title: Affymetrix SNP 6.0 data for individuals with Trisomy 21 or Down syndrome

status: Public on Oct 24 2014

city: Atlanta

first: Michael

middle: Edward

last: Zwick

state: GA

address: 615 Michael Street, Suite 301

department: Human Genetics

institute: Emory University School of Medicine

summary: Individuals with Down syndrome (DS) are at an increased risk for developing congenital heart defects especially atrioventricular septal defects (AVSD). Our goal was to identify the contribution of copy number variants (CNV) to DS-associated AVSD. We used the Affymetrix SNP 6.0 genotyping platform to comprehensively characterize CNVs in 452 ethnically matched individuals with DS, comprising of 210 cases (DS + complete AVSD) and 242 controls with a structurally normal heart (DS + NH). Results from burden and region-wise analyses using PLINK revealed that despite the 2000 fold elevated risk, common CNVs of large effect (OR > 2.0) do not account for the increased risk observed in DS-associated AVSD. In contrast, cases do harbor a significantly elevated burden of large rare variants (> 100kb, < 1% frequency) (p < 0.01) and case deletions intersect genes more often than those observed in controls (p < 0.007). Gene enrichment analysis showed a trend for enrichment among deletions impacting the ciliome pathway in cases compared to controls. Our findings suggest that the etiology of AVSD is highly complex and does not arise from the action of a few common variants of large effect. Instead, our data support a multifactorial model, wherein large rare deletions play a significant role in elevating the risk of AVSD in a trisomic background.

overall_design: Copy Number Variation Analysis of individuals with DS using Affymetrix SNP 6.0 genotyping platform. A composite reference was generated using the same dataset to derive the log2 ratios using Affymetrix Power Tols (APT). Submitting here the preliminary data from 437 subjects, 15 were excluded due to privacy concerns.


title: Dynamic profile of gene expression in rice panicle of post-meiosis under high temperature

status: Public on Nov 27 2013

city: Changsha

first: Xianwen

last: Zhang

state: Hunan

address: 1 Nongda Road Furong district

country: China

institute: Hunan Agricultural University

summary: To comprehend the gene expression profile in rice panicle under high temperature, Agilent 4×44k rice oligo microarray experiments were carried out using rice panicle of post-meiosis at 0 min, 10min, 20 min, 60 min, and 2 hr after the treatment of 40 degree centigrade, and the differentially expressed genes at the time course were involved in binding, catalysis, stress response, and cellular process. The significantly expressed genes were mainly up-regulated. Among HR genes, the predominant transcription factor gene families were Hsf, NAC, AP2/ERF, WRKY, MYB, and C2H2. The MapMan analysis demonstrated that, under heat treatment, the HR genes were enriched in the pathways related to biotic stress, abiotic stress including heat and cold, and cell cycle and development, ubiquitin-proteasome , lipid and secondary metabolisms, which revealed the great importance of cross-talk and protein homeostasis in response to heat in rice panicle of post-meiosis.

overall_design: Heat shock induced gene expression in rice panicle of late developmental stage was measured at 0min, 10min, 20min, 60min, and 2hr after the treatment of 40 degree centigrade in plant growth chamber. Two independent replicate experiments were performed at each time point.

first: Hairong

last: Xiong

first: Ailing

last: Liu

first: Jianhua

last: Xiang

first: Xinbo

last: Chen


title: Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

status: Public on May 13 2015

city: Athens

first: Robert

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

country: USA

institute: University of Georgia

type: Methylation profiling by high throughput sequencing

summary: Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. We demonstrate that the dynamic interplay between forward and backward epimutations is modulated by genomic context and show that subtle contextual differences have profoundly shaped patterns of methylation diversity in A. thaliana natural populations over evolutionary timescales. Theoretical arguments indicate that the epimutation rates reported here are high enough to rapidly uncouple genetic from epigenetic variation, but low enough for new epialleles to sustain long-term selection responses. Our results provide new insights into methylome evolution and its population-level consequences.

overall_design: MethylC-seq of Arabidopsis thaliana


title: Effect of DEL1 on endothelial cell apoptosis

status: Public on May 05 2013

city: Stanford

first: Zhen

last: Wang

state: CA

address: Campus Drive

department: Surgery

institute: Stanford University

summary: We investigated the effect of angiogenic factor DEL1 on endothelial cell apoptosis. To understand the functional roles of DEL1, we utilized human cDNA microarrays as a global approach to identify its effect on endothelial gene expression.  The arrays contained ~42,000 elements representing 27,291 unique genes, and were produced at the Stanford Functional Genomic Facility (SFGF).

overall_design:
time series design
HUVECs were plated on DEL1- and BSA-coated surfaces, and allowed to grow for 12 and 24 hours; there were three repeats for 12h time point, and 4 repeats for 24h time point.


title: Genome-wide analysis of gene expression profiles in the Rotterdam Study III

status: Public on May 31 2013

city: ROTTERDAM

first: Marjolein

middle: J.

last: Peters

address: Wytemaweg 80

department: Internal Medicine

country: Netherlands

institute: Erasmus MC

summary: Gene expression profiles were compared to investigate age-marking differential gene expression.

overall_design: We obtained Whole blood RNA of 881 participants of the Rotterdam Study III.

first: Joyce

middle: B

last: van Meurs

first: Andre

middle: G

last: Uitterlinden

first: Albert

last: Hofman


title: Identification of a radiosensitive gene signature in gastric cancer cells using microarray analysis

status: Public on Jul 31 2012

city: Seoul

first: Han Sang

last: Kim

address: Shin chon dong

department: Internal medicine

country: South Korea

institute: Yonsei Cancer Center

summary: Prediction of response prior to radiotherapy is future direction of radiotherapy and identification of druggable targets in radiotherapy could overcome resistance. In order to identify a radiosensitive gene signature and elucidate relevant signaling pathways, microarrays using gastric cancer cells were analyzed before radiotherapy

overall_design: Oligonucleotide microarray was performed using twelve gastric cancer cells and a human oligo chip containing 22,740 oligonucleotide probes before radiation.

first: Sun

middle: Y

last: Rha

first: Han

middle: S

first: Sang

middle: C

first: Jae-Joon

last: Jung


title: Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU

status: Public on Apr 30 2012

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Ross Hardison mailto:rch8@psu.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

Rationale for the Mouse ENCODE project
Our knowledge of the function of genomic DNA sequences comes from three basic approaches. Genetics uses changes in behavior or structure of a cell or organism in response to changes in DNA sequence to infer function of the altered sequence. Biochemical approaches monitor states of histone modification, binding of specific transcription factors, accessibility to DNases and other epigenetic features along genomic DNA. In general, these are associated with gene activity, but the precise relationships remain to be established. The third approach is evolutionary, using comparisons among homologous DNA sequences to find segments that are evolving more slowly or more rapidly than expected given the local rate of neutral change. These are inferred to be under negative or positive selection, respectively, and we interpret these as DNA sequences needed for a preserved (negative selection) or adaptive (positive selection) function.
The ENCODE project aims to discover all the DNA sequences associated with various epigenetic features, with the reasonable expectation that these will also be functional (best tested by genetic methods). However, it is not clear how to relate these results with those from evolutionary analyses. The mouse ENCODE project aims to make this connection explicitly and with a moderate breadth. Assays identical to those being used in the ENCODE project are performed in cell types in mouse that are similar or homologous to those studied in the human project. Thus we will be able to discover which epigenetic features are conserved between mouse and human, and we can examine the extent to which these overlap with the DNA sequences under negative selection. The contribution of DNA that with a function preserved in mammals versus that with a function in only one species will be discovered. The results will have a significant impact on our understanding of the evolution of gene regulation.
Maps of Occupancy by Transcription Factors
Maps of occupancy of genomic DNA by transcription factors (TFs) are determined by ChIP-seq. This consists of two basic steps: chromatin immunoprecipitation (ChIP) is used to highly enrich genomic DNA for the segments bound by specific proteins (the antigens recognized by the antibodies) followed by massively parallel short read sequencing to tag the enriched DNA segments. Sequencing is done on the Illumina GAIIx and HiSeq. The sequence tags are mapped back to the mouse genome (Langmead et al. 2009), and a graph of the enrichment for TF binding are displayed as the "Signal" track (essentially the counts of mapped reads per interval) and the deduced probable binding sites from the MACS program (Zhang et al. 2008) are shown in the "Peaks" track. Each experiment is associated with an input signal, which represents the control condition where immunoprecipitation with non-specific immunoglobulin was performed in the same cell type. The sequence reads, quality scores, and alignment coordinates from these experiments are available for download.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell/mouse).
The chromatin immunoprecipitation followed published methods (Welch et al. 2004). Information on antibodies used is available via the hyperlinks in the "Select subtracks" menu. Samples passing initial quality thresholds (enrichment and depletion for positive and negative controls - if available - by quantitative PCR of ChIP material) are processed for library construction for Illumina sequencing, using the ChIP-seq Sample Preparation Kit purchased from Illumina. Starting with a 10 ng sample of ChIP DNA, DNA fragments were repaired to generate blunt ends and a single A nucleotide was added to each end. Double-stranded Illumina adaptors were ligated to the fragments. Ligation products were amplified by 18 cycles of PCR, and the DNA between 250-350 bp was gel purified. Completed libraries were quantified with Quant-iT dsDNA HS Assay Kit. The DNA library was sequenced on the Illumina Genome Analyzer II sequencing system, and more recently on the HiSeq. Cluster generation, linearization, blocking and sequencing primer reagents were provided in the Illumina Cluster Amplification kits. All samples are being determined as biological replicates except time course samples. The data displayed are from the pooled reads for all replicates, but individual replicates are available by download.
The resulting 36-nucleotide sequence reads (fastq files) were moved to a data library in Galaxy, and the tools implemented in Galaxy were used for further processing via workflows (Blankenberg et al. 2010). The reads were mapped to the mouse genome (mm9 assembly) using the program bowtie (Langmead et al. 2009), and the files of mapped reads for the ChIP sample and from the "input" control (no antibody) were processed by MACs (Zhang et al. 2008) to call peaks for occupancy by transcription factors, using the parameters mfold=15, bandwidth=125. Per-replicate aligments and sequences are available for download at downloads page (http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/).

first: Ross

last: Hardison

first: Mitchell

last: Weiss

first: Gerd

middle: A

last: Blobel

first: Stephan

last: Schuster

first: James

last: Taylor

first: Anton

last: Nekrutenko


title: Histone Modifications by ChIP-seq from ENCODE/PSU

status: Public on Jun 11 2012

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Ross Hardison mailto:rch8@psu.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

Rationale for the Mouse ENCODE project
Our knowledge of the function of genomic DNA sequences comes from three basic approaches. Genetics uses changes in behavior or structure of a cell or organism in response to changes in DNA sequence to infer function of the altered sequence. Biochemical approaches monitor states of histone modification, binding of specific transcription factors, accessibility to DNases and other epigenetic features along genomic DNA. In general, these are associated with gene activity, but the precise relationships remain to be established. The third approach is evolutionary, using comparisons among homologous DNA sequences to find segments that are evolving more slowly or more rapidly than expected given the local rate of neutral change. These are inferred to be under negative or positive selection, respectively, and we interpret these as DNA sequences needed for a preserved (negative selection) or adaptive (positive selection) function.
The ENCODE project aims to discover all the DNA sequences associated with various epigenetic features, with the reasonable expectation that these will also be functional (best tested by genetic methods). However, it is not clear how to relate these results with those from evolutionary analyses. The mouse ENCODE project aims to make this connection explicitly and with a moderate breadth. Assays identical to those being used in the ENCODE project are performed in cell types in mouse that are similar or homologous to those studied in the human project. Thus we will be able to discover which epigenetic features are conserved between mouse and human, and we can examine the extent to which these overlap with the DNA sequences under negative selection. The contribution of DNA that with a function preserved in mammals versus that with a function in only one species will be discovered. The results will have a significant impact on our understanding of the evolution of gene regulation.
Maps of histone modifications
Levels of three histone modifications are being determined. H3K4me1 (monomethylation of lysine 4 of histone H3) is a mark for active chromatin and in the absence of H3K4me3, it is one indicator of an enhancer. H3K4me3 (trimethylation of lysine 4 of histone H3) is highly enriched at active promoters. One repressive (Polycomb) mark, H3K27me3, is associated with some silenced genes. Maps of genomic DNA in chromatin with these histone modifications are generated by ChIP-seq. This consists of two basic steps: chromatin immunoprecipitation (ChIP) is used to highly enrich genomic DNA for the segments bound by specific proteins (the antigens recognized by the antibodies) followed by massively parallel short read sequencing to tag the enriched DNA segments. Sequencing is done on the Illumina GAIIx and HiSeq. The sequence tags are mapped back to the mouse genome (Langmead et al. 2009), and a graph of the enrichment for histone modifications are displayed as the "Signal" track (essentially the counts of mapped reads per interval) and the deduced probable binding sites from the MACS program (Zhang et al. 2008) are shown in the "Peaks" track. Each experiment is associated with an input signal, which represents the control condition where immunoprecipitation with non-specific immunoglobulin was performed in the same cell type. The sequence reads, quality scores, and alignment coordinates from these experiments are available for download.

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols.
The chromatin immunoprecipitation followed published methods (Welch et al. 2004). Information on antibodies used is available via the hyperlinks in the "Select subtracks" menu. Samples passing initial quality thresholds (enrichment and depletion for positive and negative controls - if available - by quantitative PCR of ChIP material) are processed for library construction for Illumina sequencing, using the ChIP-seq Sample Preparation Kit purchased from Illumina. Starting with a 10 ng sample of ChIP DNA, DNA fragments were repaired to generate blunt ends and a single A nucleotide was added to each end. Double-stranded Illumina adaptors were ligated to the fragments. Ligation products were amplified by 18 cycles of PCR, and the DNA between 250-350 bp was gel purified. Completed libraries were quantified with Quant-iT dsDNA HS Assay Kit. The DNA library was sequenced on the Illumina Genome Analyzer II sequencing system, and more recently on the HiSeq. Cluster generation, linearization, blocking and sequencing primer reagents were provided in the Illumina Cluster Amplification kits. All samples are being determined as biological replicates except time course samples. The data displayed are from the pooled reads for all replicates, but individual replicates are available by download.
The resulting 36-nucleotide sequence reads (fastq files) were moved to a data library in Galaxy, and the tools implemented in Galaxy were used for further processing via workflows (Blankenberg et al. 2010). The reads were mapped to the mouse genome (mm9 assembly) using the program bowtie (Langmead et al. 2009), and the files of mapped reads for the ChIP sample and from the "input" control (no antibody) were processed by MACs (Zhang et al. 2008) to call peaks for occupancy by transcription factors, using the parameters mfold=15, bandwidth=125. Because the signal for some histone modifications is not expected to be tightly localized (compared to a transcription factor), peak calling programs may not be appropriate. Thus in addition, we provide wiggle tracks with tag counts for every 10 bp segment. Per-replicate aligments and sequences are available for download at downloads page.


title: Gene Expression Profiles of both tumor and adjacent non-tumor liver Identify Hepatocellular Carcinoma Patients at High Risk of Recurrence after Curative Hepatectomy

status: Public on Mar 20 2012

first: Cheol-Keun

last: Park

address: 50 Irwon-dong Kangnam-gu

institute: Samsung Medical Center

summary:
Progression of hepatocellular carcinoma (HCC) often leads to vascular invasion and intrahepatic metastasis, which correlate with recurrence after surgical treatment and poor prognosis.
It is crucial to identify patients with a high risk of recurrence and develop more intensified or targeted treatment strategy to improve disease outcome.

overall_design: In the training set, tumor and non-tumor liver were profiled separately, and each was used to generate a prediction model which was validated with the use of independent validation set.


title: Gene expression profile in the developing and adult mouse cochlear sensory epithelia

status: Public on Jan 01 2012

city: Montpellier

first: Said

last: Assou

address: 80, Av. Augustin Flich

country: France

institute: INSERM

summary: To understand the molecular control of development and regeneration in the mammalian cochlear sensory epithelia, we performed a comparative study of gene expression patterns between postnatal day-3 (P3) and adult stages using a microarrays approach.

overall_design: Two inner ear development stages were used in this study, Post-natal day three and eight-week-old adult. A total number of sixty Swiss mice were exploited for each stage. The cochlear sensory epithelia (CSE) were collected from the inner ears and immediately placed in RNA later solution. A total of six independent dissection experiments were carried out separately in order to obtain three biological replicates for each stage. In each experiment, the CSE from 20 mice were pooled. Total RNA was purified from each biological sample separately using RNAeasy Mini Kit and the RNA integrity was assessed by the Nanodrop 2000

first: IBTIHEL

last: SMATI

first: SAID

last: ASSOU

first: ETIENNE

last: SAVARY

first: Saber

last: MASMOUDI

first: AZEL

last: ZINE


title: Real-time quantitative PCR analysis of Wnt signalling in human prostate cancer

status: Public on Nov 10 2011

city: Dublin

first: Antoinette

last: Perry

address: Room 2.15, Institute of Molecular Medicine, Trinity Centre, St. James's Hospital

department: Clinical Medicine

country: Ireland

institute: Trinity College Dublin

summary: A comprehensive expression analysis of Wnt signaling genes was performed in a panel of prostate cancer cell lines and tissue specimens using TaqMan low density arrays. The effect of DNA methylation on gene expression was investigated using DNMT inhibitor 5-Aza-CdR. Tissue specimens from a range of disease states were used to represent the stepwise progression of prostate cancer, including benign prostatic hyperplasia (BPH), histologically benign epithelium adjacent to tumor (HB), pre-invasive high-grade prostatic intraepithelial neoplasia (HGPIN) and primary localized tumors categorized into low- and high-grade disease. Fifteen Wnt signaling related genes were idenified with significantly altered expression in prostate cancer; the majority of which were upregulated in tumors. Notably, histologically benign tissue from men with prostate cancer appeared more similar to tumour (r=0.76) than to BPH (r=0.57) (P<0.001). Overall, the expression profile was highly similar between tumors of high (≥7) and low (≤6) Gleason scores. Pharmacological demethylation of PC-3 cells reactivated 38 genes (≥2-fold); 40% of which inhibit Wnt signaling.

overall_design: qPCR gene expression profiling using TLDA Human Wnt Gene set v1.0 microfluidic card (Applied Biosystems, Foster City, CA).The TLDA consisted of 4 identical 96-gene sets preconfigured in a 384-well format. Three different malignant cell lines were profiled LNCaP, 22Rv1 and PC3 (+/- 5-Aza-2’Deoxycytidine). One benign cell line was included for comparative puposes: PWR1E. Patient samples were obtained from FFPE tissue sections from men who underwent radical prostatectomy or transrectal resection of the prostate. To overcome the limited amount of RNA obtained from FFPE tissues, RNA samples were pooled. Five different pools were generated: high grade prostate cancer (Gleason score ≥7), low grade prostate cancer (Gleason score ≤6), HGPIN, HB and BPH. Each pool consisted of DNase-treated total RNA (100ng), isolated from microdissected tissue from 4 individual cases, selected on the basis of similar histological and clinical features and previous epigenetic characterization in our laboratory. Two Biological replicates for each pool were prepared. The high capacity cDNA Archive Kit (Applied Biosystems) was used to reverse transcribe pooled RNA (400ng). TaqMan® reactions were performed in duplicate on a 7900HT Sequence Detection System. RQ data from TLDAs were analyzed using Real Time StatMiner® v3.1 (Integromics, Granada, Spain).


title: Foxa1 Reduces Lipid Accumulation in Human Hepatocytes and Is Down-regulated in Nonalcoholic Fatty Liver (HepG2 data)

status: Public on Jul 07 2011

city: Valencia

first: RAMIRO

last: JOVER

address: Avenida Fernando Abril Martorell, 106.

department: Experimental Hepatology Unit

country: Spain

institute: IIS Hospital La Fe

summary:
Triglyceride accumulation in nonalcoholic fatty liver (NAFL) results from unbalanced lipid metabolism which, in the liver, is controlled by several transcription factors. The Foxa subfamily of winged helix/forkhead box (Fox) transcription factors comprises three members which play important roles in controlling both metabolism and homeostasis through the regulation of multiple target genes in the liver, pancreas and adipose tissue. In the mouse liver, Foxa2 is repressed by insulin and mediates fasting responses. Unlike Foxa2, however, the role of Foxa1 in the liver has not yet been investigated in detail. In this study, we evaluate the role of Foxa1 in two human liver cell models, primary cultured hepatocytes and HepG2 cells, by adenoviral infection. Moreover, human and rat livers were analyzed to determine Foxa1 regulation in NAFL. Results demonstrate that Foxa1 is a potent inhibitor of hepatic triglyceride synthesis, accumulation and secretion by repressing the expression of multiple target genes of these pathways (e.g., GPAM, DGAT2, MTP, APOB). Moreover, Foxa1 represses the fatty acid transporter FATP2 and lowers fatty acid uptake. Foxa1 also increases the breakdown of fatty acids by inducing HMGCS2 and ketone body synthesis. Finally, Foxa1 is able to largely up-regulate UCP1, thereby dissipating energy and consistently decreasing the mitochondria membrane potential. We also report that human and rat NAFL have a reduced Foxa1 expression, possibly through a protein kinase C-dependent pathway. We conclude that Foxa1 is an antisteatotic factor that coordinately tunes several lipid metabolism pathways to block triglyceride accumulation in hepatocytes. However, Foxa1 is down-regulated in human and rat NAFL and, therefore, increasing Foxa1 levels could protect from steatosis. Altogether, we suggest that Foxa1 could be a novel therapeutic target for NAFL disease and insulin resistance.

To determine the global impact of Foxa1 on human liver gene transcription, microarray expression analyses were performed in HepG2 cells transfected with Ad-Foxa1 or Ad-Control.

overall_design: We used microarrays to detail the global programme of gene expression in HepG2 cells infected with Ad-Foxa1 or control adenovirus (insertless Ad-pACC).

first: Marta

last: Moya

last: Benet

first: Carla

last: Guzmán

first: Laia

last: Tolosa

first: Carmelo

last: García-Monzón

first: Eugenia

last: Pareja

first: Jose

middle: V

last: Castell

first: Ramiro

last: Jover


title: Foxa1 Reduces Lipid Accumulation in Human Hepatocytes and Is Down-regulated in Nonalcoholic Fatty Liver

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

overall_design: Refer to individual Series


title: Foxa1 Reduces Lipid Accumulation in Human Hepatocytes and Is Down-regulated in Nonalcoholic Fatty Liver (hepatocytes data)

summary:
Triglyceride accumulation in nonalcoholic fatty liver (NAFL) results from unbalanced lipid metabolism which, in the liver, is controlled by several transcription factors. The Foxa subfamily of winged helix/forkhead box (Fox) transcription factors comprises three members which play important roles in controlling both metabolism and homeostasis through the regulation of multiple target genes in the liver, pancreas and adipose tissue. In the mouse liver, Foxa2 is repressed by insulin and mediates fasting responses. Unlike Foxa2, however, the role of Foxa1 in the liver has not yet been investigated in detail. In this study, we evaluate the role of Foxa1 in two human liver cell models, primary cultured hepatocytes and HepG2 cells, by adenoviral infection. Moreover, human and rat livers were analyzed to determine Foxa1 regulation in NAFL. Results demonstrate that Foxa1 is a potent inhibitor of hepatic triglyceride synthesis, accumulation and secretion by repressing the expression of multiple target genes of these pathways (e.g., GPAM, DGAT2, MTP, APOB). Moreover, Foxa1 represses the fatty acid transporter FATP2 and lowers fatty acid uptake. Foxa1 also increases the breakdown of fatty acids by inducing HMGCS2 and ketone body synthesis. Finally, Foxa1 is able to largely up-regulate UCP1, thereby dissipating energy and consistently decreasing the mitochondria membrane potential. We also report that human and rat NAFL have a reduced Foxa1 expression, possibly through a protein kinase C-dependent pathway. We conclude that Foxa1 is an antisteatotic factor that coordinately tunes several lipid metabolism pathways to block triglyceride accumulation in hepatocytes. However, Foxa1 is down-regulated in human and rat NAFL and, therefore, increasing Foxa1 levels could protect from steatosis. Altogether, we suggest that Foxa1 could be a novel therapeutic target for NAFL disease and insulin resistance.

To determine the global impact of Foxa1 on human liver gene transcription, microarray expression analyses were performed in human hepatocytes transfected with Ad-Foxa1 or Ad-Control.

overall_design: We used microarrays to detail the global programme of gene expression in human hepatocytes infected with Ad-Foxa1 or control adenovirus (insertless Ad-pACC).


title: Gene expression in a conditionally immortalized mouse podocyte cell line

status: Public on Aug 28 2010

city: Seattle

first: Shreeram

last: Akilesh

state: Washington

address: 1959 NE Pacific St, Box 356100

institute: University of Washington

summary: The specialized glomerular epithelial cell (podocyte) of the kidney is a complex cell that is often damaged in glomerular diseases. Study of this cell type is facilitated by an in vitro system of propagation of conditionally immortalized podocytes. Here, genes that are differentially expressed in this in vitro model of podocyte differentiation are evaluated.

overall_design: Conditionally immortalized undifferentiated mouse podocytes were cultured under permissive conditions at 33*C. Podocytes that were differentiated at the non-permissive conditions at 37*C were used for comparison.

first: Andrey

last: Shaw


title: mRNA profiling reveals divergent roles of PPARa and PPARß/d in regulating mouse liver gene expression (PPARa samples)

status: Public on Oct 12 2009

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary:
Little is known about the role of the transcription factor PPARß/d in liver. Here we set out to better elucidate the function of PPARß/d in liver by comparing the effect of PPARa and PPARß/d deletion using whole genome transcriptional profiling and analysis of plasma and liver metabolites. In fed state, the number of genes altered by PPARa and PPARß/d deletion was similar, whereas in fasted state the effect of PPARa deletion was much more pronounced, consistent with the pattern of gene expression of PPARa and PPARß/d. Minor overlap was found between PPARa- and PPARß/d-dependent gene regulation in liver. Pathways upregulated by PPARß/d deletion were connected to innate immunity. Pathways downregulated by PPARß/d deletion included lipoprotein metabolism and various pathways related to glucose utilization, which correlated with elevated plasma glucose and triglycerides and reduced plasma cholesterol in PPARß/d-/- mice. Downregulated genes that may underlie these metabolic alterations included Pklr, Fbp1, Apoa4, Vldlr, Lipg, and Pcsk9, which may represent novel PPARß/d target genes. In contrast to PPARa-/- mice, no changes in plasma FFA, plasma ß-hydroxybutyrate, liver triglycerides and liver glycogen were observed in PPARß/d-/- mice. Our data indicate a role for PPARß/d in hepatic glucose utilization and lipoprotein metabolism but not in the adaptive response to fasting.

Keywords: Analysis of target gene regulation by using microarrays

overall_design: Pure-bred Sv129 PPARα -/- mice and corresponding wildtype mice were used. Male mice (n=4-5 per group) were either fed or fasted for 24 hours. At the end of the experiment, mice were anaesthetized with a mixture of isofluorane (1.5%), nitrous oxide (70%) and oxygen (30%). Blood was collected by orbital puncture, after which the mice were sacrificed by cervical dislocation. Livers were dissected, snap frozen in liquid nitrogen and kept at -80ºC until further analysis. For RNA analyses, tissue from the same part of the liver lobe was used.

first: Linda

last: Sanderson

first: Mark

last: Boekschoten

first: Beatrice

last: Desvergne

first: Michael

last: Müller

first: Sander

last: Kersten


title: Molecular characterization of hybridoma subclones spontaneously switching at high frequencies in vitro

status: Public on Mar 23 2009

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

summary:
This is a comparative microarray analysis of  36-65 hybridomas switching at normal low frequencies in vitro vs. selected variants spontaneously switching at 100 fold higher frequencies in vitro.
This analysis reveals differential gene expression of 2091 unique probe sets, 1637 of them corresponded to known genes (647 of which were up-regulated and 990 down-regulated in the variants spontaneously switching at higher frequencies), including genes known to be involved in regular class switching (such as Cd40, Lig4, H2afx,Ung, Xrcc4, Tcfe2a, Id2, Apex1, Bcl6 and Prdm1) as well as genes involved in processes known to be necessary for regular class switch recombination (CSR), such as transcription, response to DNA damage and DNA repair, DNA binding, chromatin modifications, etc.

overall_design: Two subclones of each hybridoma switching at low (L) and high (H) frequencies were analyzed.

first: Maria

middle: D

last: Iglesias-Ussel

last: Zavadil

first: Mathew

last: Scharff


title: Podocytes use FcRn to clear IgG from the glomerular basement membrane

status: Public on Jan 01 2008

summary:
The glomerular filtration barrier prevents large serum proteins from being lost into the urine. It is not known, however, why the filter does not routinely clog with large proteins that enter the glomerular basement membrane (GBM). Here we provide evidence that an active transport mechanism exists to remove immunoglobulins that accumulate at the filtration barrier. We found that FcRn, an IgG and albumin transport receptor, is expressed in podocytes and functions to internalize IgG from the GBM. Mice lacking FcRn accumulated IgG in the GBM as they aged and tracer studies showed delayed clearance of IgG from the kidneys of FcRn deficient mice. Supporting a role for this pathway in disease, saturating the clearance mechanism potentiated the pathogenicity of nephrotoxic sera. These studies support the idea that podocytes play an active role in removing proteins from the GBM and suggest that genetic or acquired impairment of the clearance machinery is likely to be a common mechanism promoting glomerular diseases.
Keywords: Unique cell type expression analysis

overall_design:
Total RNA for genechip analysis was derived from two sources:
1) Primary mouse podocytes isolated by FACS sorting of collagenase digested glomeruli
2) In vitro differentiated conditionally immortalized mouse podocyte cell line.

After obtaining genechip data, the expression of various IgG and albumin receptors was queried in the genechip data and then confirmed by RT-PCR.

first: Tobias

last: Huber

first: Hui

last: Wu

first: Gary

last: Wang

first: Bjorn

last: Hartleben

first: Jeffrey

last: Kopp

middle: H

last: Miner

first: Emil

middle: R

last: Unanue


title: PPAR Controls Gene Expression in MSC Cells

status: Public on Jan 15 2009

city: Bar Harbor

first: Keith

last: Shockley

state: ME

address: 600 Main Street

department: Computational and Systems Biology

institute: The Jackson Laboratory

summary:
Rosiglitazone (Rosi), a member of the thiazolidinedione class of drugs used to treat type 2 diabetes, activates the adipocyte-specific transcription factor peroxisome proliferator-activated receptor gamma (PPARg). This activation causes bone loss in animals and humans, at least in part due to suppression of osteoblast differentiation from marrow mesenchymal stem cells (MSC). In order to identify mechanisms by which PPARg2 suppresses osteoblastogenesis and promotes adipogenesis in MSC, we have analyzed the PPARg2 transcriptome in response to Rosi. A total of 4,252 transcriptional changes resulted when Rosi (1 uM) was applied to the U-33 marrow stromal cell line, stably transfected with PPARg2 (U-33/g2), as compared to non-induced U-33/g2 cells. Differences between U-33/g2 and U-33 cells stably transfected with empty vector (U-33/c) comprised 7,928 transcriptional changes, independent of Rosi. Cell type-, time- and treatment-specific gene clustering uncovered distinct patterns of PPARg2 transcriptional control of MSC lineage commitment. The earliest changes accompanying Rosi activation of PPARg2 included adjustments in morphogenesis, Wnt signaling, and immune responses, as well as sustained induction of lipid metabolism. Expression signatures influenced by longer exposure to Rosi provided evidence for distinct mechanisms governing the repression of osteogenesis and stimulation of adipogenesis. Our results suggest interactions that could lead to the identification of a “master” regulatory scheme controlling osteoblast differentiation.
Keywords: rosiglitazone, PPARgamma, microarray, time course, gene expression, stem cells

overall_design: U-33/g2 and U-33/c cells were cultured in the presence or absence of Rosi and gene expression was monitored at three different time points (2, 24, 72h) after exposure to the agonist. Each time point corresponds to a separate stage of Rosi-treated U-33/g2 cell conversion from the osteoblast-like phenotype to the adipocyte-like phenotype and includes induction (2h), intermediate alterations in phenotype progression (24h), and a terminally differentiated adipocytic with completely suppressed osteoblastic phenotype (72h). The experiment is a full factorial design performed in replicate.

first: Oxana

middle: P

last: Lazarenko

first: Piotr

last: Czernik

first: Clifford

last: Rosen

last: Churchill

first: Beata

last: Lecka-Czernik


title: Gene expression data from hippocampus, striatum, hypothalamus cortex, Drd2-MSNs and Drd1-MSNs in mice

status: Public on Dec 10 2009

city: New York

first: Anne

last: Schaefer

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Goal of the experiment: Analysis of gene expression changes in the cortex, striatum, hippocampus, hypothalamus, Drd2-MSNs and Drd1-MSNs of mice with a postnatal, neuron-specific ablation of GLP or G9a as compared to control mice.

overall_design: For microarray analysis, hippocampus, hypothalamus, cortex and striatum of Camk2a-Cre; GLPfl/fl, Camk2a-Cre; G9afl/fl and age (10-14 week old) and sex matched littermate controls were used for total RNA purification. Four biological replicates were performed for each experiment. Polyribosome associated mRNAs from five, age (10-14 week old) and sex matched Drd1-Cre; Drd1-bacTRAP; G9afl/fl, or Drd2-Cre; Drd2-bacTRAP; G9afl/fl and Drd1-bacTRAP; G9afl/fl or Drd2-bacTRAP; G9afl/fl control mice were used. Three biological replicates were performed for each experiment.

first: Srihari

last: Sampath

first: Adam

last: Intrator

first: Alice

last: Min

first: Tracy

last: Gertler

first: D

last: Surmeier

first: Alexander

last: Tarakhovsky

first: Paul

last: Greengard


title: MiRNA Expression Profile Study Reveals a Prognostic Signature for Esophageal Squamous Cell Carcinoma

status: Public on Aug 01 2014

city: Beijing

first: Jiagen

last: Li

address: 17 Panjiayuannanli Chaoyang District

institute: Cancer Institute, CAMS

summary: Esophageal cancer is a highly malignant and prevalent cancer worldwide. Current TNM staging system is insufficient for prognosis of esophagus squamous cell carcinoma (ESCC) patients. The aim of this study is to evaluate miRNA expression profile of ESCC and identify a miRNA signature which robustly predict the survival of ESCC patients. MiRNA expression profiles of paired frozen tissues from 119 ESCC patients were assessed by microarray. After normalization of microarray data, the patients were randomly divided into a training set (n=60) and a test set (n=59). From the training set, we identified a four-miRNA prognostic signature (including hsa-miR-218-5p, hsa-miR-142-3p, hsa-miR-150-5p, and hsa-miR-205-5p) using random forest supervised classification algorithm and nearest shrunken centroid algorithm. This signature distinguished the patients into high-risk or low-risk groups whose overall survival differed significantly (5-year survival 7.4% vs. 66.7%, p<0.001). Prognostic value of this signature was validated in the test set (5-year survival 18.8% vs. 46.5%, p=0.025) and further in an independent cohort of 58 patients assessed by a different platform (5-year survival 11.4% vs. 56.7%, p=0.003). Furthermore, multivariable Cox regression analysis revealed that this signature is an independent prognostic factor for ESCC patients. Moreover, stratified analysis showed that this signature was able to predict survival within TNM stages. The expression level of the four miRNAs measured by microarray was verified by qRT-PCR and showed high level of positive correlation (Pearson correlation coefficient>0.75, p<0.001 for all). Our results suggest that the four-miRNA signature can serve as a reliable biomarker to predict the survival of ESCC patients.

overall_design: the miRNA expression profiles of cancer and adjacent normal tissues form 119 ESCC patients were used to identify a miRNA signature that can perdict the survival of ESCC patients.

first: Zhaoli

last: Chen

first: Liqing

last: Tian


title: Transcription profiling of Esophageal tumor Samples

status: Public on Feb 09 2008

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary:
Esophageal cancer is among the 10 most common malignancies and ranks as the 6th leading cause of death from cancer. It constitutes 7% of all gastrointestinal cancers and is one of the most lethal of all cancers. The large variation in the incidence of esophageal cancer in different geographic regions has often been thought to be due to variation in exposure to environmental factors; however, hereditary factors may also contribute to the variation in rates. A positive family history was found to be associated with an increased risk of esophageal cancer in several case-control and cohort studies in China. Familial aggregation also has been observed in Iran and Japan. The cancer data generated from six hospital based cancer registries in India under National Cancer Registry Programme (NCRP, Annual Report, 2003-2004) has revealed that the occurrence of esophageal cancer in Assam is highest in India. The aggregation of esophageal cancer in families is a long-observed and well-documented phenomenon in Assam of North-east part of India (AAR=32.6). In Assam high incidence of esophageal cancer with familial aggregation need investigation for etiology. The etiology of esophageal cancer in Northeast Indian population is different from other population at India due to wide variations in dietary habits or nutritional factors, tobacco chewing and alcohol habits.
With in these high-risk regions, studies have shown a strong tendency toward familial aggregation, suggesting that genetic susceptibility, in conjunction with potential environmental exposures, may be involved in the etiology of esophageal cancer. Familial clustering of cancer has been one of the main avenues to the understanding of cancer etiology and the signal to the involvement of heritable genes. Familial clustering of cancer may be due to environmental factors shared by family members or due to shared genes. However, the familial aggregation of esophageal cancer among the population in northeast India may reflect the influence of environmental factors operating on individuals who are already genetically susceptible. Epidemiological studies indicate that tobacco smoking and alcohol consumption are the major factors for esophageal cancer, the role  of genetic factors for familial aggregation has not been elucidated.
In this study, tumor and matched normal tissue from esophageal squamous cell carcinoma patients with a family history of upper gastrointestinal cancer were analyzed using cDNA microarray containing 10,000genes to evaluate gene expression differences in esophageal squamous cell carcinoma patients with a family history of upper gastrointestinal cancer from a high- risk area in India. To identify alteration in genes and molecular functional pathways in esophageal cancer in a high incidence region of India where there is wide spread use of tobacco and betel quid with fermented areca nuts and familial aggregation cancer.
Keywords: Gene Expression

overall_design: Low RNA Input Fluorescent Linear Amplification Kit (Agilent, Santa Clara, CA) was used for labeling. Briefly, both first and second strand cDNA were synthesized by incubating 500ng of total RNA with 1.2ul of oligo dT-T7 Promoter Primer in nuclease-free water at 65 ◦C for 10 min followed by incubation with 4.0ul of 5× First strand buffer, 2ul of 0.1M DTT, 1 ul of 10mM dNTP mix, 1ul of 200 U/ul MMLV-RT, and 0.5ul of 40U/ul RNaseOUT, at 40 ◦C for 2 hour. Immediately following cDNA synthesis, the reaction mixture was incubated with 2.4 ul of 10 mM Cyanine-3-CTP or 2.4 ul of 10 mM Cyanine-5-CTP (Perkin-Elmer, Boston, MA), 20ul of 4X Transcription buffer, 8 ul of NTP mixture, 6 ul of 0.1M DTT, 0.5 ul of RNaseOUT, 0.6ul of Inorganic pyrophosphatase, 0.8 ul of T7 RNA polymerase, and 15.3ul of nuclease-free water at 40 ◦C for 2 hour. Qiagen’s RNeasy mini spin columns were used for purifying amplified aRNA samples. The quantity and specific activity of cRNA was determined by using NanoDrop ND-1000 UV-VIS Spectrophotometer version3.2.1. Samples with specific activity >8 were used for hybridization. 825ng of each Cyanine 3 or Cyanine 5 labeled cRNA in a volume of 41.8ul were combined with 11ul of 10x Blocking agent and 2.2ul of 25x Fragmentation buffer (Agilent), and incubated at 60deg C for 30 minutes in dark. The fragmented cRNA were mixed with 55ul of 2x Hybridization Buffer (Agilent). About 110ul of the resulting mixture was applied to the Microarray and hybridized at 65degC for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer II for 37C. Slides were finally rinsed with Acetonitrile for cleaning up and drying. Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol. The data was analysed by GeneSpring GX and Biointerpreter software from Genotypic Technology, Bangalore. The differential expression was considered if the Log 2 mean of at least -1 for the down regulated genes and +1 for the upregulated genes. We considered only the genes that were reproducible from all replicates.

first: Indranil

last: Chattopadhyay

first: Vasudevan

last: Madavan

first: Sujala

last: Kapur

first: Sunita

last: Saxena


title: Omics analyses of B3 pre-B cell line from STATegra Project

status: Public on Feb 28 2017

first: Ana

last: Conesa

state: Valencia

address: C/ Eduardo Primo Yúfera 3

department: Computational Genomics Program

institute: Centro de Investigaciones Príncipe Felipe (CIPF)

type: Non-coding RNA profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing