title: Avian pathogenic Escherichia coli (APEC) infection alters bone marrow transcriptome in chickens

city: Beijing

first: hongyan

last: sun

address: Poultry genetic group, College of Animal Science and Technology, China Agricultural Univeristy, Yuanmingyuan West Rd. No. 2, Haidian District, Beijing, China

country: China

institute: Iowa State University

summary:
Purpose: This study is to more comprehensively understand the genome-wide host response to avian pathogen E. coli (APEC).
Methods: Male broiler chicks were challenged with APEC (or mock-challenged as controls), and bone marrow was harvested at 1 and 5 days post-infection (dpi). Based upon necropsy-scored lesions on liver, pericardium, and air sacs, the challenged birds were assigned to mild or severe pathology categories, representing resistant and susceptible phenotypes, respectively. RNA sequence data were first analyzed using the R package EdgeR to identify differentially expressed genes.GO and pathway analysis using the R package GOseq identified many immune-related pathways.
Results: RNA sequencing resulted in 11 to 40 million single-end raw reads of 100 bp per sample. After alignment, an average of 80 % of the reads, with 5 % representing multiple mapping, were mapped to the chicken reference transcriptome. Among these detected unique transcripts, there were 2,404 novel genes mainly distributed on chromosomes 1, 2, 4, 3, Z, 5 in decreasing number. Genes were detected as differentially expressed (DE) between treatments (susceptible, resistant, and mock-challenged) at a given time point, or DE between 1 and 5 dpi within the same treatment group. Compared to mock-challenged birds on 5 dpi, susceptible birds exhibited extensive enhancement of their T cell and B cell development, as well as innate and adaptive immune response. However, for the 1 dpi group, susceptible birds exhibited a decreased gene expression of T and B cell development. The differences between the two phenotypes, susceptible and resistant birds, at 5 dpi showed that susceptible birds had increased gene expression of B-cell development and adaptive immune response.
Conclusions: This is the first report to our knowledge examining the role of bone marrow cells in responding to APEC infection in broilers. This transcriptome study provides insight and global overview into the response of genes involved in the earliest phases of the immune response to APEC infection. Our data indicate a dynamic interaction between the innate and adaptive immune responses to APEC infection in susceptible birds, providing flexibility and redundancy in the host’s induction of cytokines and chemokines. Additionally, B cell and T cell development are also extensively affected by APEC infection for susceptible birds, resulting in drastic host impairment in early response to infection. The findings of present study shed light on the underlying chicken immune modulation against APEC infection. Also, this study will build a solid foundation for identifying host genetic variation that may be manipulated to enhance resistance to infection and may be useful as colibacillosis control targets.

overall_design: Bone marrow mRNA profiles of six treatment groups were generated by deep sequencing, in four replicates, using Illumina HiSeq2000.

first: Hongyan

last: Sun

first: Susan

middle: J

last: Lamont


title: SMARCA4/Brg1 Coordinates Genetic and Epigenetic Networks Underlying Shh-type Medulloblastoma Development

status: Public on Sep 14 2016

city: Richardson

first: Zhenyu

last: Xuan

state: TX

address: 800 West Campbell

country: USA

institute: UT Dallas

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells [ChIP-Seq]

status: Public on Sep 15 2016

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

country: France

institute: IGBMC

summary: We have integrated dynamic RXRa binding, chromatin accessibility and promoter epigenetic status with the transcriptional activity inferred from RNA polymerase II mapping and transcription profiling. This demonstrated a temporal organization structure, in which early events are preferentially enriched for common GRNs, while cell fate specification is reflected by the activation of late programs in a cell-type specific manner. Furthermore, significant differences in cell lines' promoter status of genes associated with cell-line specific programs were inferred. Finally, a variety of transcription factors (TFs) playing a direct role in the signal transduction cascade downstream of the RXR/RAR initiated wiring were identified, several of them commonly regulated in both model systems, but in addition cell-type specific TF drivers were also identified.

overall_design: profiling of time series ChIP-seq datasets in two related embryonic stem cells. 5 different factors assessed in 5 timepoints in 2 different cell lines. In addition two input control samples (one per cell line): Total=52 datasets.

first: Marco-Antonio

first: Valeriya

last: Malysheva

first: Mohamed

middle: A

last: Saleem

first: Hinrich

last: Gronemeyer


title: Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells


title: Wilms Tumor cells with WT1 mutations have characteristic features of mesenchymal stem cells

status: Public on Feb 01 2010

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

country: Germany

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

summary: Wilms tumors are genetically heterogeneous kidney tumors whose cells of origin are unknown. Tumors with WT1 mutations and concomitant loss of the wild-type allele represent a distinct subgroup, frequently associated with mutations in CTNNB1. Here we describe the establishment and characterization of long-term cell cultures derived from five individual Wilms tumors with WT1 mutations. Three of these tumor cell lines also had CTNNB1 mutations and an activated canonical Wnt signaling pathway as measured by β-catenin/TCF transcriptional activity. Four of the five Wilms cell lines had a stable normal karyotype for at least 25 passages, and four lines showed loss of heterozygosity of chromosome 11p due to mitotic recombination in 11p11. Gene expression profiling revealed that the Wilms tumor cell lines are highly similar to human mesenchymal stem cells (MSCs) and FACS analysis demonstrated expression of MSC-specific surface proteins CD105, CD90 and CD73. The stem cell like nature of the Wilms tumor cells is further supported by their adipogenic, chondrogenic, osteogenic and myogenic differentiation potentials. By generating multipotent mesenchymal precursors from paraxial mesoderm (PAM) in tissue culture using embryonal stem cells, gene expression profiles of PAM and MSCs were described. Using these published gene sets we found coexpression of a large number of genes in Wilms tumor cell lines, PAM and MSCs. Lineage plasticity is indicated by the simultaneous expression of genes from the mesendodermal and neuroectodermal lineages. We conclude that Wilms tumors with WT1 mutations have specific traits of PAM, which is the source of kidney stromal cells.

overall_design: 5 different Wilms tumor cell lines with WT1 mutations, three of them with additional CTNNB1 mutations, were analyzed and compared with human mesenchymal stem cells and an established Wilms tumor cell line with wildtype WT1/CTNNB1: Wilms1 (CTNNB1 mut.; 5 replicates), Wilms2 (CTNNB1 mut.; 5 replicates), Wilms3 (4 replicates), Wilms4 (CTNNB1 mut.; 3 replicates), Wilms5 (3 replicates), MSC (5 replicates), CLS1 (4 replicates)

first: Maike

last: Busch

first: Manfred

last: Beier

first: Constanze

last: Duhme

first: Carmen

last: deTorres

first: Jaume

last: Mora

first: Arthur

last: Brandt

first: Hans-Dieter

last: Royer


title: Zebrafish (Danio rerio) catecholaminergic neuron RNA-seq based transcript profiles

status: Public on Oct 15 2012

city: Freiburg

first: Wolfgang

last: Driever

address: Hauptstrasse 1

department: Biology

institute: University of Freiburg

summary: This project aimed at identifying developmental stage specific transcript profiles for catecholaminergic neurons in embryos and early larvae of zebrafish (Danio rerio). Catecholaminergic neurons were labeled using transgenic zebrafish strains to drive expression of GFP. At stages 24, 36, 72 and 96 hrs post fertilization, embryos were dissociated and GFP expressing cells sorted by FACS. Isolated RNAs were processed using either polyA selection and libray generation or NanoCAGE. This is the first effort to determine stage specific mRNA profiles of catecholaminergic neurons in zebrafish.

overall_design: Catecholaminergic neurons were labeled by four different strategies: (1) 24 hrs old embryos: we used the ETvmat2:GFP transgenic line (Wen et al. 2007). Visualization of monoaminergic neurons and neurotoxicity of MPTP in live transgenic zebrafish. Dev Biol. 2008 Vol 314 p84-92) which at this early stage labels catecholaminergic neurons in posterior tuberculum and locus coeruleus; (2) 24 hrs old embryos: we used Tg(otpb.A:egfp)zc48 transgenic line (Fujimoto et al. Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. Dev Biol 2011, Vol 352, p393–404) which at this stage label ventral diencephalic dopaminergic neurons and some preoptic neurons. (3) For 72 and 96 hrs old zebrafish larvae we used a th:GFP BAC transgenic lines that labels catecholaminergic neurons (Tay et al., Comprehensive catecholaminergic projectome analysis reveals single-neuron integration of zebrafish ascending and descending dopaminergic systems. Nat Comms 2011 Vol 2, 171; also: T. Leng and W. Driever, unpublished). (4) for the 36 and 48 hrs old zebrafish larvae we used a th:Gal4VP16 driver and UAS:EGFP responder transgenic line system to label catecholaminergic cells (Fernandes et al., Deep brain photoreceptors control light-seeking behavior in zebrafish larvae. Curr Biol. 2012 Vol 22  DOI 10.1016/j.cub.2012.08.016). We used the different transgenic lines, because lines (3) and (4) do not efficiently label catecholaminergic neurons at early stages, while lines (1) and (2) also have GFP expression in several other non-catecholaminergic populations at later stages of development. Embryos were dissociated and catecholaminergic neurons were FACS sorted from GFP-tagged zebrafish (Manoli and Driever, 2012, Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633). RNA was either processed for NanoCAGE, or mRNA was isolated and amplified. cDNA was sequenced by Illumina technique. This data submission is a series of data files consisting of three independent experiments with diffrent RNA-Seq depth: Samples 1-4 (NanoCage): Samples 5-8 (RNA-Seq high read numbers), and SAmples 9-12 (RNA-Seq low read numbers).

first: Martha

last: Manoli

first: Piero

last: Carninci


title: SMARCA4/Brg1 Coordinates Genetic and Epigenetic Networks Underlying Shh-type Medulloblastoma Development [ChIP-Seq]

first: Zhenyu

summary: Medulloblastoma could be classified into four subtypes: Wnt, Shh, Group 3, and Group 4. Subtypes of medulloblastoma have distinct epigenetic properties. We report that a chromatin regulator SMARCA4/Brg1 controls a transcriptional program that specifically required for Shh-type medulloblastoma identity and proliferation. We show that Brg1 deletion significantly inhibited tumor formation and progression in a mouse medulloblastoma model. Genomic experiments indicate that Brg1 specifically coordinates with key transcription factors including Gli1, Atoh1, and REST to regulate the expression of both oncogenes and tumor suppressors. Shh-type medulloblastoma displays distinct H3K27me3 properties. We demonstrate that Brg1 modulates activities of H3K27me3 modifiers to regulate expression of medulloblastoma genes. Brg1 is important for the growth of a human medulloblastoma cell line and Brg1-regulated pathways are conserved in human Shh-type medulloblastoma. This study reveals a novel epigenetic mechanism that controls medulloblastoma development and provides a rationale for developing subtype-specific treatment strategies.

overall_design: ChIP-seq analysis of Brg1 binding in SmoM2 medulloblastoma.

first: Xuanming

last: Shi

first: Jiang

last: Wu


title: The Genetic Legacy of the Expansion of Turkic-Speaking Nomads Across Eurasia

status: Public on Feb 21 2015

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

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

summary: We genotyped 322 new samples from 38 Eurasian populations and combined it with previously published data to characterize the population structure of Turkic-speaking populations in the context of their geographic neighbors across Eurasia

overall_design:
322 samples were analysed with the Illumina Human610-Quad, Human660W-Quad, and HumanOmni1-Quad Genotyping BeadChips and are described herein.

Please note that the '1M_Matrix_processed_2.txt' was provided on Jul 17, 2015 to replace the original file (with more missing values).

first: Richard

last: Villems

first: Bayazit

last: Yunusbaev


title: Stress-response pathways are altered in the hippocampus of chronic alcoholics.

status: Public on Sep 05 2013

city: Indianapolis

first: Jeanette

middle: Nance

last: McClintick

state: IN

address: 635 Barnhill Dr.

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

summary:
Comparison of gene expression in post-mortem hippocampus from 20 alcoholics and 19 controls.
The chronic high-level alcohol consumption seen in alcoholism leads to dramatic effects on the hippocampus, including decreased white matter, loss of oligodendrocytes and other glial cells, and inhibition of neurogenesis. Examining gene expression in post mortem hippocampal tissue from 20 alcoholics and 19 controls allowed us to detect differentially expressed genes that may play a role in the risk for alcoholism or whose expression is modified by chronic consumption of alcohol. We identified 639 named genes whose expression significantly differed between alcoholics and controls at a False Discovery Rate (FDR) ≤ 0.20; 52% of these genes differed by at least 1.2-fold. Differentially expressed genes included the glucocorticoid receptor and the related gene FK506 binding protein 5 (FKBP5), UDP glycosyltransferase 8 (UGT8), urea transporter (SLC14A1), zinc transporter (SLC39A10), Interleukin 1 receptor type 1 (IL1R1), thioredoxin interacting protein (TXNIP), and many metallothioneins. Pathways related to inflammation, hypoxia, and stress showed activation, and pathways that play roles in neurogenesis and myelination showed decreases. The cortisol pathway dysregulation and increased inflammation identified here are seen in other stress-related conditions such as depression and post-traumatic stress disorder and most likely play a role in addiction. Many of the detrimental effects on the hippocampus appear to be mediated through NF-κB signaling. Twenty-four of the differentially regulated genes were previously identified by genome-wide association studies of alcohol use disorders; this raises the potential interest of genes not normally associated with alcoholism, such as suppression of tumorigenicity 18 (ST18), BCL2-associated athanogene 3 (BAG3), and von Willebrand factor (VWF).

overall_design: Comparison of gene expression from frozen human post-mortem hippocampus from 20 alcoholics and 19 controls using one array per sample. There were 6 females in each group. Sex and labeling batch were included in the analysis.  The hippocampus samples came from the New South Wales Tissue Resource Centre at the University of Sydney, Australia, case ID provided for the sample. The total RNA samples were labeled in 2 balanced batches (indicated by labeling_batch). Brain sample QC provided by Tissue bank: brain pH and Post mortem interval in hours.  Repoistory website: http://sydney.edu.au/medicine/pathology/trc/

middle: N

first: Howard

last: Edenberg


title: Genome-wide analysis of interferon-stimulated genes in primary cells and immortalized cell lines

status: Public on Sep 13 2013

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

summary: Analysis of interferon-stimulated genes (ISGs) in various primary cells and immortalized cell lines, following type 1 interferon (IFN) treatment. Some cell types become resistant to HIV-1 infection following type 1 interferon treatment (such as macrophages, THP-1, PMA-THP-1, U87-MG cells and to a lesser extent, primary CD4+ T cells) while others either become only partially resistant (e.g., HT1080, PMA-U937) or remain permissive (e.g., CEM, CEM-SS, Jurkat T cell lines and U937); for more information see (Goujon and Malim, Journal of Virology 2010) and (Goujon and Schaller et al., Retrovirology 2013). We hypothesized that the anti-HIV-1 ISGs are differentially induced and expressed in restrictive cells compared to permissive cells and performed a whole genome analysis following type 1 IFN treatment in cell types exhibiting different HIV-1 resistance phenotypes.

overall_design: 48 samples; design: 9 cell lines, primary CD4+ T cells and primary macrophages, untreated and IFN-treated; 2 replicate experiments per cell line; 3 replicate experiments per primary cell type

first: Caroline

last: Goujon

first: Muddassar

last: Mirza

first: Michael

middle: H

last: Malim


title: Human breast cancer SKBr-3 cells: trastuzumab-resistant vs. parental

status: Public on May 25 2013

city: Xi'an

first: Lin-Tao

last: Jia

address: 169 ChangleWest Road

institute: Fourth Military Medical university

summary: Human breast cancer SKBr-3 cells selected with trastuzumab for 6 month compared with parental SKBr-3 cells; Goal was to screen for microRNAs involved in development of trastuzumab resistance.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Human breast cancer SKBr-3 cells were continuously cultured in the presence of  5µg/ml trastuzumab for 6 months, and the resulting alive cells were regarded as trastuzumab-resistant. Total RNAs were prepared from these cells and cells cultured in parallel in control media, and were subjected to hybridization on the miRCURY LNA Array (Exiqon, version 11.0).

first: An-Gang

last: Yang

first: Xing-Ming

last: Ye


title: [E-MTAB-599] Mouse Transcriptome

status: Public on Jul 14 2011

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

summary:
Sequencing the transcriptome of DBAxC57BL/6J mice.
To study the regulation of transcription, splicing and RNA turnover we have sequenced the transcriptomes of tissues collected DBAxC57BL/6J mice. We strongly encourage researchers to contact us if there is any queries about referencing or publishing analysis based on pre-publication data. This data is part of a pre-publication release. For information on use of the data and the data release policy please see: http://www.sanger.ac.uk/resources/mouse/genomes/datarelease.html

ArrayExpress Release Date: 2011-04-09

Publication Title: Sequence variation amongst 17 classical and wild-derived mouse genomes and its effect on gene regulation and phenotypic variation.
Publication Author List: Thomas M. Keane, Petr Daneck, Leo Goodstadt, Bret Payseur, Michael White, Kim Wong, Binnaz Yalcin, Andreas Heger, Avi Agam, Guy Slater, Martin Goodson, Nick Furotte, Eleazar Eskin, Christoffer Nellaker, Helen Whitley, James Cleak, Deborah Janowitz, Polinka Hernandez-Pliego, Amartjit Bhomra, Jerome Nicod, Xiangchao Gan, Wei Yuan, Louise van der Weyden, Sendu Bala, Allan Bradley, Jim Stalker, Richard Mott, Richard Durbin, Ian Jackson, Laura Reinholdt, Chris P. Ponting, Ewan Birney, Jonathan Flint, David J. Adams

Person Roles:  submitter
Person Last Name: Service
Person First Name: Submission
Person Mid Initials:
Person Email: datahose@sanger.ac.uk
Person Phone:
Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  project owner
Person Last Name: Adams
Person First Name: David
Person Mid Initials:
Person Email: da1@sanger.ac.uk
Person Phone:
Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: individual_genetic_characteristics_design
Experimental Design: replicate_design
Experimental Design: genotyping_design
Experimental Design: organism_part_comparison_design
Experimental Factor Name: ORGANISM_PART
Experimental Factor Type: organism_part


title: Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells [Affymetrix]

first: Marco Antonio

last: Mendoza-Parra

overall_design: time series gene expression assessed over the retinoic acide induced differentiation in P19 and F9 embryonal carcinoma cells. 5 timepoints over four different treatment conditions (ATRA; RARa agonist BMS753; RARb agonist BMS641 and the RARg agonist BMS961) assessed in P19 cells and compared with those assessed in F9 cells described in a previous study: GSE30537

first: Marco-Antonio

first: Valeriya

last: Malysheva

first: Mohamed

last: Saleem

first: Hinrich

last: Gronemeyer


title: A novel unusual chromosome 11 abnormality: a homozygous somatic deletion of the entire WT1 gene within a heterozygous 11p13 deletion and UPD limited to 11p15 in a Wilms tumor and establishment of an immortalized cell line

status: Public on Jun 01 2016

first: Brigitte

last: Royer-Pokora

summary: We describe a stromal predominant Wilms tumor with a complex, tumor specific chromosome 11 aberration: a homozygous deletion of the entire WT1 gene within a heterozygous 11p13 deletion and an additional region of uniparental disomy (UPD) limited to 11p15.5-p15.2 including the IGF2 gene. The tumor carried a heterozygous p.T41A mutation in CTNNB1. Cells established from the tumor carried the same chromosome 11 aberration, but a different, homozygous p.S45Δ CTNNB1 mutation. Uniparental disomy (UPD) 3p21.3pter lead to the homozygous CTNNB1 mutation. The tumor cell line was immortalized with telomerase (TERT) and a novel triple ts mutant SV40 large T antigen (LT). This cell line is cytogenetically stable and can be grown indefinitely. It is a valuable tool to study the effect of a complete lack of WT1 in tumor cells. The tumor cell line and the immortalized cells have a limited potential for muscle/osteogenic/adipogenic differentiation similar to all other WT1 mutant cell lines.

overall_design: Array expression experiment of Wilms tumor cell lines

first: Artur

last: Brandt

first: Katharina

last: Löhers

first: Manfred

last: Beier

first: Barbara

last: Leube

first: Carmen

last: Torres

first: Jaume

last: Mora

first: Nunu

last: Arora

first: Parmjit

last: Jat


title: Response to Avian Pathogenic Escherichia coli (APEC) Infection in diverse chicken tissues

status: Public on Feb 10 2017

first: hongyan

last: sun


title: SMARCA4/Brg1 Coordinates Genetic and Epigenetic Networks Underlying Shh-type Medulloblastoma Development [gene expression]

first: Zhenyu

last: Xuan

overall_design: Examine differential gene expression in SmoM2 medulloblastoma after Smarca4/Brg1 conditional knockout

first: Xuanming

last: Shi

first: Jiang

last: Wu