title: Whole blood transcriptome during acute phase of infecion in avirulent and virulent Plasmodium chabaudi chabaudi infection

status: Public on Feb 01 2017

city: London

first: Jingwen

last: Lin

address: The Ridgeway

institute: The Francis Crick Institute

summary:
Analysis of blood samples taken throughout the acute phase of infection from mice infected with avirulent P. chabaudi AS strain or virulent CB strain
The influence of parasite genetic factors on immune responses and development of severe pathology of malaria is largely unknown. In this study, we performed genome-wide transcriptomic profiling of whole blood during blood-stage infections of two strains of the rodent malaria parasite Plasmodium chabaudi that differ in virulence. We identified several transcriptomic signatures associated with the virulent infection, including signatures for lung inflammation, stronger and prolonged anemia and platelet aggregation. The latter two signatures were detected prior to pathology. The anemia signature indicated deregulation of host erythropoiesis, and the lung inflammation signature was linked to increased neutrophil infiltration, more cell death and greater parasite sequestration in the lungs. This comparative whole-blood transcriptomics profiling of virulent and avirulent malaria infections shows the validity of this approach to inform severity of malarial infection and provide insight into pathogenic mechanisms.

overall_design: Blood samples collected from infected C57BL/6 mice via cardiac puncture into Tempus solution at 2, 4, 6, 8, (9), 10, 12 days post infection. Naïve samples were collected from age matched mice at the beginning (day 0) and the end (day 12) of the experiment. 3-4 replicates per conditon

first: Jing-wen

first: Jan

last: Sodenkamp

first: Deirdre

last: Cunningham

first: Katrien

last: Deroost

first: Tshibuayi

middle: C

last: Tshitenge

first: Sarah

last: McLaughlin

first: Tracey

last: Lamb

first: Bradley

last: Spencer-Dene

first: Caroline

last: Hosking

first: Jai

last: Ramesar

first: Chris

last: Janse

first: Christine

last: Graham

first: Anne

last: O’Garra

first: Jean

last: Langhorne


title: Brain gene expression data from High Drinking in the Dark (HDID) and HS/Npt control mice

status: Public on Jan 10 2017

city: Austin

first: Laura

last: Ferguson

state: TX

address: 1601 Trinity St Bldg. B, Rm 5.222

department: Waggoner Center for Alcohol and Addiction Research

country: USA

institute: Dell Medical School, University of Texas at Austin

summary:
Alcohol Use Disorder (AUD) is a complex psychiatric disorder with strong genetic as well as environmental risk factors. One risk factor for developing AUD is binge drinking. High Drinking in the Dark mice (HDID-1) have been selectively bred from genetically heterogeneous mice (HS/Npt stock) for attaining high blood alcohol concentrations (BAC) after a 4-hour drinking session in which a single bottle containing 20% ethanol is available and serve as a genetic model of binge drinking. To discover molecular mechanisms underlying the genetic predisposition to binge drinking, we characterized global gene expression in 7 brain regions across the addiction neurocircuit, precisely excised using laser capture microdissection from male, ethanol-naive HDID-1 and control mice
Brain regions included in the analysis are prefrontal cortex (PFC), nucleus accumbens core (AcbC), nucleus accumbens shell (AcbSh), bed nucleus of the stria terminalis (BNST), basolateral amygdala (BLA), central amygdala (CeA), and ventral tegmental area (VTA)

overall_design: Total RNA obtained from 7 brain areas implicated in addiction processes of male naïve HDID mice were compared to the same brain areas of male naïve HS/Npt control mice

first: Igor

last: Ponomarev


title: Dynamic regulation of chromatin signatures during Drosophila embryonic glial differentiation [ChIP-Seq]

status: Public on Nov 20 2016

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

country: China

institute: Shanghai Jiao Tong University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Employ affinity purification approach to capture different stages of glial-specific information on gene expression, nucleosome occupancy and histone modifications (HMs) in Drosophila melanogaster embryo

overall_design: Cell type-specific nucleosome and histone modification maps were generated from GBs and glias nuclei, which isolated from 5–7h-old gcm-Gal4,UAS-mCDGFP/cyo;UAS-3xFLAG-blrp-mCherry-RanGap and 12–14h-old repo-Gal4,UAS-3xFLAG-blrp-mCherry-RanGap/Tm3B D. melanogaster embryos by the method INTACT (Steinner et al., 2012). We determinated nucleosome occupancy in these nuclei by micrococcal nuclease sequencing (MNase-Seq). We also performed ChIP-Seq (chromatin immunoprecipitation and sequencing) for five histone modifications (H3K4me3, H3K4me1,H3K9ac, H3K27ac, and H3K27me3). Sequencing was performed on Illumina HiSeq 2000 using signle end protocol.

first: Cizong

last: Jiang


title: Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Longissimus Thoracis and subcutaneous fat transcriptome study in lambs

status: Public on Dec 12 2016

city: Zaragoza

last: González

address: Av. Montañana 930

country: Spain

institute: Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA)

summary: Feeding animals with either concentrates supplemented with vitamin E or alfalfa grazing has been proven to reduce the oxidative process that occurs in meat products. Indoor-kept lambs were fed a standard concentrate (n=7, C) or concentrate supplemented with vitamin E (n=7, VE) for 30 days before slaughtering all animals at 22–24 kg of live weight. Simultaneously, 7 unweaned lambs grazed in alfalfa paddocks (ALF) with their dams. Global transcriptomic data of longissimus thoracis (LT) muscle and subcutaneous fat (SF) with the Affymetrix® Ovine Gene 1.1 microarray was used. In LT muscle when ALF group was compared with C group, were identified 41 genes differentially expressed. Among these genes 32 were down- regulated and 9 were up- regulated. Meanwhile when VE treatment was compared with C group were identified a total of 29 genes, 26 were down- regulated and 3 genes were up- regulated. In SF when ALF treatment was compared with C, were identified only 4 genes differentially expressed, all of them up-regulated in ALF group. Meanwhile when VE treatment was compared with C group, were identified a total of 330 genes. Among them, 295 genes were up- regulated and 35 were down- regulated. In LT muscle the clusters corresponding to gene expression profiles from treatments ALF, C and VE were clearly separated from each other. In SF, ALF group, overlap with VE and C treatments, however, VE and C clearly were separate in different clusters. These differentially expressed genes were selected for a functional analysis by using DAVID. In LT muscle some of the identified significant biological processes were catabolic and lipid process (down-regulated, except CPT1B) (CPT1B, PLA2G16, SPSB1, LRTOMT, PLCD4, FBXO9, CNBP and CYP27A1) and muscle organ differentiation (down-regulated) (CPT1B, MYOD1, MYLK2 and MSTN) in ALF; whereas intracellular signaling cascade (IGF1R, DEF8, AKAP7 and CISH) was down-regulated. In SF, vitamin E supplementation had an important effect; most of the genes were up-regulated. DAVID analysis showed that biosynthesis lipid pathway was the most represented with 20 genes, such as EBP, MVD, CYP51A1, DHCR7, HMGCS1, LSS and FDFT1 implicated in cholesterol synthesis. Further exploration of the links between these genes and vitamin E will lead to a better understanding of how vitamin E affects the oxidative process that occurs in meat products.

overall_design: 21 male lambs were employed. 7 animals were fed basal concentrate, 7 animals were fed concentrate supplemented with 500 mg dl-α-tocopheryl acetate/kg concentrate and 7 animals grazed in alfalfa paddocks. Animals were slaughtered at 22-24 kg of live weight. Just after slaughter, a piece of Longissimus Thoracis muscle and a piece of subcutaneous fat were sampled from each animal.

first: Jorge

middle: H

last: Calvo


title: Circulating miRNAs in the maternal serum during early pregnancy in the pig

status: Public on Jun 23 2017

city: Olsztyn

first: Monika

middle: M

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

summary: Recently, microRNAs (miRNAs) have emerged as new players in the fine tuning of embryo development and implantation in mammals via posttranscriptional gene regulation mechanisms. There is also a growing body of evidence showing that miRNA profiles in body fluids may reflect biological processes taking place in the organism. Applying custom made multispecies arrays we aimed to analyze expression profile of circulating microRNAs in serum samples to answer the question whether some of the miRNAs found to be expressed in porcine embryos and trophoblasts or pregnant endometria could be detected in maternal serum.

platform_organism:
Homo sapiens
Sus scrofa
Bos taurus
Mus musculus

overall_design: miRNA expression profiles were analyzed in serum samples collected from pregnant and non-pregnant animals on Days 12, 16 and 20 of either pregnancy or the estrous cycle. Each group was represented by four samples.

first: Zaneta

middle: P

last: Reliszko


title: ChIP-seq from DOHH2 (ENCSR742WWB)

status: Public on Oct 14 2016

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos [ChIP-seq]

summary: Chromatin profiling of affinity-purified nuclei of neural stem cells (NSCs) and neurons from the Drosophila embryos, respectively.

overall_design: Cell type-specific nucleosome and histone modification maps were generated from NSCs and neurons nuclei, which isolated from 5–7h-old Sca-Gal4/cyo;UAS-3xFLAG-blrp-mCherry-RanGap and 12–14h-old Elav-Gal4;UAS-3xFLAG-blrp-mCherry-RanGap D. melanogaster embryos using the method INTACT (Steinner et al., 2012). We determinated nucleosome occupancy in these nuclei by micrococcal nuclease sequencing (MNase-Seq). We also performed ChIP-Seq (chromatin immunoprecipitation and sequencing) for five histone modifications (H3K4me3, H3K4me1,H3K9ac, H3K27ac, and H3K27me3). Sequencing was performed on Illumina HiSeq 2000 using signle end protocol.


title: Human Osteosarcoma Transcriptome

status: Public on Aug 26 2016

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Osteosarcoma (OS) is one of the most aggressive bone malignancy. Sub-optimal therapy has irretrievably compromised chances of survival of OS patients for years. Also lack of extensive research on this rare disease has hindered its therapeutic development. Cisplatin (CDDP) is an integral part of current treatment regime for OS. However, despite the proven benefits of CDDP, acquisition of resistance impedes therapy. Also, the molecular effects post CDDP insult in OS cells is poorly understood. Hence, we characterized molecular alterations associated with CDDP-exposure and resistance in OS cells. Resistance to CDDP in OS cells was developed and deep sequencing of mRNA was performed. It depicted an altered transcriptomic signature of resistant cells with enrichment of pathways regulating proliferation. Overall, a significant up-regulation of coding-RNAs and down-regulation of non-coding-RNAs were obtained. Further, analysis of immediate effect of CDDP-shock showed an increase in autophagy and JNK signaling, acting as a pro-survival strategy. Regulatory connections between MAPK signaling and autophagy favoring survival under CDDP-shock was elucidated. Taken together, this is the first study portraying not only global transcriptomic alterations in resistant OS cells but also showing key molecular changes associated with CDDP-insult in OS cells. Our results can be better utilized for future therapeutic benefit.

overall_design: We analyzed 5 samples, each being the representative of stages in the acquisition of chemoresistance. Control was the parental HOS cell line with which other comparisons are/will be made in future.

first: Rajdeep

last: Chowdhury

first: Sudeshna

last: Mukherjee

first: Jyothi

last: Nagraj

first: Madavan

last: Vasudevan

first: Sudhir

last: Jadhao

first: Gayatri

last: Mishra


title: Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos [RNA-seq]

summary: Expression profiles of affinity-purified nuclei of neural stem cells (NSCs) and neurons from the Drosophila embryos.

overall_design: Expression profiles were generated from NSC and neuron nuclei, which isolated from 5–7h-old Sca-Gal4/cyo;UAS-3xFLAG-blrp-mCherry-RanGap and 12–14h-old Elav-Gal4;UAS-3xFLAG-blrp-mCherry-RanGap D. melanogaster embryos using the method INTACT (Steinner et al., 2012). We examined the changes in gene expression during Drosophila embryonic neuron differentiation.


title: Next Generation Sequencing Facilitates Quantitative Analysis of HIV-1 Latency in Central Memory T Cells

status: Public on Nov 01 2016

city: Cambridge

first: Cory

middle: Haley

last: White

state: MA

address: 320 Bent St

department: DAGS

institute: Merck

summary:
Purpose: Next-generation sequencing (NGS) has become a powerful microscope to study cell models of HIV.  The goals of this study is to analyze latent HIV infection in the TCM  model of HIV latency described in Martins et al 2015 and to evaluate potential markers for HIV infection.
Methods: Peripheral blood mononuclear cells were collected from 4 healthy donors.  Naive CD4 T cells were isolated and utilized to generate a model of latent HIV infection.  During model generation, cells were sorted and collected for RNA extraction 10 days post infection along with their uninfected counterparts.  2 days after this, cells were activated with CD3/CD28 stimulation and collected for study for a total of 16 samples from 4 donors.  After cell collection, RNA was extracted from infected cells and their uninfected counterparts for deep sequencing by Expression Analysis. Sequence reads that passed quality filters were mapped using Tophat and counted using HTSeq.  In addition to human transcripts, we utilized 92 ERCC spikes as negative controls.  Any human gene which did not achieve at least 1 count per million reads in at least 4 samples or any ERCC that did not achieve at least 5 reads in at least 4 samples was discarded.  Differential expression for activated samples was not performed, but rather used to demonstrate upregulation of T-cell activation markers along with changing to the type and abundance of HIV transcripts produced.
Results: Using an custom built data analysis pipeline, 82 million reads per sample to the human genome (build hg38) and identified 13,534 human transcripts 67 ERCC spike in transcripts, and HIV NL43 transcripts were identified with the Tophat/HTSeq workflow. Differential expression analysis was performed between uninfected and latently infected cells.  826 genes were found to be differentially expressed, 275 downregulated and 551 upregulated (FDR < 0.05) with EdgeR.  GO and Pathway analysis of differential expressed genes revealed significant dysregulation of genes involved in the p53 signaling pathway.  Subsequent studies with pifithrin demonstrated a reduction in latently infected cell during model generation.
Conclusions: This study represents the first detailed analysis of HIV latency with this cell model using next generations sequencing.  These results demonstrate that the TCM model of HIV latency of Martins et al 2015 is truly reflective of HIV latency.  This study also provides a framework for which to analyze future cell models of HIV latency using next generation sequencing.  Finally, this work demonstrates that the p53 signaling pathway is a key pathway dysregulated in latency for this cell model with several genes dysregulated in HIV latency.

overall_design: TCM model of HIV latency mRNA profiles of 4 donors in 4 conditions were generated by deep sequencing by Expression Analysis.

first: Bastiaan

last: Moesker

first: Nadejda

last: Beliakova-Bethell

last: Martins

first: Celsa

middle: A

last: Spina

first: David

last: Margolis

first: Douglas

middle: D

last: Richman

first: Vicente

last: Planelles

first: Alberto

last: Bosque

first: Christopher

last: Woelk


title: ChIP-seq from DOHH2 (ENCSR052WRV)

first: ENCODE

last: DCC


title: Microarray analysis of human monocyte-derived macrophages stimulated with dexamethasone, interferon-gamma and dexamethasone/interferon-gamma

status: Public on May 30 2016

city: Cologne

first: Mario

last: Fabri

address: Kerpener Strasse 62

department: Dermatology

country: Germany

institute: University of Cologne

summary: Glucocorticoids are extensively used to treat inflammatory diseases, however their chronic intake increases the risk of mycobacterial infections. Meanwhile, the effects of glucocorticoids on innate host responses are incompletely understood. Here, we studied the direct effects of glucocorticoids on antimycobacterial host defense in primary human macrophages. We found that glucocorticoids triggered the expression of cathelicidin, an antimicrobial critical for antimycobacterial response, independent of the intracellular vitamin D metabolism. Despite upregulating cathelicidin, glucocorticoids failed to promote macrophage antimycobacterial activity. Gene expression profiles of human macrophages treated with glucocorticoids and/or IFN-gamma, which promotes induction of cathelicidin, as well as antimycobacterial activity, were investigated. Using weighted gene coexpression network analysis (WGCNA), we identified a module of highly connected genes that was strongly inversely correlated with glucocorticoid treatment and associated with IFN-gamma stimulation. This module was linked to the biological functions “autophagy”, “phagosome maturation” and “lytic vacuole/lysosome”, and contained the vacuolar H+-ATPase (v-ATPase) subunit a3, alias TCIRG1, a known antimycobacterial host defense gene, as a top hub gene. We next found that glucocorticoids, in contrast to IFN-gamma, failed to trigger expression and phagolysosome recruitment of TCIRG1, as well as to promote lysosome acidification. Finally, we demonstrated that the tyrosine kinase inhibitor imatinib induces lysosome acidification and antimicrobial activity in glucocorticoid-treated macrophages without reversing the anti-inflammatory effects of glucocorticoids. Taken together, we provide evidence that the induction of cathelicidin by glucocorticoids is not sufficient for macrophage antimicrobial activity, and identify the v-ATPase as a potential target for host-directed therapy in the context of glucocorticoid therapy.

overall_design: Peripheral blood mononuclear cells (PBMCs) of three healthy human donors were isolated by Ficoll-Paque (GE Healthcare). Monocytes were isolated via CD14+ MACS cell separation (Miltenyi Biotec) according to the manufacturers instructions. Monocyte-derived macrophages (MDMs) were prepared by culturing peripheral blood monocytes in RPMI media containing 10% FCS for four to seven days in the presence of M-CSF (50 ng/ml). Afterwards cells were cultured in fresh media with 10% vitamin D-sufficient human AB serum. Cells were stimulated with media, dexamethasone, interferon-gamma and dexamethasone/interferon-gamma for 20h. Total RNA of was isolated with TRIZOL (Life Technologies) and RNA quality was confirmed using micro capillary electrophoresis (2100 Bioanalyzer, Agilent). 100ng RNA was labeled and hybridized to Sureprint G3 human GE 8x60K whole genome mRNA microarray according to the manufacturer’s specifications. The arrays were scanned (Agilent G2595C scanner), data extracted and processed using the Genespring XII software (Agilent).

first: Bent

last: Brachvogel


title: ChIP-seq from DOHH2 (ENCSR350RYG)


title: Major differences between human atopic dermatitis and murine models as determined by global genomic profiling

status: Public on Jan 02 2017

city: Kongens Lyngby

first: David Adrian

last: Ewald

address: Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

type:
Expression profiling by array
Third-party reanalysis

summary:
In this study we applied genomic profiling to evaluate the transcriptomic differences between murine models ot atopic dermatitis.
We evaluated the expression data of five models and their respective controls, and one previously published murine dataset (GSE50400).
The included models were groupe 1 (Lesional: Flaky tail and FLG mutant; Control: C57BL/6NCrSlc), Group 2 (Lesional: NC/Nga(+mite); Control: NC/Nga(-mite)), Group 3 (Lesional: OVA-ODT 24h; Control: C57BL/6NCrSlc), and Group 4 (Lesional: OXA 2h; Control: BALB/c,Acetone).

overall_design: Expression profiles for mice with five murine models were contrasted to their respective controls.

first: Mayte

last: Suárez-Fariñas

first: Thomas

middle: W

last: Litman


title: Acute loss of TET function results in aggressive myeloid cancer in mice

status: Public on Nov 26 2015

city: La Jolla

first: Anjana

last: Rao

address: 9420 Athena Circle

department: Signaling and Gene Epression

institute: La Jolla institute

type: Methylation profiling by high throughput sequencing


title: Systematic mapping of functional enhancer-promoter connections with CRISPR interference

status: Public on Nov 11 2016

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

institute: Stanford University

summary: Gene expression in mammals is regulated by noncoding elements that can impact physiology and disease, yet the functions and target genes of most noncoding elements remain unknown. We present a high-throughput approach that uses CRISPR interference (CRISPRi) to discover regulatory elements and identify their target genes. We assess >1 megabase (Mb) of sequence in the vicinity of 2 essential transcription factors, MYC and GATA1, and identify 9 distal enhancers that control gene expression and cellular proliferation. Quantitative features of chromatin state and chromosome conformation distinguish the 7 enhancers that regulate MYC from other elements that do not, suggesting a strategy for predicting enhancer-promoter connectivity. This CRISPRi-based approach can be applied to dissect transcriptional networks and interpret the contributions of noncoding genetic variation to human disease.

overall_design: We examined the effects of using CRISPRi to inhibit a putative enhancer of GATA1, eHDAC6. We performed RNA sequencing on K562 cells expressing individual sgRNAs targeting the transcription start site of GATA1 (2 sgRNAs), eHDAC6 (2 sgRNAs) and non-targeting, negative controls (4 sgRNAs). We generated paired-end RNA sequencing libraries from 3 biological replicates for each sgRNA.

first: Charles

last: Fulco

first: Mathias

last: Munschauer

first: Rockwell

last: Anyoha

first: Glen

last: Munson

first: Sharon

middle: R

last: Grossman

first: Elizabeth

last: Perez

first: Michael

last: Kane

first: Brian

last: Cleary

first: Eric

middle: S

last: Lander


title: HLA peptides derived from tumor antigens induced by inhibition of DNA methylation for development of drug-facilitated immunotherapy

status: Public on Jul 19 2016

city: Haifa

first: Arie

last: Admon

state: select a state

address: Kiryat Technion- Emerson building

department: Department of Biology

country: Israel

institute: Technion - Israel Institute of Technology, Haifa, Israel

summary: Treatment of cancer cells with anti-cancer drugs often fails to achieve complete remission. Yet, such drug treatments may induce alteration in the tumor’s gene expression patterns, including those of Cancer/Testis Antigens (CTA). The degradation products of such antigens can be presented as HLA peptides on the surface of the tumor cells and be developed into anti-cancer immunotherapeutics. For example, the DNA methyl transferase inhibitor, 5-aza-2'-deoxycytidine (Decitabine) has limited anti-tumor efficacy, yet it induces the expression of many genes, including CTAs that are normally silenced in the healthy adult tissues. In this study, the presentation of many new HLA peptides derived from CTAs and induced by Decitabine was demonstrated in three human Glioblastoma cell lines. Such presentation of CTA-derived HLA peptides can be exploited for development of new treatment modalities, combining drug treatment with anti-CTA targeted immunotherapy. The Decitabine-induced HLA peptidomes include many CTAs that are not normally detected in healthy tissues or in cancer cells, unless treated with the drug. In addition, the study included large-scale analyses of the simultaneous effects of Decitabine on the transcriptomes, proteomes and HLA peptidomes of the human Glioblastoma cells. It demonstrates the poor correlations between these three levels of gene expression, both in their total levels and in their response to the drug.

overall_design: The transcriptomes, proteomes and HLA peptidomes of the U-87, T98G and LNT-229 GBM human cell lines were analyzed before and after treatment with Decitabine. Overall, the RNA-Seq transcriptome analyses resulted in the identification of above 26000 transcripts, the proteome analyses identified about 7500 proteins and the HLA class I peptidome analyses resulted in above 25000 identified HLA peptides. Two biological repetitions of the transcriptome, three of the proteome and three of the HLA peptidome were performed with each of the cell lines and treatment, resulting in highly reproducible datasets.

first: Bracha

last: Shraibman

first: Dganit

last: Kadosh

first: Eilon

last: Barnea


title: RNA-seq of porcine inner ear stria vascularis

status: Public on May 31 2016

city: Chongqing

first: Ting

middle: huan

last: zhang

address: Rongchang

institute: Chongqing Academy of Animal Science

summary: To clarify the effect of Mitf mutation on stria vascularis transcriptome and identify downstream-genes of Mitf pathway which responsible for hearing development, we employed high-throughput sequencing to analyze the transcriptome of MitfR/r and Mitfr/r stria vascularis.

overall_design: Compare the transcriptome difference between MITF mutated homozygous and heterozygous pigs.

first: Lei

last: Chen

first: Weiwei

last: Guo

first: Tinghuan

last: Zhang

first: Qianzi

last: Tang


title: Effects of long-term intake of RPS on gene expression in the colon and liver of pigs

status: Public on Jul 25 2015

city: Nanjing

first: Yong

last: Su

address: Weigang 1#

institute: Nanjing Agricultural University

summary: To investigate effects of long-term intake of RPS on gene expression in the colon and liver of pigs,thirty-six Duroc × Landrace × Large White growing barrows were randomly allocated to corn starch (CS) and RPS groups. Each group consisted of six replicates (pens), with three pigs per pen. Pigs in the CS group were offered a corn/soybean-based diet, while pigs in the RPS group were put on a diet in which 230 g/kg (growing period) or 280 g/kg (finishing period) purified corn starch was replaced with purified RPS during a 100-day trial. Liver transcriptomic results showed that the expression of CD36, CPT1B and ACADM was down-regulated, while AGPAT4, GPAT, FABP1 and FABP3 were up-regulated by the RPS diet, indicating a decrease in fatty acid intake and synthesis, and an increase in fatty acid oxidation and glycerophospholipid synthesis.Analysis of the colonic transcriptome profiles revealed that the RPS diet changed the colonic expression profile of the host genes mainly involved in immune response pathways. RPS significantly increased proinflammartory cytokine IL-1β gene expression and suppressed genes involved in lysosome.

overall_design: Thirty-six Duroc × Landrace × Large White growing barrows (70 days of age, 23.78 ± 1.87 kg) were randomly allocated to two groups, each group consisting of three pigs per pen, and six replicates. Pigs in the control group were offered a corn/soybean-based diet, while 230 g/kg purified corn starch (CS) was replaced with purified RPS in the RPS diet group. Diets were formulated according to the nutrient requirements of the National Research Council (1998). When animals reached the age of 120 days, diets were adapted to the nutrient requirements of the animals (finishing diet) and the amount of purified starch increased to 280 g of CS or RPS per kilogram of feed. Pigs had unlimited access to feed and water throughout the experimental period, which consisted of two 50-day trials in which the pigs consumed the growing diet (days 0-50) and finishing diet (days 51-100), respectively. On day 100, one pig from each replicate that met the target slaughter weight (105 to 110 kg) was slaughtered. The liver and colonic mucosa tissues were collected and preserved in liquid nitrogen for gene expression analysis.

first: Yue

last: Sun


title: IL-27 receptor signaling regulated stress hematopoiesis drives Abdominal Aortic Aneurysm development

status: Public on Oct 14 2019

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Abdominal Aortic Aneurysm (AAA) is a prevalent life-threatening disease, where aortic wall degradation is mediated by accumulated immune cells. Though cytokines regulate inflammation within the aorta, their contribution to AAA via distant alterations, particularly in the control of hematopoietic stem cell (HSC) differentiation remains poorly defined. Here we report a pathogenic role for the interleukin-27 receptor (IL-27R) in AAA as genetic ablation of IL-27R protects mice from the disease development, where the mitigation of AAA is associated with a blunted accumulation of myeloid cells in the aorta due to the attenuation of Ang II-induced HSC expansion. The loss of IL-27R engages transcriptional programs that promote HSCs quiescence and suppresses differentiation decreasing mature myeloid cell production and accumulation in the aorta.  Our studies illuminate how a prominent vascular disease can be distantly driven by cytokine dependent regulation of bone marrow precursors.

overall_design: RNA-seq for long-term progenitors (LT-HSC), short-term progenitors (ST-HSC) from   in Apoe-/-, Apoe-/-Il27ra+/- and Apoe-/-Il27ra-/- mice  treated with PBS or AngII

first: Ekaterina

middle: K

last: Koltsova

first: Iuliia

middle: O

last: Peshkova


title: Biomarkers for radiation-induced renal toxicity following 177Lu-octreotate administration in mice

status: Public on Aug 31 2015

city: Göteborg

first: Emil

last: Schüler

address: Gula stråket 2B

country: Sweden

institute: University of Gothenburg

summary: Transcriptomic profiling of normal mouse tissue and blood following 177Lu irradiation

overall_design: Total RNA was isolated from fresh-frozen tissue samples

first: Maria

last: Larsson

first: Toshima

middle: Z

last: Parris

first: Khalil

last: Helou

first: Eva

last: Forssell-Aronsson


title: Dynamic regulation of chromatin signatures during Drosophila embryonic glial differentiation [RNA-Seq]

first: Youqiong

last: Ye

summary: Expression profiles of affinity-purified nuclei of GBs and glias from the Drosophila embryos.

overall_design: Expression profiles were generated from GBs and glias nuclei, which isolated from5–7h-old gcm-Gal4,UAS-mCDGFP/cyo;UAS-3xFLAG-blrp-mCherry-RanGap and 12–14h-old repo-Gal4,UAS-3xFLAG-blrp-mCherry-RanGap/Tm3B D. melanogaster embryos using the method INTACT (Steinner et al., 2012). We profiled gene expression during Drosophila embryonic glial differentiation.

first: Cizong

last: Jiang


title: RNA sequencing of matched nephrectomy samples [RNA-seq]

status: Public on Jul 02 2015

city: Rochester

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

institute: Mayo Clinic

summary: To address the need to study frozen clinical specimens using next-generation RNA, DNA, chromatin immunoprecipitation (ChIP) sequencing and protein analyses, we developed a biobank work flow to prospectively collect biospecimens from patients with renal cell carcinoma (RCC). We describe our standard operating procedures and work flow to annotate pathologic results and clinical outcomes. We report quality control outcomes, nucleic acid yields of our RCC submissions (N=16) to The Cancer Genome Atlas (TCGA) project, as well as newer discovery platforms by describing mass spectrometry analysis of albumin oxidation in plasma and 6 ChIP sequencing libraries generated from nephrectomy specimens after histone H3 lysine 36 trimethylation (H3K36me3) immunoprecipitation. From June 1, 2010, through January 1, 2013, we enrolled 328 patients with RCC. Our mean (SD) TCGA RNA integrity numbers (RINs) were 8.1 (0.8) for papillary RCC, with a 12.5% overall rate of sample disqualification for RIN <7. Banked plasma had significantly less albumin oxidation (by mass spectrometry analysis) than plasma kept at 25°C (P<.001). For ChIP sequencing, the FastQC score for average read quality was at least 30 for 91-95% of paired-end reads. In parallel, we analyzed frozen tissue by RNA sequencing and after genome alignments, only 0.2-0.4% of total reads failed the default quality check steps of Bowtie2, which was comparable to the disqualification ratio (0.1%) of the 786-O RCC cell line, prepared under optimal RNA isolation conditions. The overall correlation coefficients for gene expression between the Mayo Clinic vs. TCGA tissues ranged from 0.75 to 0.82. These data support the generation of high-quality nucleic acids for genomic analyses from banked RCC. Importantly, the protocol does not interfere with routine clinical care. Collections over defined time points during disease treatment further enhance collaborative efforts to integrate genomic information with outcomes.

overall_design: Examination of RNA expression in ccRCC

first: Thai

last: Ho

first: Huihuang

last: Yan


title: A transcriptome-based classifier to identify developmental toxicants by stem cell testing: design, validation, and optimization for histone deacetylase inhibitors

status: Public on Jul 21 2015

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

summary: Test systems to identify developmental toxicants are urgently needed. A combination of human stem cell technology and transcriptome analysis was used here to provide proof-of-concept that toxicants with a related mode of action can be identified, and grouped for read-across. We chose a test system of developmental toxicity, related to the generation of neuroectoderm from pluripotent stem cells (UKN1), and exposed cells for six days to benchmark concentration (BMC) of histone deacetylase inhibitors (HDACi) valproic acid, trichostatin-A, vorinostat, belinostat, panobinostat and entinostat. To provide insight into their toxic action, we identified HDACi consensus genes, assigned them to superordinate biological processes, and mapped them to a human transcription factor network constructed from hundreds of transcriptome data sets. We also tested a heterogeneous group of ‘mercurials’ (methylmercury, thimerosal, mercury(II)chloride, mercury(II)bromide, 4-chloromercuribenzoic acid, phenylmercuric acid) (BMCs). Microarray data were compared at the highest non-cytotoxic concentration for all 12 toxicants. A support vector machine (SVM)-based classifier predicted all HDACi correctly. For validation, the classifier was applied to legacy data sets of HDACi, and for each exposure situation, the SVM predictions correlated with the developmental toxicity. Finally, optimization of the classifier based on 100 probe sets showed that eight genes (F2RL2, TFAP2B, EDNRA, FOXD3, SIX3, MT1E, ETS1, LHX2) are sufficient to separate HDACi from mercurials. Our data demonstrate, how human stem cells and transcriptome analysis can be combined for mechanistic grouping and prediction of toxicants. Extension of this concept to mechanisms beyond HDACi would allow prediction of human developmental toxicity hazard of unknown compounds with the UKN1 test system.

overall_design: We applied a test system (next referred as the UKN1 test system) of developmental toxicity, related to the generation of neuroectoderm from human embryonic stem cells (hESCs), and exposed cells for six days to the histone deacetylase inhibitors (HDACi) valproic acid, trichostatin-A, vorinostat, belinostat, panobinostat and entinostat, as well as to the mercurial compounds methylmercury, thimerosal, mercury(II)chloride, mercury(II)bromide, 4-chloromercuribenzoic acid and phenylmercuric acid. After 6 days, total RNA has been isolated and gene expression studies were performed applying the human Genome U133 plus 2.0 arrays. Untreated and vehicle controls (Ethanol and DMSO) have been also investigated. At least four independent experiments have been performed.

first: Marcel

last: Leist


title: HT-SuperSAGE of the gut tissue of a Vip3A-resistant Heliothis virescens F. (Lepidoptera: Noctuidae) strain provides insights into its evolution and toxin adaptation

status: Public on Aug 21 2015

city: Havana

first: Camilo

last: Ayra-Pardo

country: Cuba

institute: CIGB

summary: Summary: Multi-toxins Bt-crops carrying insecticidal toxins with similar host spectrum and different mode of action e.g. Cry and Vip, are expected to improve resistance management in target pests. Control failure has been informed for Cry toxins but not for Vip3A, of which no mechanism of resistance has yet been identified. Here we applied HT-SuperSAGE to analyze the transcriptome profiling in the midgut tissue of a tobacco budworm Heliothis virescens (F.) strain laboratory-selected for Vip3A resistance. A total of 1324252 26-bp tags were sequenced representing 17751 unique transcripts (UniTags) from genetically similar Vip3A-resistant (Vip-Sel) strain and susceptible control (Vip-Unsel) strain. Differential expression was found significant (≥ 2.5-fold or ≤ 0.4) for 1845 unigenes that constitute 10.4% of the total number of UniTags, where 277 represented overexpressed (OE) and 1568 underexpressed (UE) genes in Vip-Sel compared to Vip-Unsel. BLASTN searches mapped 1141 of these UniTags to H. virescens EST sequences, of which, 816 (143 OE and 673 UE) were unambiguously annotated to proteins in NCBI non-redundant protein databases. Gene ontology revealed Vip3A adaptation induced major constitutive transcriptional differences in serine-proteases (SP)-mediated proteolysis, ribosome biogenesis and metabolic processes. Several unigenes homologous to a particular member of the REsponse to PAThogen (REPAT) family were found to be predominantly OE. Since UniTags related to SP and ribosomal proteins (RP) were the most represented in the libraries, they were further analyzed in details. Interestingly, UniTags related to the putative Vip3A-binding protein RpS2 were underexpressed, while, the tumorigenesis suppressor RpL37 accounted for the 35% of total overexpressed RP. A subset of unigenes was chosen to confirm the HT-SuperSAGE data by qRT-PCR. The present study is the first providing a lepidopteran gut transcriptome associated with Vip3A resistance and a foundation for future attempts to elucidate the resistance mechanism.

overall_design: Methods: Midgut transcriptional profiles of third-instar larvae from genetically similar Vip3A-resistant (Vip-Sel) and susceptible control (Vip-Unsel) strains were generated by HT-SuperSAGE. RNA pools of Vip-Sel and Vip-Unsel samples (five RNA preparations each) were prepared and used for the construction of SuperSAGE libraries HvR_GCCT and HvS_GCAC, respectively, according to the procedure described by [Matsumura et al., 2010]. Purified PCR products were mixed and applied to Illumina Genome Analyzer II sequencing with GEX (DpnII) primer in the sequencing reactions as recommended by the manufacturer. Sorting of sequence reads based on index sequences and the subsequent extraction of sequence tags from reads was conducted using a script written in Perl. Fold-change for each tag was calculated as in [Gilardoni et al., 2010]. qRT–PCR validation was performed using TaqMan and SYBR Green assays.

first: Denis

last: Wright

first: Ben

last: Raymond

middle: E

last: Ochogavia

first: Lianet

last: Rodriguez-Cabrera

first: Ryohei

last: Terauchi

first: Kentaro

last: Yoshida

first: Hideo

last: Matsumura


title: RNA-seq analysis of flg22-induced gene expression changes in wild type, asr3-1 mutant and OX9 overexpression line

status: Public on Aug 26 2015

city: College Station

first: Libo

last: Shan

state: Texas

address: Norman Borlaug Center 136, TAMU2123

department: Department of Plant Pathology and Microbiology

institute: Texas A&M University

summary: The correlation coefficient (R) for the expression profile of all transcripts between WT and asr3-1, and between WT and OX9 without flg22 treatment is close to linear, suggesting that ASR3 does not affect general gene transcription. Hierarchical clustering analysis flg22-induced genes in any of the three genotypes suggested that the asr3-1 mutant displayed overall enhanced flg22 response whereas OX9 displayed overall reduced responses compared to WT plants.

overall_design: RNA-seq analysis was performed with 10-day-old seedlings of WT, asr3-1 and 35S:ASR3-HA transgenic line OX9 with or without 100 nM flg22 treatment for 30 min. Two independent repeats were performed for RNA-seq analysis. For each repeat, equal amount of RNA from two biological replicates was pooled for RNA-seq library construction. RNA-seq library preparation and sequencing were carried out on an Illumina HiSeq 2500 platform with 100 nt single end reads.

first: Bo

last: Li

first: Shan

first: Xiao

last: Yu

first: Cheng

last: Cheng

first: Sixue

last: Chen

first: Yanbing

first: Joshua

last: Yuan

first: Daohong

first: Ping

last: He


title: Transcriptional response of Streptococcus mutans in chemically defined medium (CDM) towards the autoinducers CSP and XIP

status: Public on Jun 01 2015

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

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

summary: S. mutans UA159 was cultivated in chemically defined medium. Changes in the transcriptome in response to the autoinducing peptides CSP and XIP were monitored for 30 minutes.

overall_design: Time series of Streptococcus mutans UA159 cultivated in CDM after treatment with CSP, XIP or uninduced. Time points: before treatment, 5, 15, 30 min after treatment. Two biological replicates

first: Michael

last: Reck

first: Irene

last: Wagner-Döbler


title: MicroRNA profiling of neurons generated using induced pluripotent stem cells derived from patients with schizophrenia and 22q11.2 deletion

status: Public on Aug 01 2015

city: ny

first: mingyan

last: lin

address: 1925 morris park ave

institute: aecom

type: Non-coding RNA profiling by high throughput sequencing

summary: We are using induced pluripotent stem cell (iPSC) technology to study neuropsychiatric disorders associated with 22q11.2 microdeletions (del), the most common known schizophrenia (SZ) -associated genetic factor. Several genes in the deleted region have been implicated; one of the more promising candidates is DGCR8, which codes for a protein involved in microRNA (miRNA) biogenesis. We carried out miRNA expression profiling (miRNA-seq) on neurons generated from iPSCs derived from controls and SZ patients with 22q11.2 del.

overall_design: miRNA profiling of 7 SZ samples and 9 Control samples derived from iPSCs

first: Mingyan

last: Lin

first: Herb

last: Lachman


title: Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells

status: Public on May 26 2015

city: Worcester

first: Troy

middle: W.

last: Whitfield

address: 55 Lake Ave. N.

institute: University of Massachusetts Medical School

summary: This study characterizes the genome-side occupancy of AML1, AML1-ETO and the cofactors N-CoR and p300 in leukemics cells (Kasumi-1) to discover novel regulatory mechanisms involving genes bound by the t(8:21) fusion protein AML1-ETO. A significant discovery of our study is the co-localization of AML1-ETO with the N-CoR co-repressor on genomic regions that are primarily distal to the transcriptional start sites (TSSs). These regions exhibit over-representation of the PU.1 motif: PU.1 is a key hematopoietic regulator and member of the ETS family of transcription factors.  Functionally, genes co-occupied by AML1-ETO and N-CoR (e.g., TYROBP and LAPTM5) are associated with the leukemic phenotype, as determined by analyses of gene ontology and by the observation that these genes are predominantly up-regulated upon AML1-ETO depletion. To further probe the regulatory context of these leukemic cells, genome-wide enrichment of the transcriptional initiation-associated histone modification H3K4me3 was also measured.

overall_design: Genome-wide study of transcription factor-DNA binding for AML1 (RUNX1) and the t(8;21) fusion protien AML1-ETO (RUNX1T1) in the Kasumi-1 leukemia cell line.  The genome-wide binding of the disease-related cofactors N-CoR and p300 was assayed, along with enrichments of the H3K4me3 and H3K27me3 histone modifications.

first: Daniel

last: Trombly


title: 4T1 vs. MMP3-low 4T1

status: Public on Apr 22 2015

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

summary: Molecular comparison between control 4T1 cells with MMP3-low 4T1 cells

overall_design: RNA extracted from biological triplicates of each of the above mentioned cell populations were subjected to microarray analysis

first: Scott

last: Abrams

first: Debarati

last: Banik

first: Colleen

last: Netherby

first: Song

last: Liu


title: Genome-wide maps of H3K36me3 in ccRCC and RNA-seq of matched nephrectomy samples

first: Jeff

last: Nie

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

overall_design: Refer to individual Series


title: Genome wide analysis of AR binding sites and histone modifications in prostate cancer

status: Public on Feb 08 2015

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

summary: Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation.We performed ChIP-seq analysis to investigate the role of AR and histone modifications.In addition, by siRNA mediated knockdown of AR-associated factors, changes of AR-binding sites in prostate cancer cells were analyzed..

overall_design: ChIP-sequence analysis of AR and its associated factors in prostate cancer cells

first: Satoshi

last: Inoue

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani


title: RNA expression profiling of human mPB or CB-derived CD34+ cells treated with UM171 at different doses

status: Public on Oct 21 2014

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: RNASeq data for mPB or CB-derived CD34+ exposed to UM171

overall_design: human mobilized peripheral blood or cord blood-derived CD34(+) cells were cultured for 16 hours with vehicle (DMSO),  dose response of UM171 [11.9nM, 19nM, 30.5nM, 48.8nM, 78.1nM and 125nM], SR1 [500nM] and combination of( UM171  [48.8nM]+SR1 [500nM])

first: Iman

last: Fares


title: Differential gene expression in heart tubes of hand[173] null mutants vs. w[1118]

status: Public on Mar 01 2015

city: Cologne

first: Julia

last: Hoffmann

address: Joseph-Stelzmann-Str. 9b

department: Partridge

institute: MPI for Biology of Ageing

summary:
Hand proteins belong to the highly conserved family of basic Helix-Loop-Helix transcription factors and are critical for distinct developmental processes, including cardiogenesis and neurogenesis in vertebrates. In Drosophila melanogaster a single orthologous hand gene is expressed with absence of the respective protein causing semilethality during early larval instars. Surviving adult animals suffer from shortened lifespan associated with a disorganized myofibrillar structure being apparent in the dorsal vessel, the wing hearts and in midgut tissue. Based on these data, the major biological significance of Hand seems to be related to muscle development, maintenance or function; however, up to now the physiological basis for Hand functionality remained elusive. Thus, the identification of genes whose expression is, directly or indirectly, regulated by Hand has considerable relevance with respect to understanding its biological functionality in flies and vertebrates. Beneficially, hand mutants are viable and exhibit affected tissues which renders Drosophila an ideal model to investigate up- or downregulated target genes by a comparative microarray approach focusing on the respective tissues from mutant specimens.
Our present work reveals for the first time that Drosophila melanogaster Hand regulates the expression of numerous genes of diverse physiological relevancy including distinct factors required for proper muscle development and function, such as Zasp52 or Msp-300. These results relate Hand activity to muscle integrity and functionality and may thus be highly beneficial in order to understand hand phenotypes described earlier.

overall_design: For  hand[173] null mutants and w[1118] heart tissues of wandering 3d instar larvae were dissected, RNA was isolated and samples were subjected to microarray analysis.

first: Benjamin

last: Hallier

first: Thomas

last: Roeder

first: Markus

last: Tögel

first: Heiko

last: Meyer

first: Achim

last: Paululat


title: Single-cell RNA-Seq transcriptome analysis of circular RNAs in mouse embryos

status: Public on Jun 16 2015

city: Beijing

first: Xiaoying

last: Fan

state: Beijing

address: 5 Yiheyuan Road

department: College of Life Sciences

institute: Peking University

summary: We reported a new method of single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) to obtain single cell whole transcriptome analysis that covers both poly(A) plus and poly(A) minus RNA species. We built libraries of single mouse ESC , 10pg, 100pg and 1ng diluted mouse ES total RNA, single HEK293T cell and mouse early embryos before 4-cell stage. We analyzed these data using bioinformatics and find a good coverage of non-polyadenylated RNAs, circular RNA for example. to make a comparison,we also used mouse ES cells and HEK293T cells to build libraries using the protocol publish by F.Tang in 2009(sample name Tang2009_*). We also de novo assembled new genes in mouse ESCs and early embryo samples, further validated known and novel zygotic genes with a-Aminatine treated 2-cell embryos(sample name SUPeR-seq_a-AM_treated_2-cell*).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 3 Single mouse ES cells, 7 single HEK293T cells, 8 diluted mouse ES total RNA samples and 19 mouse embryo samples are performed using SUPeR-seq to evaluate its ability to detect genes in single RNAs and to cover poly(A)- RNA species.

first: Xiannian

last: Zhang


title: Expression data from human carcinoma (MCF7) derived cells that have been exposed to insulin analogues

status: Public on Jan 29 2015

city: Leiden

first: Steven

last: Wink

state: Zuid Holland

address: Einsteinweg 55

department: Division of Toxicology

country: Netherlands

institute: LACDR

summary: Insulin analogues are designed to improve the pharmacokinetic parameters compared to regular human insulin. This provides a sustained control of blood glucose levels in diabetic patients. All novel insulin analogues are tested for their mitogenic side effects, however these assays do not take into account the molecular mode-of-action of different insulin analogues. Insulin analogues can bind the insulin receptor (INSR) and the insulin-like growth factor-1 receptor (IGF1R) with different affinities and consequently will activate different downstream signaling pathways. Here we used a panel of MCF7 human breast cancer cell lines that selectively express either one of the isoforms of the INSR (IRA or IRB) or the IGF1R. We sought to study the role of the different receptors (IRA, IRB and IGF1R) in the mitogenic signaling of insulin-like molecules (including insulin, glargine, X10 (or AspB10) and IGF1).

overall_design: MCF7 IRA, MCF7 IRB or MCF7 IGF1R cells (as described in Arch Toxicol. 2014 Apr;88(4):953-66. doi: 10.1007/s00204-014-1201-2. Epub 2014 Jan 25.) were cultured in RPMI supplemented with 5% (v/v) CDFBS (Hyclone) and used for experiments. Cells have been exposed for 1 or 6 hours to 10 nM of the indicated insulin-like molecule. As a control sample a vehicle stimulation was performed that contained everything except the active compound.

first: Bas

last: Ter Braak

first: Esmee

last: Koedoot

first: Chantal

last: Pont

first: Christine

last: Siezen

first: Jan

last: van der Laan

first: Bob

last: van de Water


title: Genome-wide maps of H3K36me3 in clear cell renal cell carcinoma (ccRCC) [ChIP-seq]

first: Jeff

last: Nie

overall_design: Examination of H3K36me3 in ccRCC

first: Thai

last: Ho

first: Huihuang

last: Yan


title: Heat shock-induced changes in chromatin binding of SUMO2/3 modified proteins

city: Kuopio

first: Einari

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: Heat shock induces rapid modification of proteins with SUMO2/3. This study concentrated in charaterizing how these changes are reflected on SUMOylation of chromatin bound proteins, trancsription, and chromatin binding of SUMO ligase PIAS1.

overall_design: Comparison of chromatin SUMO2/3 modification pattern in non-stressed and heat shocked K562 and VCaP cells. All samples were done as biological replicates. In K562 cells, SUMO2/3 ChIP-seq was done in non-stressed (37C) and heat shocked (30min at 43C) cells. The effect of heat shock factor 1 (HSF1) to chromatin SUMOylation in HS was studied in HSF1 silenced (shHSF1) K562 cells (non-stressed vs. heat shocked) using scramble shRNA transfected cells as control (shSCR). SUMO2/3, SUMO ligase PIAS1,and RNA polymerase II binding in HS (30 min at 43C) and recovery from HS (1h at 37C after HS) was studied using ChIP-seq. Effect of PIAS1 for chromatin SUMOylation was studied in PIAS1 silenced (siRNA for PIAS1, siPIAS1) cells (non-stressed or heat shocked) using non-targeting siRNA transfected cells as a control (siNON). Effect of SUMOylation to chromatin binding of RNA polymerase II was studied in UBE2I silenced (siRNA for UBE2I) and control (non-targeting siRNA transfected, siNON) VCaP cells (non-stressed or heat shocked). Effect of transtription inhibition for chromatin SUMOylation was studied in TRP (triptolide; 1 micromolar, 3h) and DRB (5,6-Dichlorobenzimidazole 1-beta-D-ribofuranosidase; 100 micromolar, 3h) treated VCaP cells. GRO-seq was used to determine HS-induced changes in nascent transcription in K562 cells.

first: Marjo

last: Malinen

first: Päivi

last: Sutinen

first: Sari

last: Toropainen

first: Ville

last: Paakinaho

first: Anniina

last: Vihervaara

first: Jenny

last: Joutsen

first: Minna

middle: U

last: Kaikkonen

first: Lea

last: Sistonen

first: Jorma

last: Palvimo


title: Identification of genes differentailly expressed in cancer stem-like cells of ovarian serous carcinoma and its clinical significance

status: Public on Aug 27 2014

city: Seongnam-si

first: Ah-Young

last: Kwon

state: Gyeonggi-do

address: 351 Yatap-dong, Bundang-gu

department: Department of Pathology

country: South Korea

institute: College of Medicine, CHA University

summary: We found gene expression profiling of spheroid-forming cell (cancer stem-like cell) by cDNA microarray and validated the genes as prognostic markers of ovarian serous carcinoma.

overall_design: Total RNA obtained from four different spheroid-forming cell (S3, S4, S5, and sample 7) compared to corresponding parent cancer cell (control3-1, C4, C5 and control7) by cDNA microarray.

first: Hee

last: An

first: Mi-jung

last: Lee

first: Ah-young


title: Transcriptome and translatome profiling of MCF7 vector cells after p53 activation

status: Public on Apr 17 2014

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

summary:
Several genome-wide transcriptome analyses that focused on p53-induced cellular responses in many cellular contexts have continued to expand the already vast p53-regulated transcriptional networks. To investigate post-transcriptional controls as an additional dimension of p53-directed gene expression responses we performed translatome analysis by polysomal profiling on MCF7 cells treated with Doxorubicin and Nutlin-3a. A comparison between the transcriptome and the translatome revealed a large number of uncoupled genes, whose transcription changes did not correlate with translation changes. Overall, we establish p53 as a master regulator of translational control and identify many p53 target genes affecting translation that can contribute to p53-dependent cellular responses.
Keywords: p53,  transcriptome,  translatome, polysomal RNA, subpolysomal RNA, uncoupling, Doxorubicin, Nutlin-3a

overall_design: Total RNA (tot) was extracted from MCF7 vector cells after 16h of treatment with Doxorubicin (1.5uM) and Nutlin-3a (10uM) or DMSO (solvent, as control treatment). Polysomal profiling was performed after the same conditions. We collected all subpolysomal mRNA fractions (sub) and the polysomal ones (pol) after sucrose gradient fractionation of cytoplasmic lysates to analyze separately mRNAs that are not actively translated from those that are considered in active translation, respectively. Experiments were performed in three biological replicates.

first: Sara

last: Zaccara

first: Alessandra

last: Bisio

first: Yari

last: Ciribilli

first: Alberto

last: Inga


title: Thalidomide induced early gene expression perturbations indicative of human embryopathy in mouse embryonic stem cells

status: Public on May 31 2015

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

country: USA

institute: US FDA

summary:
To unravel the mechanisms of thalidomide developmental toxicity, we used microarrays to study transcriptomic changes induced by thalidomide during mouse embryonic stem cell (mESC) differentiation.
C57BL/6 mESCs were allowed to differentiate spontaneously and global gene expression changes were studied using microarrays at at different time points after exposure to 0.25 mM thalidomide (THD).

overall_design: RNA of control smaples (unexposed) and THD-exposed samples was collected at 24, 48, 72 h post-exposure. Three replicates were included for each experimental condition.

first: Robert

middle: L

last: Sprando

first: Jeffrey

last: Yourick


title: Single cell RNA-seq analysis of melanoma

status: Public on Apr 05 2016

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

institute: WEIZMANN INSTITUTE OF SCIENCE

summary: To understand the diversity of expression states within melanoma tumors, we obtained freshly resected samples, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq.

overall_design:
Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2.

*Raw data files absent for samples GSM1851356 and GSM1851494.*

**Submitter declares reads will be made available through dbGaP.**

Please note that the processed data file (melanoma_single_cell_revised_v2.txt) contains two additional sample characteristis ("classification (based on inferred cnvs)" and "cell types for non-malignant cells").

first: Ben

last: Izar


title: Setdb1 is required for persistence of H3K9me3 and repression of endogenous retroviruses in mouse primordial germ cells

status: Public on Sep 01 2014

city: Vancouver

first: Matthew

last: Lorincz

state: BC

address: 2350 Health Sciences Mall

department: Medical Genetics

institute: University of British Columbia

summary: Transcription of endogenous retroviruses (ERVs) is inhibited by de novo DNA methylation during gametogenesis, a process initiated after birth in oocytes and at ~E15.5 in prospermatogonia. Earlier in germline development however, the genome, including most retrotransposons, is progressively demethylated, with young ERVK and ERV1 elements retaining intermediate methylation levels. As DNA methylation reaches a low point in E13.5 primordial germ cells (PGCs) of both sexes, we determined whether retrotransposons are marked by H3K9me3 and H3K27me3 using a recently developed low input ChIP-seq method. Although these repressive histone modifications are predominantly found on distinct genomic regions in E13.5 PGCs, they concurrently mark partially methylated LTRs and LINE1 elements. Germline-specific conditional knock-out (KO) of the H3K9 methyltransferase SETDB1 yields a decrease of both histone marks and DNA methylation at H3K9me3 enriched retrotransposon families. Strikingly, Setdb1-KO E13.5 PGCs show concomitant de-repression of many marked ERVs, including IAP, ETn and ERVK10C elements and ERV-proximal genes, a subset in a sex-dependent manner. Furthermore, Setdb1 deficiency is associated with a reduced number of male PGCs and postnatal hypogonadism in both sexes. Taken together, these observations reveal that SETDB1 is an essential guardian against proviral expression prior to the onset of de novo DNA methylation in the germline.

overall_design: H3K9me3, H3K27me3 and expression profiles in Setdb1 WT, Het and KO male and female E13.5 PGCs.

first: Sheng

last: Liu

first: Julie

last: Brind'Amour

first: Mohammad

middle: M

last: Karimi

first: Kenjiro

last: Shirane

first: Aaron

last: Bogutz

first: Louis

last: Lefebvre

first: Hiroyuki

last: Sasaki

first: Yoishi

last: Shinkai

middle: C


title: The role of the ETS factor ERG in prostate cancer

status: Public on Mar 18 2014

city: Boston

first: M. Simo

last: Arredouani

address: 330 Brookline Ave.

department: Surgery

institute: Beth Israel Deaconess Medical Center

summary: Prostate cancer cell lines that express ERG acquire a neuron-like phenotype.

overall_design: The human prostate tumor cell line LNCap was transfected with lenti-ERG or control lenti-vector. Gene expression profiling was performed to establish the ERG-associated phenotype.

first: M.


title: Map the causative gene of hearing loss in Chinese Rongchang pigs by GWAS

status: Public on May 01 2015

city: Chongqing

first: Ting

last: zhang

address: Rongchang

country: China

institute: Chongqing Academy of Animal Science

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

summary: Whole genome genotyping (WGG) arrays are the powerful tools for GWAS in farm animal. Here we take advantage of the commercial Illumina PorcineSNP60 BeadChips, a mapping population including 101 individuals were genotyped. Association analysis and linkage analysis were followed to map the causative gene of hearing loss in Chinese Rongchang pigs.

overall_design: To map the causative gene of hearing loss in Chinese Rongchang pigs, we genotyped 60000 markers in the genome of a mapping population including 101 individuals. Illumina 60K BeadChips were used. Sample types were normal blood samples.

first: Lei

last: Chen


title: Integrative miRnome and transcriptome analysis in human malignant prolactin pituitary tumors identify miR-183 as driving gene for tumor progression to malignancy.

city: Lyon

first: magali

last: roche

address: 8 avenue Rockfeller

country: France

institute: university lyon 1

summary: miRNAs expression is known to be deregulated in many types of cancer leading to suspect them implication in crucial steps occurring during tumor progression and maybe as potential driving genes. In this study we tried to decipher the place of miRNA in the hierarchical events cascade occurring  in prolactinoma-tumours  progression toward malignancy by using an integrative genomic approach performed on the same samples associating global miRNA expression, transcriptomic, DNA structure and methylation analyses.   By this approach, we observed the down-regulation of 3 miRNAs (miR-183, miR-98, and miR-744) in A vs. NA tumors. MiR-98 and miR-744 were demonstrated to regulate respectively E2F2 and TGFB1 which are up-regulated in the A vs. NA prolactinomas. Moreover we demonstrated that KIAA0101 is a new target of miR-183 and that miR-183 is regulated by the transcription factor ETS2. KIAA0101 is up-regulated in the A vs. NA prolactinomas. KIAA0101, E2F2 and TGFB1 are interconnected in a pathway controlling cell proliferation and invasion that is over-activated in A PRL tumors. Thus the down-regulation of these three miRNAs is involved in the tumoral progression of human prolactinoma towards aggressiveness.     The integrative genomic approach used here allowed us to propose a model of PRL tumoral progression towards aggressiveness. Moreover it revealed the potential of integrative genomic strategy applied in the same human tumors to identify the molecular mechanisms responsible for tumor progression  even from a  small cohort of patients.

overall_design: miRNA signatures was assessed on 4 aggressive, 8 non-aggressive human prolactin secreting pituitary tumors and 1 normal pituitary for data normalization.

first: M

last: Roche

first: N

last: Nazaret

first: J

last: Lachuer


title: c-Jun Targets Cockayne Syndrome protein B to Specific Genomic Region for Transcription Regulation

status: Public on Mar 06 2014

city: Philadelphia

first: Jieun

last: Jeong

address: 3400 Civic Center Blvd

institute: The University of Pennsylvania

summary: Cockayne syndrome is an inherited premature aging syndrome associated with developmental and neurological disorders.  Mutations in the genomic locus encoding CSB are associated with 80% Cockayne syndrome cases.  Transcription profiling assays reveal the association of mis-regulation of gene expression with Cockayne syndrome, highlighting the importance of CSB in transcription regulation.  However, many questions remain unanswered as how CSB regulates transcription.  In this study, we dissect the mechanisms by which CSB regulates transcription during normal growth.  By anti-CSB chromatin immunoprecipitation followed by deep sequencing, we found CSB is enriched at genomic regions containing TGASTCA motifs, to which the immediate early gene product C-Jun binds specifically.  We further demonstrate that c-Jun co-immunoprecipitates with CSB.  In addition, the targeting of CSB to genomic region containing TGASTCA motifs was drastically reduced in cells treated c-Jun shRNA.  Reverse transcription followed by quantitative PCR indicates that CSB can regulate gene expression nearby its binding sites, both in activation and repression.  The remodeling defective CSB∆N1 mutant is also targeted to TGASTCA motifs, but cannot always substitute CSB function in transcription regulating, suggesting the importance of remodeling by CSB in transcription regulation.  Notably, the Cockayne syndrome related mutation encoding protein CSBR670W, which is defective in ATP hydrolysis but is targeted to TGASTCA motifs efficiently, indicating that ATP hydrolysis is dispensable for c-Jun mediated CSB targeting, in sharp contrast to the ATP-dependent targeting mechanism by which CSB is relocated to DNA lesion stalled transcription. Together, these results reveal a second CSB targeting mechanism in which DNA sequence specific transcription factor c-Jun targets CSB to specific genomic region and regulate gene expression.

overall_design: Genomic localization of CSB and remodeling deficient CSB∆N1

first: K-J

last: Won

first: Robert

last: Lake

first: Erica

last: Boetefuter

first: Pei-Fang

last: Tsai

first: Hua-Ying

last: Fan


title: Identification of stable markers of the EMT:MET process

status: Public on Jan 30 2014

city: West Lafayette

first: Michael

last: Wendt

state: IN

address: 201 S. University St.

department: MCMP

institute: Purdue University

summary: Epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) facilitate breast cancer (BC) metastasis, however stable molecular changes that result as a consequence of these processes remain poorly defined. Therefore, we sought to identify molecular markers that could distinguish tumor cells that had completed the EMT:MET cycle in the hopes of identifying and targeting unique aspects of metastatic tumor outgrowth.Therefore, normal murine mammary gland (NMumG) cells transformed by overexpression of EGFR (NME) cells were cultured in the presence of TGF-beta1 (5 ng/ml) for 4 weeks, at which point TGF-beta1 supplementation was discontinued and the cells were allowed to recover for an additional 4 weeks (Post-TGF-Rec). Total RNA was prepared from unstimulated cells (Pre-TGF) of similar passage and compared by microarray analysis.

overall_design: The two groups were analyzed in triplicate, three Pre-TGF samples and three Post-TGF-Rec samples.

first: Wendt

last: Michael


title: cGvHD vs. non-cGvHD gene expression profiling in peripheral blood

status: Public on Jul 11 2013

city: Stanford

first: Li

last: Li

state: CA

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

summary: We performed peripheral blood gene expression profiling to identify an array of transcriptional biomarkers that discriminate presence of active cGvHD requiring immunosuppression following allogeneic HCT. Peripheral blood mononuclear cells were prepared by Ficoll gradient and cryopreserved from 63 patients (median age 50 yrs; range 19-64) following allogeneic HCT (median 475 days post-HCT) on an IRB approved protocol. Samples were randomly selected into a training set (23 cGvHD and 19 without cGvHD) and test set (12 cGvHD and 9 without cGvHD) and processed on the Aligent whole human genome 44k microarray platform. Bioinformatics programs including AILUN, GeneSpring, SAM, and PAM were used to select a minimum gene-set (FDR <5%) to predict cGvHD in the training set. Patient characteristics in the two groups were collected for confounder/interaction analysis across the following parameters: age, gender, disease histology, disease status at HCT, graft source, conditioning regimen, white blood count (WBC) at sample, and follow-up status including relapse and survival. Type, grade, and activity of acute cGvHD and cGvHD at time of sample and at most recent follow-up were determined by two independent investigators by standard clinical criteria.

overall_design: Three-condition experiment, 35 cGvHD vs. 28 non-cGvHD samples vs. 7 controls (cGvHDnoIS; no immunosuppression drug).

first: Holbrook

last: Kohrt

first: Sue

last: Heish

first: Arash

last: Alizadeh

first: Samuel

last: Strober

first: Minnie

last: Sarwal

last: Lowsky


title: A comprehensive study to understand the effects of climate warming, simulated by soil transplant, on soil microbial community and its feedback responses

status: Public on Oct 30 2013

first: Zhao

last: Mengxin

address: Haidian District, Zhongguancun Street

institute: Tsinghua University

summary:
Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research.
Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling.

overall_design: Fifty four samples were collected from three soil types (Phaeozem,Cambisol,Acrisol) in three sites (Hailun, Fengqiu and Yingtan) along a latitude with reciprocal transplant; Both with and without maize cropping in each site; Three replicates in every treatments.

first: Mengxin

last: Zhao

first: Shanshan

last: Liu

first: Yunfeng

last: Yang

first: Kai

last: Xue

first: Feng

last: Wang

first: Jizhong

last: Zhou

first: Bo

last: Sun

first: Joy

last: Van Nostrand

first: Zhili

last: He

first: Yuguang

last: Zhang

first: Shijie

last: Bai


title: Gene-regulatory networks activated by pattern-specific generation of action potentials in dorsal root ganglia neurons

status: Public on Jul 26 2016

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Development and plasticity in the nervous system are regulated by specific patterns of neural impulse activity.  Patterned activity orchestrates spatial and temporal changes in the expression of networks of genes.  These gene regulatory networks underlie the long-term changes in cell specification, growth of synaptic connections, and frequency adaptation that occur throughout neonatal and postnatal life. We show that the temporal nature of action potentials and downstream signaling differentially regulate the expression of hundreds of diverse neuronal genes through distinct gene regulatory networks.  Analysis of upstream regulatory regions showed enrichment in transcription factor binding sites for NF-Kappa that was action potential firing pattern specific.  Our new findings demonstrate spike-frequency decoding by action potentials at the transcriptional level by pattern-specific activation of transcription factors and associated gene-regulatory networks that operate to adjust the modalities of sensory neurons.

overall_design:
We analyzed the transcriptomic changes in primary cultures of embronic dorsal root ganglia (DRG) neurons subjected to four electric stimulation patterns with respect to their non-stimulated counterparts.
We have adopted the multiple yellow strategy in which differently fluorescent labeled biological replicas are co-hybridized with each array and then similarly labeled samples from cells subjected to different conditions are compared and results averaged over the two labels.

first: Philip

last: Lee

first: Jonathan

last: Cohen

first: Sanda

first: R

last: Fields


title: Affymetrix SNP array data for 29 MCL cases

status: Public on Nov 04 2013

city: Barcelona

first: Sílvia

last: Beà

state: Barcelona

address: Rossello, 153

department: HematoPathology

country: Spain

institute: Hospital Clinic

summary:
DNA from four 29 cases, 38 tumor samples (23 PB, 12 LN, 1 Tonsil, 1 colonic biopsy, 1 spleen) and 29 normal DNA from the same patients were analyzed with Affymetrix SNP 6.0 platform for copy number alterations study.
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples, lymph nodes and other tissues like spleen, tonsil and colonic biopsy

overall_design: Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 29 MCL cases samples and their respective matched non-tumor DNA, which were used as references for copy number inference.

first: Silvia

first: Elias

last: Campo


title: Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [NimbleGen ChIP-chip]

status: Public on Feb 17 2013

city: Edinburgh

first: Nick

last: Gilbert

address: Crewe Rd South

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: The University of Edinburgh

type: Genome binding/occupancy profiling by genome tiling array

summary:
This study was designed to investigate DNA supercoiling across the human genome and to understand how supercoiling domains impact on higher levels of genome organisation.
DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, “open” chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes.

overall_design: The binding of bTMP, as a reporter for DNA supercoiling, was investigated in RPE1 cells. Experiments were biological replicates

first: Catherine

last: Naughton


title: Abrupt scrib- vs. Abrupt and RasV12 (RasACT) scrib-, NotchICD (NACT) scrib- +/- JNK (Bsk) expression profiles

status: Public on Aug 15 2013

city: East Melbourne

first: Helena

middle: Elizabeth

last: Richardson

state: Victoria

address: 7 St Andrew's place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Center

summary:
Drosophila mosaic eye-antennal discs from the listed genotypes generated using the MARCM system were dissected from 3rd instar larvae at day 5 after egg deposition.
20 pairs of discs for the Abrupt and scrib- + Abrupt samples and 50 pairs from FRT control, NACT scrib- +/- BskDN and RasACT scrib- +/- BskDN were used to prepare RNA. Samples were prepared in triplicate, and the RNA isolated using TRIZOL, before being column purified (Qiagen). Probes were hybridized to GeneChip Drosophila 2.0 Genome Arrays (Affymetrix).

overall_design: To compare the expression profile of Abrupt when overexpressed in the eye-antennal discs with tumours formed by Abrupt overexpression in scrib- clones, and to reveal JNK responsive genes in RasV12 (RasACT) scrib- versus NotchICD (NACT) scrib- eye-antennal mosaic discs

first: Jason

last: Ellul


title: Mantle Cell Lymphoma

status: Public on Jun 25 2013

first: Pedro

last: Jares

address: c/ Villarroel 170

department: Genomics Unit

institute: IDIBAPS

summary:
Gene expression analyis of primary MCL including IGHV mutated and unmutated cases
Gene set analysis was perfomed in  MCL samples, comparing IGHV mutated cases vs. IGHV unmutated cases

overall_design: In total 38 MCL samples were processed with the HU133plus 2.0 microarray. Twenty four cases had a IGHV mutations and 14 were unmutated.

first: Elías

first: Alba

last: Navarro


title: Chemokine expression in retinal pigment epithelial cells in response to co-culture with activated T Cells

status: Public on Nov 19 2012

city: Copenhagen

first: Carsten

last: Faber

address: Blegdamsvej 3

department: Fac. of Health Science, ISIM

country: Denmark

institute: University of Copenhagen

summary:
Purpose: To investigate the effects of T cell-derived cytokines on gene and protein expression of chemokines in a human RPE cell line (ARPE-19).

Methods: We used an in vitro co-culture system in which the RPE and CD3/28-activated T cells were separated by a membrane. Differential gene expression in the RPE cells of chemokine genes was quantified using three different microarrays. Protein expression was determined by single- and multiplex ELISA and immunoblotting.

Results: Co-culture with activated T cells increased RPE mRNA and protein expression of chemokines CCL2 (MCP-1), CCL5 (RANTES), CCL7 (MCP-3), CCL8 (MCP-2), CXCL1 (GRO-α), IL8 (CXCL8), CXCL9 (MIG), CXCL10 (IP10), CXCL11 (ITAC), and CX3CL1 (fractalkine). The secretion of CCL7 and CXCL9, 10, and 11 was polarized in the apical direction. Using recombinant human cytokines and neutralizing antibodies we identified IFNgamma and TNFalpha as the two major T cell-derived cytokines responsible for the RPE response. For CCL5, CXCL9, 10, 11, 16, and CX3CL1 we observed a synergistic effect of IFNgamma and TNFalpha in combination. CCL20, CXCL1 and 6, and IL8 were negatively regulated by IFNgamma.

Conclusions: RPE cells responded to exposure to T cell-derived cytokines by upregulating expression of several chemokines related to microglial, T cell, and monocyte chemotaxis and activation. This inflammatory stress response may have implications for immune homeostasis in the retina, and for the further understanding of inflammatory ocular diseases such as uveitis and age-related macular degeneration.

overall_design: Differentiated ARPE19 grown on inserts in serum-free media was basolaterally stimulated for 48h with activated T cells or recombinant cytokines (IFNg and/or TNFa) or neutralizing antibodies (aIFNg and/or aTNFa)

first: Helene

middle: B

last: Juel

first: Maja

last: Udsen

first: Lasse

last: Folkersen

first: Mogens

middle: H

last: Nissen


title: LGR5 positivity defines stem-like cells in colorectal cancer [Expression]

status: Public on Apr 19 2013

city: Bethesda

first: Yue

last: Hu

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

summary:
To further elucidate the role of the intestinal stem cell marker Leucine-rich-repeat-containing G-protein-coupled receptor 5 (LGR5) in colorectal cancer (CRC), we exposed Lgr5-EGFP-IRES-Cre-ERT2 mice to azoxymethane/dextrane sodium sulfate (AOM/DSS) which induces inflammation-driven colon tumors. Tumors were then flow-sorted into fractions of epithelial cells that expressed high or low levels of Lgr5 and were characterized using gene expression profiling. In the AOM/DSS-induced mouse colon tumors Lgr5 high cells showed higher levels of several stem cell-associated genes and higher Wnt signaling than Lgr5 low tumor cells and Lgr5 high normal colon epithelial cells.
To further elucidate the role of the intestinal stem cell marker Leucine-rich-repeat-containing G-protein-coupled receptor 5 (LGR5) in colorectal cancer (CRC), we transduced SW480 CRC cells with lentiviral shRNA constructs to silence LGR5 expression. This resulted in a depletion of spheres but did not affect adherently growing cells. Spheres expressed higher levels of several stem cell-associated genes than adherent cells. Notch signaling was down-regulated upon LGR5 silencing. This was confirmed by immunohistochemistry against cleaved NOTCH1.

overall_design:
Normal mouse colons and AOM/DSS-induced mouse colon tumors were flow-sorted into Lgr5 high and low cells before gene expression was measured. Fifteen independent experiments were performed using seven individual mice for normal colons and eight for tumors.
Appropriate LGR5 status was confirmed by real-time qRT-PCR before measuring silencing induced gene expression. Three independent experiments were performed for each cell fraction using separately cultured cells for each experiment.

first: Daniela

middle: D

last: Hirsch

first: Timo

last: Gaiser

first: Thomas

last: Ried


title: Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [Agilent ChIP-chip]


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

status: Public on Apr 11 2012

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

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

This track shows probable binding sites of the specified transcription factors (TFs) in the given cell types as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq). 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. For each experiment (cell type vs. antibody) this track shows a graph of enrichment for TF binding (Signal), along with sites that have the greatest evidence of transcription factor binding, as identified by the PeakSeq algorithm (Peaks).
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). For details on the chromatin immunoprecipitation protocol used, see Euskirchen et. al., (2007), Rozowsky et. al. (2009) and Auerbach et. al. (2009).
DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa) sequencing platform and mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length ~30 bps) that align uniquely to the human genome. From the mapped tags, a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome. Reads were pooled from all submitted replicates to generate the Peak and Signal files. Per-replicate aligments and sequences are available for download at downloads page (http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/).
For each 1 Mb segment of each chromosome, a peak height threshold was determined by requiring a false discovery rate <= 0.01 when comparing the number of peaks above said threshold to the number of peaks obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value = 0.01 are considered to be significantly enriched compared to the input DNA control.

first: Michael

last: Snyder

first: Sherman

last: Weissman

first: Philip

last: Cayting


title: Methylome Analysis and Epigenetic Changes Associated with Menarcheal Age

status: Public on Sep 21 2013

city: London

first: Gianluca

last: Campanella

address: Norfolk Place

department: Epidemiology and Biostatistics

institute: Imperial College London

summary: Epigenome-wide association study of age at menarche in a group of 329 women from the EPIC-Italy cohort.

overall_design: A total of 329 samples from the EPIC-Italy cohort were analyzed. No replicates are available.

first: Christiana

middle: A

last: Demetriou

first: Jia

last: Chen

first: Silvia

last: Polidoro

first: Karin

last: van Veldhoven

first: Cyrille

last: Cuenin

first: Kevin

last: Brennan

first: Françoise

last: Clavel-Chapelon

first: Laure

last: Dossus

first: Marina

last: Kvaskoff

first: Dagmar

last: Drogan

first: Heiner

last: Boeing

first: Rudolf

last: Kaaks

first: Angela

last: Risch

first: Dimitrios

last: Trichopoulos

first: Pagona

last: Lagiou

first: Giovanna

last: Masala

first: Sabina

last: Sieri

first: Rosario

last: Tumino

first: Salvatore

last: Panico

first: José

middle: R

last: Quirós García

first: María-José

last: Sánchez Perez

first: Pilar

last: Amiano

last: Huerta Castaño

first: Eva

last: Ardanaz

first: Charlotte

last: Onland-Moret

first: Petra

last: Peeters

first: Kay-Tee

last: Khaw

first: Nick

last: Wareham

first: Timothy

last: Key

first: Ruth

last: Travis

first: Isabelle

last: Romieu

first: Valentina

last: Gallo

first: Marc

last: Gunter

first: Zdenko

last: Herceg

first: Kyriacos

last: Kyriacou

first: Elio

last: Riboli

first: James

last: Flanagan

first: Paolo

last: Vineis


title: CTCF regulates positioning of the human cystic fibrosis gene in association with a histone deacetylase

status: Public on Dec 31 2013

city: Umeå

first: Joscha

last: Muck

address: Analysvägen 1

department: UCMM

institute: Umeå University

summary:
Treatment with the histone deacetylase inhibitor trichostatin a (TSA) changes the radial positioning of the CFTR gene in HeLa S3 cells. The gene relocates from the nuclear periphery to the nuclear interior. In Calu-3 cells the gene is located in the nuclear interior. To identifiy potential regulatory elements for the positioning of CFTR, the histone h3 and h4 acetylation patterns of untreated and TSA-treated HeLa S3 and untreated Calu-3 cells were determined by ChIP-chip.
A CTCF site close to the CFTR promoter displayed consistent histone H3 hyperacetylation in TSA treated HeLa S3 cells and Calu-3 cells.

overall_design:
Four Agilent 4x 44K DNA-chips (DNA-Chips: REP_1 - REP_4).
HeLa untreated and TSA treated: H3ac/H3pan (Cy5/Cy3): hybridized together on four sectors - 1x regular 3x dye swap;
H4ac: 3 sectors, respective H3pan reference on different sectors on the same DNA-chips (labeled with the identical fluorophore).
Calu-3: H3ac/h3pan: one sector each on the same DNA-chip (labeled with the identical fluorophore)
H4ac/H3pan: two sectors each on the same DNA-chips (two each on two DNA-Chips, labeled with the identical fluorophore)


title: Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers [expression data]

status: Public on Feb 01 2012

city: Cambridge

first: Ana Teresa

last: Maia

state: Cambridgeshire

address: Robinson Way

department: Department of Oncology

institute: University of Cambridge

summary: Introduction: Cis-acting regulatory single nucleotide polymorphisms (SNPs) at specific loci may modulate penetrance of germline mutations at the same loci by introducing different levels of expression of the wild-type allele. We have previously reported that BRCA2 shows differential allelic expression and we hypothesize that the known variable penetrance of BRCA2 mutations might be associated with this mechanism.  Methods: We combined haplotype analysis and differential allelic expression of BRCA2 in breast tissue to identify expression haplotypes and candidate cis-regulatory variants. These candidate variants underwent selection based on in-silico predictions for regulatory potential and disruption of transcription factor binding, and were functionally analysed in-vitro and in-vivo in normal and breast cancer cell lines. SNPs tagging the expression haplotypes were correlated with the total expression of several genes in breast tissue measured by Taqman and microarray technologies. The effect of the expression haplotypes on breast cancer risk in BRCA2 mutation carriers was investigated in 2754 carriers.  Results: We identified common haplotypes associated with differences in the levels of BRCA2 expression in human breast cells. We characterised three cis-regulatory SNPs located at the promoter and two intronic regulatory elements, which affect the binding of the transcription factors C/EBPα, HMGA1, DBP and ZF5. We showed that the expression haplotypes also correlated with changes in the expression of other genes in normal breast. Furthermore, there was suggestive evidence that the minor allele of SNP rs4942440, which is associated with higher BRCA2 expression, is also associated with a reduced risk of breast cancer (per-allele HR=0.85, 95%CI=0.72-1.00, P-trend=0.048).  Conclusion: Our work provides further insights into the role of cis-regulatory variation in the penetrance of disease-causing mutations. We identified small-effect genetic variants associated with allelic expression differences in BRCA2, which could possibly affect the risk in mutation carriers through altering expression levels of the wild-type allele.

overall_design:
Total gene expression of normal breast sample from healthy controls.

This submission represents transcriptome component of study.

first: Ana

middle: T


title: Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers [SNP data]

overall_design: Genotype of normal breast sample from healthy controls.


title: Affymetrix SNP array data for Pediatric malignant glioma samples

status: Public on Nov 23 2011

city: Pittsburgh

first: Aleksandr

last: Lisovich

state: PA

address: 5150 Centre Ave.

department: DBMI

institute: University of Pittsburgh

summary: Data includes all available Affymetrix SNP data from a cohort of Pediatric malignant glioma samples, isolated from Formalin-fixed Paraffin embedded tissue. No clinical data is available.

overall_design: Copy number analysis of Affymetrix 250K Sty SNP arrays was performed for 28 pediatric malignant gliomas. The VN algorithm was used to generate the reference signal based on 48  Mapping 500k HapMap Trio Dataset template.

middle: I

first: Uma

last: Chandran

first: Maureen

last: Lyons-Weiler

first: William

last: LaFramboise

first: Ashley

last: Brown

first: Regina

last: Jakacki

first: Ian

middle: F

last: Pollack

first: Robert

middle: W

last: Sobol


title: Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale

status: Public on Sep 20 2011

first: ENCODE

last: DCC

summary:
This track shows probable locations of the specified histone modifications in the given cell types as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq). 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. For each experiment (cell type vs. antibody) this track shows a graph of enrichment for histone modification (Signal), along with sites that have the greatest evidence of histone modification, as identified by the PeakSeq algorithm (Peaks).

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. For details on the chromatin immunoprecipitation protocol used, see Euskirchen et. al., (2007), Rozowsky et. al. (2009) and Auerbach et. al. (2009).
DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa) sequencing platform and mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length ~30 bps) that align uniquely to the human genome. From the mapped tags a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome.
For each 1 Mb segment of each chromosome, a peak height threshold was determined by requiring a false discovery rate <= 0.01 when comparing the number of peaks above said threshold to the number of peaks obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value <= 0.01 are considered to be significantly enriched compared to the input DNA control.

first: Michael

last: Snyder

first: Sherman

last: Weissman

first: Philip

last: Cayting