiating vascular smooth muscle cell (VSMC) calcification.  In the present study, we performed miRNA microarray analysis to identify the dysregulated miRs between MV and VSMC derived from CKD rats to understand the role of post-transcriptional regulatory networks governed by these miRNAs in vascular calcification and to uncover the differential miRNA content of MV.  The percentage of miRNA to total RNA was increased in MV compared to VSMC.  Comparison of expression profiles of miRNA by microarray demonstrated 33 miRs to be differentially expressed with the majority (~ 57%) of them down-regulated.   Target genes controlled by differentially expressed miRNAs were identified utilizing two different complementary computational approaches Miranda and Targetscan to understand the functions and pathways that may be affected due to the production of MV from calcifying VSMC thereby contributing to the regulation of genes by miRs. We found several processes including vascular smooth muscle contraction, response to hypoxia and regulation of muscle cell differentiation to be enriched.   Signaling pathways identified included MAP-kinase and wnt signaling that have previously been shown to be important in vascular calcification.   In conclusion, our results demonstrate that miRs are concentrated in MV from calcifying VSMC, and that important functions and pathways are affected by the miRs dysregulation between calcifying VSMC and the MV they produce.  This suggests that miRs may play a very important regulatory role in vascular calcification in CKD by controlling an extensive network of post-transcriptional targets.

overall_design: Compare miRNA from matrix vesicles to miRNA from vascular smooth muscle cells that gave rise to the matrix vesicles from 3 sets of MV and VSMC derived from 3 normal and 3 CKD rats

first: Sharon

middle: M

last: Moe


title: Gene expression analysis of cervical cancer progression

status: Public on Jul 01 2015

city: Madison

first: Johan

last: den Boon

state: WI

address: 330 North Orchard Street

department: Virology

institute: Morgridge Institute for Research

summary:
Affymetrix-U133-plus2.0-based gene expression analysis of laser-captured epithelium from 128 cervical tissue specimens from women enrolled in SUCCEED
Cervical cancer (CC) is the second most frequent cancer in women and the third leading cause of cancer death in women worldwide. Our analysis of normal, precancerous, and cancerous cervical tissue shows that progress of the disease is a cascade of increased DNA replication/repair and cell proliferation followed by substantial metabolic shifts. The data show a sharp decrease in estrogen receptor alpha (ERα) in tumor cells, and ranking tissue specimens by estrogen-responsive gene expression correlates remarkably closely with histological pathology.
Johan, den Boon, Morgridge Institute for Research at University of Wisconsin-Madison
Paul, Ahlquist, Howard Hughes Medical Institute and Morgridge Institute for Research at University of Wisconsin-Madison
Nicolas, Wentzensen, National Cancer Institute

overall_design: 24 normal, 14 CIN1 lesions, 22 CIN2 lesions, 40 CIN3 lesions, and 28 cancers specimens were cryosecrtioned and used for laser-capture, RNA extraction, two rounds of T7-mediated amplification, and cRNA biotinylation. Bio-cRNA was hybridized to Affymetrix U133-Plus2.0 arrays, scanned signals were processed through GC-RMA

first: Paul

last: Ahlquist

first: Nicolas

last: Wentzensen


title: Expression of subtelomeric lncRNAs links telomeres maintenance with RNA decay in S. cerevisiae

status: Public on Apr 30 2015

city: Paris

first: Marc

last: Descrimes

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Long non-coding RNAs (lncRNAs) have been shown to regulate gene expression, chromatin domains and chromosome stability in eukaryotic cells. Recent observations have reported the existence of telomere associated long ncRNAs (TERRA, telomeric repeat containing RNA) in mammalian and yeast cells but their function(s) remain(s) poorly characterized. Here, we report the existence in S. cerevisiae of several sense and antisense Cryptic Unstable Transcripts (CUTs) and Xrn1-sensitive Unstable Transcripts (XUT) initiating within the subtelomeric repeated region Y’. We show that the Y’ ncRNAs, subTERRA, are distinct from TERRA and are mainly destabilized by the general cytoplasmic and nuclear 5’- and 3’- RNA decays in a sense-dependent manner. subTERRA transcription is mainly sustained by RNAPII and subTERRA accumulate preferentially during the G1/S transition and in C-terminal rap1 mutants independently of Rap1p function in silencing. The accumulation of subTERRA in RNA decay mutants coincides with telomere misregulation: shortening of telomere length, loss of telomeric clustering in mitotic cells, indicating that subTERRA might compete with factors involved in telomere elongation, tethering and/or clustering. We propose that subtelomeric RNAs expression links telomere maintenance with RNA degradation pathways.

overall_design: Exmination of two yeast mutants for RNA decay.

first: Marta

last: Kwapisz

first: Erwin

last: Van Dijk

first: Antonin

last: Morillon


title: The conserved organization of the human and mouse transcriptomes

status: Public on Nov 20 2014

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: We characterized by RNA-seq the transcriptional profiles of a large and heterogeneous collection of mouse tissues, augmenting the mouse transcriptome with thousands of novel transcript candidates. Comparison with transcriptome profiles obtained in human cell lines reveals substantial conservation of transcriptional programs, and uncovers a distinct class of genes with levels of expression across cell types and species, that have been constrained early in vertebrate evolution. This core set of genes capture a substantial and constant fraction of the transcriptional output of mammalian cells, and participates in basic functional and structural housekeeping processes common to all cell types. Perturbation of these constrained genes is associated with significant phenotypes including embryonic lethality and cancer. Evolutionary constraint in gene expression levels is not reflected in the conservation of the genomic sequences, but it is associated with strong and conserved epigenetic marking, as well as to a characteristic post-transcriptional regulatory program in which sub-cellular localization and alternative splicing play comparatively large roles.

overall_design: Comparison of human and mouse transcriptome profiles has uncovered a distinct class of genes (6600- one third of all expressed genes in both human and mouse) whose variation in expression levels have been constrained irrespective of cell types and species that they are express in. Such constraint appears to have been developed early in vertebrate evolution since it seen in multiple other species. This constraint is not associated with the conservation of the genomic sequences found in each species. Finally, this core set of genes helps in interpreting how non-human organisms like the mouse can better be used as models for human disease and why perturbation of these constrained genes is associated with significant phenotypes including embryonic lethality and cancer.

first: Dmitri

last: Pervouchine

first: Sarah

last: Djebali

first: Alessandra

last: Breschi

first: Carrie

last: Davis

first: Pablo

last: Barja

first: Alex

last: Dobin

first: Andrea

last: Tanzer

first: Julien

last: Lagarde

first: Chris

last: Zaleski

first: Lei-Hoon

last: See

first: Meagan

last: Fastuca

first: Jorg

last: Drenkow

first: Huaien

last: Wang

first: Giovanni

last: Bussotti

first: Baikang

last: Pei

first: Suganthi

last: Balasubramanian

first: Jean

last: Monlong

first: Arif

last: Harmanci

first: Mark

last: Gerstein

first: Micheal

last: Beer

first: Cedric

last: Notredame

first: Roderic

last: Guigo

first: Thomas

middle: R

last: Gingeras


title: Transcriptional response to heat shock in Pkh-depleted yeast cells.

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

institute: Universitat Autonoma de Barcelona

summary:
	The yeast proteins Pkh1 and Pkh2 are functional counterparts of the mammalian 3-phosphoinositide-dependent protein kinase 1 (PDK1). Cells carrying simultaneous deletion in both genes, PKH1 and PKH2 are not viable, at least in some genetic backgrounds (Casamayor et al., 1999; Inagaki et al., 1999). Consequently, a different strategy is needed to study the function of these apparently redundant gene products. The approach that has been successfully used to dissect the functions of these proteins consist in the use of a strain that combine the disruption of PKH2 with the temperature sensitive pkh1D398G allele (Inagaki et al., 1999). Since Pkh1 and Pkh2 phosphorylate Pkc1 in vitro in its activation loop (Thr983), and the cell lysis defects of the pkh1D398G pkh2 strain at the restrictive temperature are partially restored by constitutive activation of the Pkc1-Slt2 MAPK pathway, it has been suggested that the Pkh activity is important for maintenance of the cell wall integrity in S. cerevisiae (Inagaki et al., 1999; Friant et al., 2001). We considered it necessary that a different genetic strategy would be convenient in order to carry out specific studies about the functions of the Pkh proteins. In order to avoid incubations at temperatures that activate the Slt2 pathway, and induce cellular lysis, we decided to use a strategy based on the use of a regulatable promoter. We replaced 487 bp located immediately upstream the start PKH2 codon by a cassette containing the doxycycline-repressed promoter tetO7. This substitution is positioned in a 1.3 kbp intergenic region containing divergent promoters and it seems unlikely that may affect expression of the IZH4, the upstream gene, which encode a family of four paralogous membrane proteins involved in zinc ion homeostasis and whose expression is regulated by fatty acids and zinc altered levels. In this strain (MB002) the PKH2 expression could be switched off by addition of doxycycline. In order to deplete the cell for the Pkh activity, we disrupted both, the PKH1 and PKH3 coding regions, obtaining the new SDP8 strain.
Our results show that depletion of Pkh results in a differential transcriptional response in front of a heat shock stress. The general transcriptional response was attenuated in the SDP8 when compared when WT cells, but lack of Pkh activity did not affect the repression of the ribosomal proteins.

overall_design:
	Four samples were analyzed: the SDP8 strain, a tetO7 conditional mutant, and its isogenic WT strain both, in the presence and in the absence of doxycyline (for 8 and 24 h).

We compared the expression profile of:
1) WT + 16h Dox + 40 min heat shock vs WT + 16h Dox.
2) SDP8 + 16h Dox + 40 min heat shock vs SDP8 + 16h Dox.

A Dye-swap was carried out for each comparison of samples.

Total number of chips analyzed: 4.

first: Daniel

last: Pastor-Flores

first: Jofre

last: Ferrer-Dalmau

first: Anna

last: Bahí

first: Ricardo

last: Biondi


title: Genomic aberrations of high-grade and low-grade gliomas from Chinese patients

status: Public on Jan 03 2015

city: Beijing

first: Dapeng

address: No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

institute: Beijing Institute of Genomics

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

summary: We carried out the analyses of chromosome variations between low-grade  and high-grade gliomas in Chinese population. We found out the differences in chromosomes, cytobands, genes, pathways and GO functions.

overall_design: To identify the glioma tissue-specific genomic alterations and compare the genomic variations between low-grade and high-grade gliomas.

first: Yunbo

last: Li


title: Gene expression in Escherichia coli treated with human PGRP, gentamicin, and CCCP

status: Public on Jul 25 2014

city: Gary

first: Roman

last: Dziarski

address: 3400 Broadway

institute: Indiana University School of Medicine-Northwest

summary:
Human Peptidoglycan Recognition Proteins (PGRPs) kill bacteria, likely by over-activating stress responses in bacteria. To gain insight into the mechanism of PGRP killing of Escherichia coli and bacterial defense against PGRP killing, gene expression in E. coli treated with a control protein (bovine serum albumin, BSA), human recombinant PGRP (PGLYRP4), gentamicin (aminoglycoside antibiotic), and CCCP (membrane potential decoupler) were compared. Each treatment induced unique and somewhat overlapping pattern of gene expression. PGRP highly increased expression of genes for oxidative and disulfide stress, detoxification and efflux of Cu, As, and Zn, repair of damaged proteins and DNA, methionine and histidine synthesis, energy generation, and Fe-S clusters repair. PGRP also caused marked decrease in the expression of genes for Fe uptake and motility.
Gene expression microarray in E. coli exposed to a human bactericidal innate immunity protein, PGRP, showed induction of oxidative stress response and defense genes, with different expression pattern than E. coli exposed to an aminoglycoside antibiotic and a membrane potential decoupler.

overall_design: E. coli was treated with PGRP (human recombinant PGLYRP4), gentamicin, or CCCP (carbonyl cyanide 3-chlorophenylhydrazone). RNA was obtained from each culture and assayed for gene expression using whole genome Affymetrix E. coli Genome 2.0 Array. Each experiment was repeated 3 times.

first: Des

last: Kashyap

first: Dipika

last: Gupta


title: Integrated miRNA-mRNA analysis revealing the potential roles of miRNAs in chordomas

status: Public on Mar 29 2014

city: Beijing, China

first: zhongjun

last: Liu

state: Beijing

address: 49 North Garden Rd, Haidian, 100191, Beijing, China.

department: Department of Orthopedics

institute: Peking University Third Hospital

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

summary:
Emerging evidence suggests that microRNAs (miRNAs) are crucially involved in tumorigenesis and that paired expression profiles of miRNAs and mRNAs can be used to identify functional miRNA-target relationships with high precision.However, no studies have applied integrated analysis to miRNA and mRNA profiles in chordomas.
The purpose of this study was to provide insights into the pathogenesis of chordomas by using this integrated analysis method

platform_organism:
Homo sapiens
synthetic construct

overall_design: Differentially expressed miRNAs and mRNAs of chordomas (n = 3) and notochord tissues (n = 3) were analyzed by using microarrays with hierarchical clustering analysis. Subsequently, the target genes of the differentially expressed miRNAs were predicted and overlapped with the differentially expressed mRNAs. Then, GO and pathway analyses were performed for the intersecting genes

first: Cheng

last: Long

first: Liang

last: Jiang

first: Feng

last: Wei

first: Chuan

last: Ma

first: Hua

last: Zhou

first: Shaomin

last: Yang

first: Xiaoguang

first: Zhongjun


title: Cytokine stimulation systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates.

status: Public on Aug 31 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Background: The recent emergence of a novel coronavirus in the Middle East (designated MERS-CoV) is a reminder of the zoonotic potential of coronaviruses and the severe disease these etiologic agents can cause in humans. Clinical features of Middle East respiratory syndrome (MERS) include severe acute pneumonia and renal failure that is highly reminiscent of severe acute respiratory syndrome (SARS) caused by SARS-CoV. The host response is a key component of highly pathogenic respiratory virus infection. Here, we computationally analyzed gene expression changes in a human airway epithelial cell line infected with two genetically distinct MERS-CoV strains obtained from human patients, MERS-CoV-EMC (designated EMC) and MERS-CoV-London (designated LoCoV).   Results: Using topological techniques, such as persistence homology and filtered clustering, we characterized the host response system to the different MERS-CoVs, with LoCoV inducing early kinetic changes, between 3 and 12 hours post infection, compared to EMC. Robust transcriptional changes distinguished the two MERS-CoV strains predominantly at the late time points. Combining statistical analysis of infection and cytokine-stimulated treatment transcriptomics, we identified differential innate and pro-inflammatory responses between the two virus strains, including up-regulation of extracellular remodeling genes following LoCoV infection and differential pro-inflammatory responses between the two strains.   Conclusions: These transcriptional differences may be the result of amino acid differences in viral proteins known to modulate innate immunity against MERS infection.

overall_design: Triplicate wells of Calu-3 2B4 cells were infected with Human Coronavirus EMC 2012 (HCoV-EMC) or time-matched mock infected.  Cells were harvested at 0, 3, 7, 12, 18 and 24 hours post-infection (hpi), RNA extracted and transcriptomics analyzed by microarray.

first: Christian

last: Selinger

first: Jennifer

last: Tisoncik-Go

first: Vineet

last: Menachery

first: Jean

last: Chang

first: Victoria

last: Carter

first: Chris

last: Williams

first: Pavel

last: Sova

first: Ralph

middle: S

last: Baric


title: Transcriptional response of virus-infected cassava and identification of putative sources of resistance for cassava brown streak disease

status: Public on Apr 03 2014

city: Chatham Maritime

first: sophie

last: BOUVAINE

state: kent

address: Central Avenue

institute: Natural resources Institute

summary: Analysis of transcriptional response of virus-infected cassava and identification of putative sources of resistance for cassava brown streak disease

overall_design: transcriptome analysis of two varieties of cassava that differ in their level of resistance to cassava brown streak virus.

first: M

last: Maruthi

last: Bouvaine

first: Hale

middle: A

last: Tufan

first: I

middle: U

last: Mohammed

first: R

last: Hillocks


title: The novel NLR-related protein NWD1 is associated with prostate cancer progression and impacts androgen receptor signaling.

status: Public on Mar 07 2014

city: La Jolla

first: Roy

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: Characterization of NWD1; a novel NLR-related protein and further correlate it as a putative Prostate Cancer marker.  NLRs (NACHT and Leucine Rich Repeat domain containing proteins) constitute a major subfamily of innate immunity proteins  mostly acting as cytosolic pattern recognition receptors (PRRs), involved in the detection of cytoplasmic pathogen-associated molecular patterns (PAMPs) and endogenous danger signals. The recognition of the signals initiates a variety of host defense pathways through the activation of NF-kappaB, stress kinases, interferon response factors (IRFs) and/or inflammatory caspases. Despite the importance in host immune response, deregulation on NLR activities has been described in a variety of maladies, including chronic inflammation and cancer predisposition. For instance, NOD1 was one of the first NLR members shown to possibly play a role in tumorigenesis, since NOD1 stimulation induces apoptosis in MCF-7 breast carcinoma cells, and NOD1-/- MCF-7 cells generate larger tumors after injection in SCID mice. Mice deficient in NLR member NLRP3, and/or its interacting partners ASC or caspase-1, are also shown to be more susceptible to colitis-associated cancer (CAC). Polymorphisms along NLR genes NOD1 and NOD2 have also been correlated with altered cancer risk. NOD1 SNPs have been associated with gastric cancer, lymphoma, ovarian, prostate, and lung cancer due to the recognition of H. pylori (etiologic agent in gastric cancer and MALT lymphoma), C. trachomatis (putative etiologic agent in ovarian cancer), P. acnes (possible causative agent in PCa) and C. pneumonia (plausible etiological agent in lung cancer) as NOD1 ligands. Particularly, NOD1 and NOD2 have been shown to be fully operative in prostate epithelial cells and, in cooperation with TLRs, may elicit immune response during PCa progression.

overall_design: To access a tissue-specific gene expression profile for NWD1, quantitative PCR analysis was performed using a normalized cDNA panel derived from 48 human tissues (TissueScan Tissue qPCR Array, Origene). Two apparently independent expression patterns were detected, respectively related to neurological related organs (brain, pituitary and retina) and male reproductive system (prostate, epididymis and testis), where the highest mRNA levels was observed in prostate tissue. Results were confirmed using a second set of NWD1-specific qPCR primers (data not shown). Moreover, a similar expression pattern was virtually observed using the SAGE database from the Cancer Genome Anatomy Project (CGAP) of the National Cancer Institute (not shown).  Comparative gene expression microarray data was analyzed systematically by Ingenuity Pathway Analysis (IPA) to set up potential networks based on NWD1 regulated genes. The eventual participation of NWD1 in signaling transduction pathways was further examined by microarray analysis (Human WG-6v3 Expression BeadChip, Illumina) comparing the expression profile of PPC-1 cells lacking NWD1 expression (sh184 & sh3922) versus control cells  (shGFP). According to the differential expression profile that was generated and analyzed by the Ingenuity PathwaysTM software (IPA version 7.1, Ingenuity Systems), NWD1 is presumably associated with biological networks related, for instance, to tissue morphology, organogenesis, cancer and neurological diseases .

first: Ricardo

last: Correa

first: John

last: Reed


title: Expression data from muscle transcriptome of pigs on low protein and control diets

status: Public on Jan 31 2014

city: Dublin 15

first: Ruth

middle: Marie

last: Hamill

address: Teagasc Food Research Centre, Ashtown

department: Food Chemistry and Technology

country: Ireland

institute: Teagasc

summary:
The ratio of energy to protein in the finishing diet of growing pigs can impact on IMF content with consequences for pork quality. The objective of this study was to compare gene expression profiles of Musculus semimembranosus (SM) of animals divergent for IMF as a consequence of protein dietary restriction in an isocaloric diet. The animal model was derived through the imposition of low or high protein diets during the finisher stage in Duroc gilts.
RNA was extracted from post mortem SM tissue, processed and hybridised to Affymetrix porcine GeneChip® arrays.

overall_design: Eleven purebred Duroc gilts were blocked on the basis of initial body weight and assigned to one of two dietary treatments. High (HP) and low protein (LP) diets were formulated to contain 217 and 128 g/kg crude protein (CP) respectively. The HP and LP diets contained 13.0 and 7 g/kg of total lysine, respectively. Downward adjustment of CP was achieved by increasing the wheat:soyabean meal ratio. Diets were isocaloric, formulated to an estimated digestible energy (DE) density of 14 MJ/kg.


title: Rhizobium etli CFN42 wild type transcriptional profiling was compared between free living and symbiosis conditions

status: Public on Feb 03 2014

city: Cuernavaca

first: Sergio

middle: Manuel

last: Encarnación

state: Morelos

address: Av. Universidad S/N

department: Centro de Ciencias Genomicas

country: Mexico

institute: Universidad Nacional Autonoma de México

summary: Rhizobium etli is a bacteria that fix nitrogen in symbiotic activity with Phaseolus vulgaris, the common bean plant. In order to accomplish this nitrogen reduction a especial environment is induced in nodules such that gene expression of bacteroid suffer a significant change with respect to its wild type life style. With the purpose to identify genetic alterations between these physiological states, replicates of microarray data were accomplished in similar conditions between bacteria cultivated in free-life (succinate-ammonia) and those carrying on nitrogen fixation inside nodule.

overall_design: Three independent biological materials with one dyeswap were performed.

first: Osbaldo

last: Resendis-Antonio

first: Magdalena

last: Hernández

first: Emmanuel

last: Salazar

first: Sandra

last: Contreras

first: Gabriel

last: Martínez-Batallar

first: Yolanda

last: Mora


title: Remodeling of DNA transcription genomic fabric in Capridine-treated LNCaP human prostate cancer cell line

status: Public on Aug 27 2015

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Capridine is a chemotherapeutic agent with specificity towards prostate cancer and minimal bone marrow toxicity. Capridine structure is consistent with a classical DNA intercalating agent, although its DNA intercalation property does not fully correlate with its anti prostate cancer specific activity. We have used Agilent human gene expression arrays to identify the cellular targets of Capridine on androgen responsive LNCaP cells, a classical cell lines for prostate cancer studies. We found that expression of 142 unigenes genes was altered by Capridine. Interestingly, the most altered category was that of transcription regulators: 10 down and 16 upregulated. Our data confirm that, in addition to DNA intercalation, Capridine targets DNA transcription via histone modulation in a cell-specific manner.

overall_design: Two-conditions: LO = not treated, LA = Capridine-treated LNCaP cells. Four biological replicates of each condition. Differently labeled biological replicates were cohybridized with each array. Results of similarly labeled different conditions were compared then averaged for the two fluorescent labels. For instance: LO1 & LO3 were compared with LA1 & LA3, LO2 & LO4 were compared  with LA2 & + LA4, and the results of the comparisons averaged. This design uses 100% of the resources, has a better normlaiztion and allows all possible comparisons among the conditions.

first: Robert

last: Suriano

first: Priyanka

last: Mukherjee

first: Tanay

last: Gupta

first: Anvita

first: Sanda

middle: T

last: Fallon

first: Jan

last: Geliebter

first: Abraham

last: Mittelman

first: Raj

middle: K

last: Tiwari


title: The relationship between expression imbalance of adhesion molecules and asthma pathogenesis

status: Public on Feb 01 2014

city: Changsha

first: Yang

last: Xiang

state: Hunan

address: 110 Xiangya Road

department: Physiology

institute: Central South University

summary: Accumulated research has suggested the importance of the adhesion molecules modulation as therapeutic approach for bronchial asthma. Adhesion molecules expression alteration contributes to the pathogenesis of asthma. In order to probe the relationship between expression imbalance of adhesion molecules and asthma pathogenesis, expression profiling of adhesion molecules was performed using cDNA microarray. The results showed that there were various adhesion molecules with abnormal expressions in peripheral blood leucocytes of asthma patients.

overall_design: RNA was extracted from leucocytes in peripheral blood of 4 normal adults and 6 asthma patients by using TRIzol Reagent. Microarray expression studies were performed using the GEArray Q Series Human Extracellular Matrix & Adhesion Molecules Gene Array (SABiosciences Corporation, USA). This microarray profiles the expression of 96 genes key to the functions of cell adhesion. A negative control (PUC18DNA and blank), and the housekeeping genes including β-actin, GAPDH, Cyclophilin A and ribose body protein L13a were spread on each chip.

first: Xiaoqun

last: Qin


title: Real-time quantitative PCR analysis of human PBMCs from HCV+ patients and healthy donors

status: Public on Jan 28 2014

city: roma

first: antonella

last: minutolo

address: viale del policlinico

country: Italy

summary: Human livers biopsies from HCV+ patients and healthy donors were collected . RNA and Protein were extract  and The Human Adipogenesis RT² Profiler™ PCR Array was used to compare the gene expression in the two group. At the same time PBMCs were collected and the same array were used to compare the adipogenesis expression in the two system.

overall_design: qPCR gene expression profiling.  Fresh Livers from 40 HBV+ and 20 HD patients were used . Equal amount total RNA from each samples were used.

first: Antonella

last: Minutolo

first: Beatrice

last: Conti

first: Carmela

last: Viscomi

first: Grelli

last: Sandro

first: Clara

last: Balsano


title: Real-time quantitative PCR analysis of human PBMCS from HBV+ patients and healthy donors

summary: Human livers biopsies from HBV+ patients and healthy donors were collected . RNA and Protein were extract  and The Human Adipogenesis RT² Profiler™ PCR Array was used to compare the gene expression in the two group. At the same time PBMCs were collected and the same array were used to compare the adipogenesis expression in the two system.

overall_design: qPCR gene expression profiling.  PBMCs from 20 HBV+ and 20 HD patients were used . Equal amount total RNA from each samples were used


title: Real-time quantitative PCR analysis of human liver biopsies from HBV+ patients and healthy donors

overall_design: qPCR gene expression profiling.  Fresh Livers from 20 HBV+ and 20 HD patients were used . Equal amount total RNA from each samples were used.


title: Differential miRNA expression profiling of urinary exosomes from normo- and microalbuminuric type 1 diabetic patients

status: Public on Feb 14 2014

city: Turin

first: Gabriella

last: Gruden

address: C/so AM Dogliotti 14

department: Medical Science

institute: University of Turin

summary: The aim of this study was to compare miRNA expression in urinary exosomes from type 1 diabetic patients with and without incipient diabetic nephropathy. Overnight urine collections were obtained from normo- and microalbuminuric type 1 diabetic patients. Urines were pre-cleared by both centrifugation and filtration, urinary exosomes were isolated by two consecutive ultracentrifugation steps and total RNA extracted. Differential miRNA profiling was performed using a Human TaqMan miRNA Array A on an 7900HT Fast Real-Time PCR System. Results showed that expression of 22 urinary exosomal miRNAs differed  in incipient diabetic nephropathy.

overall_design: Differential qPCR miRNA profiling was performed on urinary exosomes from 2 pairs of micro/normoalbuminuric type 1 diabetic patients comparable for age, sex, diabetes duration, and tightly matched for HbA1c (1° pair: 8.1 vs. 8.1, 2° pair: 8.7 vs. 8.7). MiRNAs were considered differentially expressed if they exhibited greater than twofold expression differences in both pairs.

first: Federica

last: Barutta


title: Gene expression profiling of blood in ruptured intracranial aneurysms

status: Public on Jan 01 2014

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

summary: In the present study we aimed to investigate the systemic response to a rupture of intracranial aneurysms by an analysis of global gene expression profiles in peripheral blood cells. In addition, we sought to determine whether this approach could provide biomarkers related to clinical status of subarachnoid hemorrhage patients.

overall_design: Patients with subarachnoid hemorrhage from ruptured aneurysm were prospectively recruited from patients consecutively admitted to the Departments of Neurology or Neurosurgery and Neurotraumatology, University Hospital, Krakow, Poland in 2010 and 2011. Control subjects were recruited from patients of the Department of Neurology suffered from headaches.

first: Joanna

last: Pera

first: Michal

last: Korostynski


title: Real-time quantitative PCR analysis of human liver biopsies and PBMCs from HBV+ patients, HCV+ patients and healthy donors

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

overall_design: Refer to individual Series


title: Loss of soluble guanylate cyclase, the major nitric oxide receptor, leads to moyamoya and achalasia.

status: Public on Jun 19 2014

city: PARIS

first: Anne

last: Philippi

address: 10 avenue de Verdun

institute: INSERM

summary: Background: Moyamoya is a cerebrovascular condition of unknown mechanism characterized by a progressive stenosis of the terminal part of the internal carotid arteries (ICA) and the compensatory development of abnormal “moyamoya” vessels. It leads to ischemic and hemorrhagic stroke. We describe a novel autosomal recessive disease leading to severe moyamoya and early onset achalasia and report its cause in 3 unrelated families.  Methods: We used a combination of genetic linkage and exome sequencing in 2 consanguineous to identify rare shared variants. Sanger sequencing of GUCY1A3, the sole gene mutated in both families, was then conducted in the third family. Platelets from one of the patients and controls were used to carry out functional studies.  Results: Homozygous mutations of GUCY1A3 gene encoding the alpha1 subunit of soluble guanylate cyclase (sGC), the major receptor for Nitric Oxide (NO), were identified in all 3 families. Platelet analysis showed a complete loss of the mutated protein and showed an unexpected stimulatory role of sGC within platelets.   Conclusion: The NO/sGC/cGMP pathway is a major pathway controlling vascular smooth muscle (VSMC) relaxation, vascular tone and vascular remodeling. Our data suggest that alterations of this pathway may lead to an abnormal vascular remodeling process in sensitive vascular areas with low blood

overall_design: A total of 17 samples (8 affected and 9 unaffected) were used for this study. Linkage analysis was performed in a single informative consanguine family composed of 2 unaffected parents, 4 affected siblings and 3 unaffected siblings. Two affected samples in two different families were used for the exome sequencing analysis and results were compared to 20 control exomes (in-house exomes from IntegraGen, Evry, France) and 8 HapMap exomes. All samples were used for Sanger Sequencing confirmation.

first: Dominique

last: Hervé

first: Reda

last: Belbouab

first: Michel

last: Zerah

first: Stéphane

last: Chabrier

first: Francoise

last: Bergametti

first: Aurore

last: Essongue

first: Eliane

last: Berrou

first: Valérie

last: Krivosic

first: Christian

last: Sainte Rose

first: Emmanuel

middle: E

last: Houdart

first: Kareen

last: Billiem

first: Sabine

last: Roman

first: Frédéric

last: Adam

first: Marilyne

last: Lebret

first: Sandrine

last: Passemard

first: Gwenola

last: Boulday

first: Audrey

last: Delaforge

first: Stéphanie

last: Guey

first: Xavier

last: Dray

first: Hugues

last: Chabriat

first: Peter

last: Brouckaert

first: Maryjke

last: Bryckaert

first: Elisabeth

last: Tournier-Lasserve


title: Effect of LOX-PP on the gene expression profile of the A673 cell line (Ewing sarcoma)

status: Public on Dec 31 2013

city: MAJADAHONDA

first: Javier

last: Alonso

state: MADRID

address: CTRA. MAJADAHONDA-POZUELO KM 2

department: AREA DE GENÉTICA HUMANA

institute: INSTITUTO DE SALUD CARLOS III - IIER

summary: In this study we show that lysyl oxidase (LOX), an enzyme involved in maintaining structural integrity of the extracellular matrix, is expressed at low levels in Ewing sarcoma cells and primary tumors and is downregulated by the EWS/FLI1 oncoprotein characteristic of these tumors. Using a doxycycline inducible system to restore LOX expression in an Ewing sarcoma derived cell line, we show that LOX displays tumor suppressor activities. Interestingly, we show that the tumor suppressor activity resides in the propeptide domain of LOX (LOX-PP), an N-terminal domain produced by proteolytic cleavage during the physiological processing of LOX. Finally, we show that LOX-PP inhibits ERK/MAPK signalling pathway, and that many pathways involved in cell cycle progression were significant deregulated by LOX-PP, providing a mechanistic explanation to the cell proliferation inhibition observed upon LOX-PP expression. In summary, our observations indicate that deregulation of the LOX gene participates in Ewing sarcoma development and identify LOX-PP as a new therapeutic target for one of the most aggressive paediatric malignancies. These findings suggest that therapeutic strategies based in the administration of LOX propeptide or functional analogues could be useful in the treatment of this devastating paediatric cancer.

overall_design: A673 cells derived from Ewing sarcoma were genetically enginereed to express LOX-PP upon doxycycline stimulation (72 hours). Three independent experiments from control cells and three independent experiments from A673 cells expressing LOX-PP were done. Gene expression profile in A673 cells expressing LOX-PP vs control cells were compared.

first: N

last: Agra

first: F

last: Cidre

first: J


title: Expression data from a new lymphoid stromal population

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

summary:
Lymph node (LN) stromal cells provide survival signals and adhesive substrata to lymphocytes. During an immune response, B cell follicles enlarge, questioning how LN stromal cells manage these cellular demands. Herein, we used a murine fate mapping system to describe a new stromal cell type that resides in the T cell zone of resting LNs.
We used microarrays to detail the global programme of gene expression characterizing this new population of lymphoid stromal cells.

overall_design: Mice lymph nodes were collected and digested before cell sorting and RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of lymphoid stromal cells in order to increase expression profiles.

first: Marc

last: Bajénoff

first: Cyrille

last: Mionnet


title: Expression data for lymph node lymphatic endothelial cells and blood endothelial cells

status: Public on Dec 28 2013

city: Charlottesville

first: Stefan

last: Bekiranov

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry & Molecular Genetics

institute: University of Virginia

summary: Lymphatic endothelial cells (LEC) residing in lymph nodes (LN) have been shown to express genes normally restricted to one or a few tissues, termed peripheral tissue antigens (PTA). The expression of one of these PTA, tyrosinase, by LN-resident LEC has been shown to mediate peripheral T cell tolerance. We used a microarray approach to determine the gene expression profile of LN-resident LEC and blood endothelial cells as a comparison with the objective of determining the global PTA repertoire in these LN stromal populations.

overall_design: Skin draining and mesenteric lymph nodes were pooled from 6 week old adult C57BL/6 mice, minced, and enzymatically digested yielding single cell suspensions. Lymph node stromal cells were purified via CD45 magnetic bead negative selection and pure populations of lymphatic endothelial cells (LEC) and blood endothelial cells (BEC) were obtained via electronic cell sorting according to their expression of gp38 and CD31 (LEC: gp38+ CD31+, BEC: gp38- CD31+). Total RNA was extracted, amplified, and hybridized to Affymetrix microarrays. 3 paired independent samples of purified lymph node LEC and BEC were analyzed.

first: Cynthia

last: Guidi

first: Jarish

last: Cohen

first: Xiaojiang

last: Xu


title: Toxicogenomics and phenotypic characterization of adult female zebrafish liver treated with cadmium (II)

city: Singapore

first: Choong Yong

last: UNG

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

summary: We performed microarray-based expression profiling on liver of female zebrafish exposed to 30 µg/L of cadmium (II) chloride for 8-96 h, to identify global transcriptional programs and biological pathways involved in cadmium-induced adaptive responses under in vivo environment.

overall_design: We analyzed 10 arrays of Cadmium-treated adult female zebrafish liver and 12 arrays of control fish.

first: Choong

middle: Y

last: Ung

first: Siew

middle: H

last: Lam

first: Hlaing

last: Myintzu

first: Sinnakarupan

last: Mathavan

first: Zhiyuan

last: Gong


title: Toxicogenomics and phenotypic characterization of adult male zebrafish liver treated with cadmium (II)

summary: We performed microarray-based expression profiling on liver of male zebrafish exposed to 30 µg/L of cadmium (II) chloride for 8-96 h, to identify global transcriptional programs and biological pathways involved in cadmium-induced adaptive responses under in vivo environment.

overall_design: We analyzed 10 arrays of Cadmium-treated adult male zebrafish liver and 12 arrays of control fish.


title: A broad array of anticancer activities of the immunosuppressive drug mycophenolic acid (MPA) is suggested by pathway analyses of gene expression and validated by proteomic and functional assays

status: Public on Oct 28 2013

city: Augusta

first: Jin-Xiong

last: She

state: GA

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

summary: Gene expression microarray was performed to assess the global changes coupled to targeted validation of proteomic profiling to reveal the broad anticancer activities of the immunosuppressive drug Mycophenolic acid (MPA) and elucidate the molecular mechanisms underlying these activities.

overall_design: We conducted gene expression microarray experiments on AGS cancers cells treated with Mycophenolic acid (MPA). A concentration of 2ug/ml was selected to treat AGS cells and the treated cells were harvested at 0, 12, 24, 48 and 72 hours of culture with the drug.  Gene expression analyses were carried out using Illumina Human 12 Beadchips.

first: Boying

last: Dun

first: Ashok

last: Sharma

first: Yong

last: Teng

first: Haitao

last: Liu

first: Sharad

last: Purohit

first: Heng

first: Lingwen

last: Zeng

first: Jin


title: Toxicogenomics and phenotypic characterization of adult female and zebrafish liver treated with cadmium (II)


title: Dietary supplementation to a plant-based diet for Atlantic salmon

status: Public on Oct 31 2013

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: The study evaluated effects of dietary cholesterol (CH), taurocholate (TC), choline (CN) and taurine (TA)  in Atlantic salmon fed a plant based diet for 77 days. The additives did not affect growth or organ weights of Atlantic salmon, but promoted induction of cholesterol and plant sterol efflux in the intestine, whereas sterol uptake was suppressed. Microarray analyses in the liver indicated decreased cholesterol biosynthesis and enhanced conversion to bile acids. The marked effect of cholesterol on bile acid synthesis suggests that dietary cholesterol can be used to stimulate bile acid synthesis in fish. The study clearly demonstrated how Atlantic salmon adjusted metabolic functions in response to the dietary load of cholesterol, and has expanded our understanding of sterol metabolism and turnover that adds to the knowledge of these processes in fish. Feed supplementation with choline improved lipid absorption and suppressed abnormal accumulation of fat in the gut.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Atlantic salmon received feeds based on plant ingredients with (CH, TC, CN and TA) and without (K) supplementation. Liver samples were collected after 77 days. Five individuals from each group were analyzed with microarrays, pooled liver sample of salmon fed with commerical fish meal based feed was used as a reference.

first: Krasnov

last: Aleksei

first: Trond

last: Kortner


title: Effect of osteoblast-specific constitutive activation of beta-catenin or deletion of FoxO1 on gene expression in mice

status: Public on Jan 21 2014

city: New York

first: Stavroula

last: Kousteni

state: NY

address: 650 West 168th Street

department: Physiology and Cellular Biophysics

institute: Columnia University

summary: The gene expression of mice with osteoblast-specific beta-catenin activation or FoxO1 deactivation are each compared to that of Wt.

overall_design:
A. Wt mice (n=4)
B. Osteoblast specific beta-catenin constitutively expressed mice (n=3)
C. Osteoblast specific FoxO1 deleted mice  (n=3)

first: Aruna

last: Kode

first: Sanil

middle: J

last: Manavalan

first: Ioanna

last: Mosialou

first: Chozha

last: Rathinam

first: Govind

last: Bhagat

first: Murty

last: Vundavalli

first: Richard

last: Friedman

first: David

last: Pickard

first: Ronald

last: DePinho

first: Naomi

last: Galil

first: Azra

last: Raza

first: Siddhartha

last: Mukherjee

first: Julie

last: Teruya-Feldstein

first: Ellin

last: Berman


title: Progressive epigenetic changes in milk protein gene loci during functional differentiation of the mammary gland: ChIP-Seq part II

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: The role of chromatin in mammary gland development and differentiation has not been defined. Here we have studied the changes in chromatin conformation in the mammary gland during the lactation cycle at milk protein gene loci, whose gene expression marks functional differentiation of the mammary gland.

overall_design: histone modification patterns were studied using ChIP-seq in Lactating (day 8) mammary gland tissue, Mammary epithelial cells Isolated from 12 week virgin (diestrus) mammary gland tissue, and liver from 8 day lactating female.

first: Monique

last: Rijnkels


title: Genome-wide analysis of gene expression in mouse spleen stroma

status: Public on Nov 13 2013

city: Moscow

first: Marina

middle: Alekseevna

last: Afanasyeva

address: Vavilova 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, RAS

summary: Comparison between gene expression profiles of splenic stroma from wild type and lymphotoxin beta receptor knockout mice. The goal was to identify a set of genes which expression in splenic stroma is under lymphotoxin control and which can potentially be important for proper stroma development and function in secondary lymphoid organs.

overall_design:
Total RNA isolated from mechanically separated stroma and splenocytes of wild type and LTbR-KO mice, as well as cultured spleen stroma cells from wild type mice.
technical replicate - extract: A,B
technical replicate - extract: C,D
technical replicate - extract: E,F
technical replicate - extract: G,H

first: Lyudmila

middle: V

last: Britanova

first: Anna

last: Kuchmiy

first: Dmitry

last: Kuprash


title: Bovine mammary epithelial cells: control vs. stimulated by S. aureus or LPS

status: Public on Jan 11 2014

city: Castanet Tolosan

first: Rachel

last: Rupp

address: chemin de borde rouge

department: animal genetics

institute: INRA

summary:
Differential response of bovine mammary epithelial cells to Staphylococcus aureus or Escherichia coli agonists of the innate immune system.

Mastitis caused by Escherichia coli and Staphylococcus aureus is a major pathology of dairy cows. To better understand the differential response of the mammary gland to these two pathogens, we stimulated bovine mammary epithelial cells (bMEC) with either E. coli crude lipopolysaccharide (LPS) or with S. aureus culture supernatant (SaS) to compare the transcriptomic profiles of the initial bMEC response (3 and 6 h of exposure to agonists). By using HEK 293 cells transfected with human pattern recognition receptors, the LPS preparation was found to stimulate TLR2 and TLR4 but not TLR5, Nod1 or Nod2, whereas SaS stimulated TLR2. Biochemical analysis revealed that lipoteichoic acid, protein A and alpha-hemolysin were all present in SaS, and bMEC were found to be responsive to each of these molecules. Transcriptome profiling by a microarray and confirmation by RT-qPCR revealed an innate immune response which was common to both LPS and SaS. However, LPS induced expression of a significant higher number of genes and the fold changes were of greated magnitude than those induced by SaS. Overall, the analysis of microarray data suggests that the activation pathways and the early chemokine and cytokine production preceded the defense and stress responses. Chemokines were among the most up-regulated genes, in particular ELRCXC chemokines that target neutrophils. A major differential response was the activation of the type I IFN pathway by LPS but not by SaS. This was in accordance with the much stronger up-regulation of Cxcl10, Ccl5 and Nos2 by LPS than by SaS. The higher upregulation of chemokines that target mononuclear leucocytes (CXCL10, CCL2, CCL5 and CCL20) by LPS than by SaS is likely to be related to the differential activation of the type I IFN pathway, and could induce a different profile of the initial recruitment of leucocytes. It is noteworthy that at the protein level, secretion of TNF-alpha and IL-1-beta was not induced by either stimulus. These results suggest that the response of MEC to diffusible bacterial stimuli is able to contribute to the onset of the response with differential leucocyte recruitment but does not account directly for the differential production of major pro-inflammatory cytokines.

overall_design: Transcriptional profiling of bovine mammary epithelial cells (Holstein breed) comparing untreated control with mammary epithelial cells (MECs) stimulated by Staphylococcus aureus (SA) versus Escherichia coli lipopolysaccharide (LPS). 16 microarrays (2 stimuli * 2 times * quadruplicate) in a two-color dye-swap experimental design. Untreated cells served as the control. One replicate per array. Log2-intensity of each dye was analyzed separately => 32 samples.

first: Pascal

last: Rainard


title: Real-time quantitative PCR analysis of human liver biopsies from HCV+ patients and healthy donors

first: antonella

last: minutolo

summary: Human livers biopsies from HCV+ patients and healthy donors were collected . RNA and Protein were extract  and The Human Adipogenesis RT² Profiler™ PCR Array was used to compare the gene expression in the two group. At the same time PBMCs were collected and the same array were used to compare the adipogenesis expression in the two system.

overall_design: qPCR gene expression profiling.  Fresh Livers from 40 HBV+ and 20 HD patients were used . Equal amount total RNA from each samples were used.

first: Antonella

last: Minutolo

first: Beatrice

last: Conti

first: Carmela

last: Viscomi

first: Grelli

last: Sandro

first: Clara

last: Balsano


title: PAO1 gene expression at 22°C and 37°C in Lysogeny broth

first: Mariette

last: Barbier

address: 345 Crispell Drive

department: Microbiology, Immunology and Cancer Biology

summary: Pseudomonas aeruginosa strain PAO1 was grown at 22°C and 37°C in Lysogeny broth (LB) and RNA was hybridized on the Affymetrix P. aeruginosa chip.

overall_design: PAO1 was grown in triplicate in Lysogeny broth at 22°C or 37°C.  Total RNA from each sample was pooled and amplified then assayed in triplicate resulting in 6 total samples.

first: Piotr

last: Bielecki

first: Jacek

last: Puchałka

first: Vitor

last: Dos Santos

first: Roberts

last: Geffers

first: Sebastian

last: Albertí

first: Joanna

middle: B

last: Goldberg


title: CXCR4/YinYang1/Hsa-let-7a axis functions as tumor suppressor in acute myeloid leukemia

status: Public on Dec 01 2013

city: Columbus

first: Ramiro

last: Garzon

address: 460 12th street

institute: Ohio State University

summary: Surface expression of C-X-C chemokine receptor type 4 (CXCR4) in acute myeloid leukemia (AML) has been reported to be an independent prognostic factor for disease relapse and survival. We previously reported that targeting the stromal-derived factor 1α (SDF-1α)/CXCR4 axis could overcome resistance of AML cells to chemotherapy both in vitro and in vivo. To further explore the mechanism of targeting CXCR4, in the current study we focused on the regulation of microRNA. Microarray analysis revealed that the hsa-let-7a microRNA was down-regulated in OCI-AML3 cells by SDF-1α treatment and increased after CXCR4 inhibition. To further investigate the role of hsa-let-7a in leukemia biology, we overexpressed it in AML cell lines, which resulted in decreased Bcl-xL protein expression and consequently enhanced cell sensitivity to the chemotherapeutic agent cytarabine, both in vitro and in vivo. We also identified the transcription factor Yin Yang 1 (YY1) as a mediator that links the SDF-1α/CXCR4 axis with hsa-let-7a. Western blotting and immunocytochemistry demonstrated a correlation between YY1 and CXCR4 activation. ChIP assay confirmed the binding of YY1 to pri-let-7a DNA fragments. In primary AML samples (n=50), high CXCR4 surface expression was associated with low hsa-let-7a levels (r2=0.53). Improved effects of cytarabine treatment associated with greatly extended survival of human AML carrying mice was observed in primary human AML overexpressing hsa-let-7a. On the basis of these results, we propose that CXCR4 regulation of hsa-let-7a microRNA through YY1 and transcriptional silencing of the Bcl-xL protein together identifies a novel mechanism by which CXCR4 functions to induce chemoresistance in AML cells.

overall_design: MicroRNA expression profiling of OCI-AML3 cell lines treated with CXCR4 antagonist or SDF-1α. OCI-AML3 cells were treated with 100 ng/mL SDF-1α or 250 nM POL6326 (a CXCR4 antagonist, Allschwil, Switzerland), total RNA was extracted at specific time points (1, 2, 4, and 8 h), and miRNA expression profiling was performed

first: Ye

last: Chen

first: Rodrigo

last: Jacamo

first: Marina

last: Konopleva

first: Carlo

last: Croce

first: Michael

last: Andreeff


title: Expression of the IL-17/Th17 axis in the development of acute renal allograft rejection

city: Stanford

first: Silke

last: Roedder

address: 300 Pasteur Dr

department: Pediatric

institute: Stanford University

summary:
Genesets for the IL-17 pathway and Th17 T-helper cell subtype showed increasing enrichment in 33 pre-transplant donor biopsies and 33 matching post-transplant biopsies from patients with increasing Banff grades of acute rejection (no signficant abnormalities, n=17; borderline, n=4; ARIA, n=7; ARIB, n=6) in gene set analysis using SAM (GSA, FDR 0.5; 1000 permutations, log rank regression) for a total of 3307 publically available and manually curated gene-sets. 14 genes of the IL-17 pathway gene-set and 132 genes of the Th17 gene set segregated patients according to their histological diagnosis by unsupervised hierarchical clustering and principal component analysis.
This study demonstrates a significant role for the IL-17 pathway in the development of acute renal allograft rejection. Therapeutically targeting the IL-17 pathway presents a promising option in transplantation medicine and can be acchieved through drug reposittioning. Keywords: IL-17 pathway, drug repositioning, gene set enrichment analysis

overall_design: A total of 66 human renal allograft protocol biopsies were included in this study, 33 biopsies obtained at implantation prior to revascularization and 33 protocol biopsies obtained after transplantation. Whole genome expression profiles were assessed using microarrays.

first: Naoyuki

last: Kimura

first: Homare

last: Okamura

first: Yongquan

last: Fong

first: Robert

middle: C

last: Robbins

first: Minnie

middle: M

last: Sarwal

first: Mike

last: Fischbein


title: Single-cell RNA-seq of mouse cerebral cortex

status: Public on Feb 20 2015

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

summary: We have applied a recently developed, highly accurate and sensitive single-cell RNA-seq method (STRT/C1) to perform a molecular census of two regions of the mouse cerebral cortex: the somatosensory cortex and hippocampus CA1.

overall_design: We isolated cells fresh from somatosensory cortex (S1) and hippocampus CA1 area of juvenile (P22 - P32) CD1 mice, 33 males and 34 females. Cells were collected without selection, except that 116 cells were obtained by FACS from 5HT3a-BACEGFP transgenic mice. A total of 76 Fluidigm C1 runs were performed, each attempting 96 cell captures and resulting in 3005 high-quality single-cell cDNAs, containing Unique Molecular Identifiers allowing counting of individual mRNA molecules, even after PCR amplification.

first: Amit

last: Zeisel

first: Ana

last: Muñoz Manchado

first: Peter

last: Lönnerberg


title: Identification of dysregulated genes in 3D culture of BRIP1 knockdown cells

status: Public on Oct 21 2013

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

summary: To identify down-stream target genes of BRIP1 during acinar morphogenesis of human mammary epithelial cells, we carried out microarray analysis of BRIP1 knockdown cells.

overall_design: Changes in gene expression in 3D culture of non-target and BRIP1 shRNA-transduced cells were analyzed. Samples were harvested from three different clones of non-target and BRIP1 shRNA-transduced cells at three time points, 4, 8, and 12 days, after cell seeding in Matrigel.

first: Tatsuhiko

last: IMAOKA

first: Takamitsu

last: MORIOKA

first: Daisuke

last: IIZUKA

first: Mayumi

last: NISHIMURA

first: Yoshiya

last: SHIMADA


title: Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors

status: Public on Oct 24 2013

city: Oslo

first: Miriam

middle: Ragle

last: Aure

address: Ullernchauséen 70

department: Dept. of Cancer Genetics

institute: Oslo University Hospital Radiumhospitalet

summary:
Background: The global effect of copy number and epigenetic alterations on miRNA expression in cancer is poorly understood. In the present study, we integrate genome-wide copy number, DNA methylation and miRNA expression and identify genetic mechanisms underlying miRNA dysregulation in breast cancer.

Results: We identify 70 miRNAs whose expression was associated with aberrations in copy number or methylation, or both. Among these, five miRNA families are represented. Interestingly, the members of these families are encoded on different chromosomes and are complementarily altered by gain or hypomethylation across the patients. In an independent breast cancer cohort of 123 patients, 41 of the 70 miRNAs were confirmed with respect to aberration pattern and association to expression. In vitro functional experiments were performed in breast cancer cell lines with miRNA mimics to evaluate the phenotype of the replicated miRNAs. let-7e-3p, which in tumors is found associated with hypermethylation, is shown to induce apoptosis and reduce cell viability, and low let-7e-3p expression is associated with poorer prognosis. The overexpression of three other miRNAs associated with copy number gain, miR-21-3p, miR-148b-3p and miR-151a-5p, increases proliferation of breast cancer cell lines. In addition, miR-151a-5p enhances the levels of phosphorylated AKT protein.

Conclusions: Our data provide novel evidence of the mechanisms behind miRNA dysregulation in breast cancer. The study contributes to the understanding of how methylation and copy number aberrations influence miRNA expression, emphasizing miRNA functionality through redundant encoding, and suggests novel miRNAs important in breast cancer.

overall_design: The miRNA expression profiling of 149 breast cancer samples was performed using the 8x15k “Human miRNA Microarray Kit (V2)” with design id 019118 from Agilent (Agilent Technologies, Santa Clara, CA, USA). In brief, 100 ng total RNA was dephosphorylated, labeled and hybridized for 20 hours, following the manufacturer’s protocol. Scanning was performed on Agilent Scanner G2565A, signals were extracted using Feature Extraction v9.5 and the subsequent data processing was performed using the GeneSpring software v12.0 (Agilent Technologies). In brief, the miRNA signal intensities were log2-transformed and normalized to the 90th percentile, and miRNAs that were detected in less than 10% of the samples were excluded. This resulted in 448 unique mature miRNAs.

middle: R

first: Suvi-Katri

last: Leivonen

first: Thomas

last: Fleischer

first: Qian

last: Zhu

first: Jens

last: Overgaard

first: Jan

last: Alsner

first: Trine

last: Tramm

first: Riku

last: Louhimo

first: Grethe

middle: I

last: Alnæs

first: Merja

last: Perälä

first: Florence

last: Busato

first: Nizar

last: Touleimat

first: Jörg

last: Tost

first: Anne-Lise

last: Børresen-Dale

first: Sampsa

last: Hautaniemi

first: Olga

middle: G

last: Troyanskaya

first: Ole

last: Lingjærde

first: Kristine

last: Sahlberg

first: Vessela

middle: N

last: Kristensen


title: Mutant p53 attenuates the anti-tumorigenic activity of fibroblasts secreted interferon (IFN) beta

status: Public on Oct 10 2013

city: Rehovot

first: Shlomi

last: Madar

address: Hertzl

country: Israel

institute: Weizmann institute of science

summary: Mutations in the p53 tumor suppressor protein are highly frequent in tumors and often endow cells with tumorigenic capacities. We sought to examine a possible role for mutant p53 in the cross-talk between cancer cells and their surrounding stroma, which is a crucial factor affecting tumor outcome. Here we present a novel model which enables to individually monitor the response of cancer cells and stromal cells (fibroblasts) to co-culturing. We found that fibroblasts elicit the interferon beta (IFNβ) pathway when in contact with cancer cells, thereby inhibiting their migration. Mutant p53 in the tumor was able to alleviate this response via SOCS1 mediated inhibition of STAT1 phosphorylation. IFNβ on the other hand, reduced mutant p53 RNA levels by restricting its RNA stabilizer, WIG1. These data underscore mutant p53 oncogenic properties in the context of the tumor microenvironment and suggest that mutant p53 positive cancer patients might benefit from IFNβ treatment.

overall_design: As we planned to investigate the effect of mutant p53 we chose to work with lung cancer cells (H1299)  which are null for p53 expression and introduce them with two p53 ‘hotsopt’ mutations residing within the DNA binding domain namely R175H and R248Q (H1299175 and H1299248 respectively, Figure 1A and B). The cells were then labeled with a red fluorescent protein (dsRed), while lung CAFs (HK3-T) were labeled with a green fluorescent protein (GFP).  The labeled populations were co-cultivated for 24 hours and separated by Fluorescence Associated Cell Sorting (FACS) based on their specific fluorescent marker. RNA was extracted and samples were loaded on chips. Samples were loaded against a common reference sample which contained equal amount of RNA from all samples.

first: Shalom

first: Varda

last: Rotter


title: Affymetrix SNP array data for pulmonary adenocarcinomas with or without ALK fusion

city: Tokyo

first: Hironori

last: Ninomiya

address: 3-8-31 Ariake, Koutou ward

department: pathology

institute: The Japanese Foundation for Cancer Research

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

summary: ALK fusion positive tumor constitutes a unique entitiy in lung adenocarcionmas. We compared the allelokaryotypes of ALK fusion positive and negative tumors with SNP array to get insight into the difference of genomic background of them.

overall_design: Copy number analysis with Affymetrix 250K SNP arrays of 35 ALK fusion positive and 95 ALK fusion negative lung adenocarcinomas was performed with annonymous references.

first: Motohiro

last: Kato


title: Time dependent changes of gene expression in surgical specimen of colorectal cancer

status: Public on Sep 11 2013

first: Aya

last: Yamagishi

address: 1-1-5 Sendagi Bunkyo-ku

department: department of surgery

institute: Nippon medical school

summary: To investigate time-dependent changes the comprehensive gene expressions in colorectal normal and tumor surgical specimen within two hours.

overall_design: Both normal and tumor tissues were extracted at 0, 30, 60, 120 min after surgical removal in seven patients with locally advanced colorectal cancer and stabilized. RNA was extracted and calculated, time dependent changes of gene expression were examined by microarray data.

first: Satoshi

last: Matsumoto


title: RNA-seq for gastric cancer and normal tissues/cells

city: Daejeon

first: Seongmin

last: Park

address: 111 Gwahangno, Yuseong-gu

country: South Korea

institute: KRIBB

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed RNA-seq experiments to identify differentially expressed intergenic transcripts between gastric cancer and normal tissues/cells.

overall_design: Three primary cell culture samples from gastric cancer tissues, three gastric cancer cell lines and two normal tissue samples were used for the experiments.

first: Seong-Min

first: Hee-Jin

last: Kim

first: Tae-Wook

last: Kang

first: Seon-Young


title: Kindler syndrome microarray study

city: London

first: Charles

last: Mein

address: Charterhouse Square

department: Genome Centre

institute: Queen Mary University

summary: Characterization of gene expression profile of normal human and Kindler Syndrome (KS) patients skin biopsies samples, to extend the knowledge of transcriptional changes in the Kindler syndrome disease.

overall_design: For this micro array three age-, site - and sex-matched biopsies form control and Kindler Syndrome patients were analyzed.

first: Joey

last: Lai-Cheong

first: John

last: McGrath

middle: A

first: Rosamond

last: Nuamah


title: Gene expression profiling of A549 cells that undergo cell death

status: Public on Sep 16 2013

city: Pusan

first: Ho Sung

address: 30, Jangjeon-dong

department: Departmemt of Molecular Biology

institute: Pusan National University

summary: Gene expression profiling was analyzed using A549 cells that were treated with glucose deprivation (GD) or GD + phorbol-12-myristate-13-acetate (PMA).

overall_design: Gene expression levels were determined by comparing the gene expression of the experimental samples (GD or GD+PMA) with that of the control sample.

first: Ho

middle: S


title: MicroRNA expression data from muscle samples of the pig commercial herd Pix(DLxDE)

status: Public on Dec 08 2013

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary: In this study, we analyzed the miRNA expression pattern in muscle and constructed miRNA coexpression networks. Target of miRNA networks were enriched for biological pathways.

overall_design: 190 crossbred pig muscle samples were hybridized to Affymetrix miRNA arrays.

first: Siriluck

last: Ponsuksili


title: Comparison of gene expression (hESC, PGC-like cell from hESC, SSC from testis)

city: Seoul

first: LIM

last: JUNG JIN

address: 606-5 Yeoksam-dong, Gangnam-gu

department: Fertility Center of CHA Gangnam Medical Center

institute: CHA University

summary: Microarray analysis to identify the similarity of gene expression between ESC-derived PGC-like cells and testis-derived SSCs

overall_design: hESCs were differentated into PGC-like cell. And those cell campared with SSC from testis

first: Jung

last: Lim

first: Dong

last: Lee


title: Molecular Characterization of Heat Intolerance in Mice (microRNA data)

status: Public on Sep 01 2013

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

country: USA

institute: Children's National Medical Center

summary:
Prolonged exposure to high temperatures may cause heat-related illnesses, such as cramps, syncope, exhaustion or even stroke in some individuals.  Heat-related injuries remain a threat to the health and operational effectiveness of military personnel, athletes and the general public. Heat injury victims experience long-term complications that may include multi-system organ (liver, kidney, muscle) and neurologic damage, as well as reduced exercise capacity and heat intolerance.  Findings from our laboratory using a developed heat stress model show that about 1/3 of mice are heat-intolerant and vulnerable to heat injury even though they are from the same mice litter.
We examined if there is any genetic causation to this pattern of observation between the two groups of mice classified (Heat Intolerant and Heat Tolerant). We would like to screen Heat Tolerant and Heat Intolerant mice samples using microarray technology and examine their microRNA and mRNA for possible gene-specific differences between the two groups (6 mice per group). The results from this proposed animal research will help identify and select potential markers that can be used as a pre-screen to identify heat intolerance and assess heat injury recovery in humans.

overall_design: Heat-induced physiological and biochemical changes were assessed to determine heat tolerance levels in mice. We performed mRNA and microRNA expression profiling on mouse gastrocnemius muscle tissue samples to determine novel biological pathways associated with heat tolerance.

first: Aminul

last: Islam


title: Molecular Characterization of Heat Intolerance in Mice: microRNA (Affymetrix) and mRNA (Illumina) platforms

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Mining gene expression data for low doses of radiation and pollutants (dioxin, toluene, formaldehyde)

status: Public on Aug 30 2013

first: Anna

last: Kudravsteva

address: Vavilova, 32

institute: EIMB RAS

summary: Expression profiles of  Drosophila melanogaster in response to ionizing radiation, formaldehyde, toluene, and 2,3,7,8-tetrachlorodibenzo-p-dioxin.

overall_design: RNA-seq analysis on 25,415 transcripts to measure the change in gene expression in males and females separately. An analysis of the genes unique to each treatment yielded a list of genes as a gene expression signature. In the case of radiation exposure, both sexes exhibited a reproducible increase in their expression of the transcription factors  sugarbabe  and  tramtrack.

first: A

last: Moskalev

last: Kudryavtseva


title: Molecular Characterization of Heat Intolerance in Mice (mRNA data)


title: ZNF-mediated resistance to imatinib mesylate in gastrointestinal stromal tumor

status: Public on Aug 01 2013

city: Baltimore

first: Michael

middle: F

last: Ochs

state: MD

address: 550 North Broadway, Ste 1103

department: Oncology Biostatistics

institute: Johns Hopkins University

summary: siRNA knock-down of ZNF genes determined to impact gastrointestinal stromal tumor response to imatinib were used to determine functional significance of ZNFs and identify key targets related to imatinib resistance.

overall_design: exploratory array design to identify candidate effector genes for targeted study

first: Lori

last: Rink

first: Andrew

middle: K

last: Godwin