title: Comparative analysis of co-evolving host-parasite associations reveal unique expression patterns and pathways underlying slavemaker raiding and host defensive behavior in ants

status: Public on Jul 01 2017

city: Mainz

first: Austin

last: Alleman

address: Joh.-v.-Müller-Weg 6

department: Evolutionary Biology

institute: Feldmeyer-Foitzik Group

summary: The transition to parasitism is a drastic shift in lifestyle, involving rapid changes in gene structure, function, and expression. Evolutionarily 'young' parasites are ideal models for the elucidation of the early steps of this transition. After the establishment of an antagonistic relationship, parasite and host co-evolve through reciprocal adaptations resulting in an evolutionary arms-race. Repeated evolution of social parasitism and slavery among Temnothorax ants allows us to examine gene expression patterns characterizing slavemaker raiding and reciprocal host defensive behavior. Previous studies of Temnothorax provide evidence for co-evolving adaptations between parasites and hosts, as well as diverging raiding strategies between slavemakers. However, under parasite pressure, host defense portfolios shift similarly, suggesting diverging evolution of defensive traits. Through comparative gene expression analyses, we find that slavemaker raiding behavior is characterized by a down-regulation of numerous genes relative to their non-raiding state. Moreover, only a small number of genes shared expression between slavemaking species. In contrast, hosts possess a higher ratio of commonly-to-privately over-expressed genes and metabolic pathways during raids, suggesting that genes of similar function control defensive behavior. Additionally, a number of candidate genes were identified, each potentially playing a major role in shaping slavemaker- and host-specific behaviors. Finally, in two slavemaking species, functional enrichment analyses indicate that genes over-expressed during raiding behavior are associated with ribosomal structure, oxidation-reduction, and metabolic processes. Overall, our analysis revealed evidence for divergent evolution among closely-related ant species, where species-specific gene expression characterize raiding and defensive behavior.

sample_organism:
Temnothorax curvispinosus
Temnothorax longispinosus
Temnothorax duloticus
Temnothorax ambiguus
Temnothorax pilagens
Temnothorax americanus

overall_design:
Gene expression analysis using RNA-Seq data. Six species examined, two behaviors per species, and four replicates per behavior.

Please note that 2017July_TemnoClusters.fas-gb.tar.gz includes 5,197 OrthoMCL homologous cluster files (.fas-gb) containing all previously-identified contigs that are present within all six Temnothorax species.

first: Barbara

last: Feldmeyer

first: Susanne

last: Foitzik


title: Gene expression data from meningioma samples and healthy meningial cell line

status: Public on Feb 01 2017

city: IStanbul

first: Sukru

last: Gulluoglu

address: Acibadem Mah. IStek vakfi binasi

country: Turkey

institute: Yeditepe University

summary: Although meningioma is a common disease, there is a lack of understanding of the underlying molecular mechanisms behind its initiation and progression. We used combined miRNA-mRNA transcriptome analysis to discover novel genes and networks in meningiomas.

overall_design: Fourteen fresh-frozen meningioma samples and one human meningeal cell line were analyzed by using gene expression microarray chips. Data was filtered and analyzed.

first: Emre

middle: C

last: Tuysuz

first: Omer

middle: F

last: Bayrak


title: Genome-wide DNA methylation analysis of liver tissue samples obtained from patients with hepatitis virus-related hepatocellular carcinomas

status: Public on Apr 15 2017

city: Shinjyuku-ku

first: Yae

last: Kanai

state: Tokyo

address: 35, Shinano-machi

country: Japan

institute: Keio University School of Medicine

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling was performed in paired samples of non-cancerous liver tissue and the corresponding cancerous tissue obtained from patients with hepatitis virus-related hepatocellular carcinomas using the Illumina Infinium HumanMethylation450 Beadchip.

overall_design: 37 paired genomic DNA was extracted form fresh-frozen tissue specimens obtained from partial hepatectomy materials of 37 patients, who had provided written informed consent and suffered from hepatitis virus-related hepatocellular carcinomas. Genomic DNA was subjected to bisulfite conversion followed by Infinium assay.

first: Eri

last: Arai


title: Identifying RNA cargo of Drosophila S2 exosomes

status: Public on Jan 09 2018

city: Worcester

first: Travis

last: Thomson

state: Massachusetts

address: UMMS, 364 Plantation, LRB 760B

department: Neurobiology

country: USA

institute: Umass Medical School

type: Expression profiling by high throughput sequencing

summary: We isolated exosomes from Drosophila S2 cells, and sequenced RNAs in exosomes and compared them to cells.

overall_design: Isolated RNAs from exosomes and cells for 4 separate experiments.

first: Vivian

last: Budnik


title: Coordinated regulation of mitochondrial turnover by estrogen related receptor alpha and and thyroid hormone

status: Public on Mar 01 2017

city: Singapore

first: Brijesh

middle: Kumar

last: Singh

address: CVMD Level-8, 8 College Road

department: Cardiovascular and Metabolic Disorders Program

country: Singapore

institute: Duke-NUS Gradiate Medical School

summary: Transcriptome analysis showed that majot mitochondrial pathways are co-regulated by ESRRA and TH together.

overall_design: Mice received daily intraperitoneal injection of XCT790 (ESRRA inverse agonist; Sigma) for 4 days and L-T3 (liothyronine; Sigma) for last 3 days, and were sacrificed.

first: Paul

middle: M

last: Yen

middle: K

first: Madhulika

last: Tripathi

first: Sujoy

last: Ghosh


title: Real-time quantitative PCR analysis of murine splenic chemokines and cytokines [common cytokines assay]

status: Public on Jul 12 2016

city: Guangzhou

first: Chong

last: Wu

address: 135 Xin Gang Xi Road

country: China

institute: Sun Yat-sen University

summary: C57BL/6 mice were subjected to sham surgery or orthotopic Hepa1-6 hepatic tumor inoculation. Spleen tissues from mice subjected to sham surgery (control mice), mice bearing a 2-week orthotopic hepatoma, and mice bearing a 4-week othotopic hepatoma were collected. Total RNA was extracted from the spleen tissues, and we used the RT² Profiler PCR array-mouse common cytokines (SABioscience) array panels to quantitate gene expression of cytokine genes from the spleens.

overall_design: qPCR gene expression profiling. Spleen tissues from 5 mice per group were used as indicated in the summary.

first: Limin

last: Zheng


title: Real-time quantitative PCR analysis of murine splenic chemokines and cytokines

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

overall_design: Refer to individual Series


title: miRNA and gene expression data from meningioma samples and healthy meningial cell line

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

platform_organism:
Homo sapiens
synthetic construct


title: CDKN2B is an important tumor suppressor in pancreatic cancer

status: Public on Nov 09 2016

city: Kunming

first: Junjun

last: Hao

address: 32 Jiaochang Donglu Kunming

institute: Kunming Institute of Zoology

summary: This study demonstrates a critical role for CDKN2B inactivation in the development of pancreatic cancer and provides a potential adult animal model by mimicking the frequent genetic alterations of human pancreatic cancer in fully mature adult mouse.

overall_design: Examination the differental expression of 4 different development and pancreatic cancer in mouse.

first: Qiu

last: Tu


title: Analysis of the global transcriptome of 'sijimi' longan (Dimocarpus longan Lour.) using Illumina paired-end sequencing

status: Public on Mar 10 2017

city: Shenzhen

first: Zhangyan

address: Yantian district, Shenzhen

institute: Beijing Genomics Institute

summary: To improve the gene annotation and address a series of biological questions, we generated 490,502,822 clean reads of RNA-Seq data from nine tissue types of 'sijimi' longan, including root, stem, leaf, flower_bud, flower, young fruit, pericarp, pulp, and seed, and used them for mapping, and annotation of the longan genome sequence. About 53.55 ~79.40 % of the unique RNA sequences from nine RNA-seq data could be mapped to the genome. RNA-Seq data confirmed a majority of annotated introns, identified thousands of novel alternatively spliced mRNA isoforms, extend gene, SNP and indel, indicative of more functional variation than represented by the gene set alone, and a collection of potentially new and longan-specific gene. A comparative analysis of differential expression in the gene family at the nine different developmental stages showed that most of significant  differentially expressed genes were mainly involved in the metabolic pathway, plant- pathogen interaction, and biosynthesis of secondary metabolities, which was fully consistent with the standpoint of D. longan specise containing a lot of plant pahtogen resistant genes, and in particular containing high levels of polyphenolic compounds

overall_design:
 For Illumina sequencing, total RNA was extracted from 9 tissues using the TRIzol Reagent kit (Invitrogen, USA) according to the manufacturer's instructions. Samples then were treated with DNase I to remove any genomic DNA. Extracted RNA was quantified using a Agilent 2100(the Agilent Technologies 2100 Bioanalyzer)and checked for integrity using denaturing agarose gel electrophoresis with ethidium bromide staining. Only the RNA samples with A260/A280 ratios between 1.9 and 2.1, RNA 28S:18S ratios higher than 1.0 and RIN (RNA integrity number)=8.5 were used for further analysis. The poly (A)+ RNA was isolated from the total RNA of longan using Dynal oligo (dT) 25 beads according to the manufacturer’s instructions. Following purification, fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, N6 random hexamer-primer was used to synthesize first-strand cDNA using SuperScript III reverse transcriptase. Subsequently, the second-strand cDNA was synthesized using buffer, dNTPs, RNaseH and DNA polymerase I, respectively. The double-stranded cDNA were further processed by an end- repair using T4 DNA polymerase, the Klenow fragment, and T4 polynucleotide kinase, then ligated with adapters using T4 DNA ligase. The products were purified for the section of 200± 25 bp long using QiaQuick PCR extraction kit and resolved with EB buffer for adaptor-ligated fragments. And, after the agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification as templates. Then, the cDNA library was detected by Illumina HiSeq™ 2000.
Please note that this study is a part of Dimocarpus longan Lour. WGS project (Bioproject PRJNA305337) and was used for gene annotation improvement and gene expression analysis. The whole-genome shot gun sequenced reads of D. longan have been deposited at NCBI SRA database under Bioproject PRJNA305337 (SRA: SRA315202; sample accessions  SRS1272137-40). However, the identifiers in the processed data (e.g. Dlo_021756.1, Dlo_019949.1etc.) are not yet searchable in a public database. The longan genome data is being submittetd to GigaDB. The records will be updated in near future.

first: Zhong

middle: X

last: Lai


title: miRNA expression data from meningioma samples and healthy meningial cell line

first: Sukru

overall_design: Fourteen fresh-frozen meningioma samples and one human meningeal cell line were analyzed by using miRNA microarray chips. Data was filtered and analyzed.


title: Genome-wide EBF1 occupancy in pro-B cells

status: Public on May 09 2016

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

type: Genome binding/occupancy profiling by high throughput sequencing

summary: EBF1 ChIP in Rag2(-/-) pro-B cells

overall_design: Rag2 (-/-) pro-B cells were derived from mouse fetal liver and cultured on OP9 cells for short term

first: Sören

last: Boller

first: Rudolf

last: Grosschedl


title: Integrative Single-Cell Transcriptomics Reveals Molecular Networks Defining Neuronal Maturation during Neurogenesis

status: Public on Feb 29 2016

city: Madison

first: Xinyu

last: Zhao

state: Wisconsin

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

summary: Neurogenesis in the adult hippocampus contributes to information processing critical for cognition, adaptation, learning and memory, and is implicated in numerous neurological disorders. New neurons are continuously produced from neural stem cells via a well-controlled developmental process. The immature neuron stage defined by doublecortin (DCX) expression is the most sensitive to regulation by extrinsic factors. However, little is known about the dynamic biology within this critical interval that drives maturation and confers susceptibility to regulating signals. This study aims to test the hypothesis that DCX-expressing immature neurons in adult mouse hippocampus progress through developmental stages via activity of specific transcriptional networks. Using single-cell RNA-seq combined with a novel integrative bioinformatics approach, we discovered that individual immature neuron can be classified into distinct developmental subgroups based on characteristic gene expression profiles and subgroup-specific markers. Comparisons between immature and more mature subgroups revealed novel pathways involved in neuronal maturation. Genes enriched in more immature cells shared significant overlap with genes implicated in neurodegenerative diseases, while genes positively associated with neuronal maturation were enriched for autism-related gene sets. Our study thus discovers molecular signatures of individual adult-born immature neurons and unveils potential novel targets for therapeutic approaches to treat neurodevelopmental and neurological diseases.

overall_design: mRNA sequencing and expression estimation in 64 individual DCX-dsRed+ cells isolated from transgenic DCX-dsRed mice by FACS sorting

first: Yu

last: Gao

first: Feifei

last: Wang

first: Brian

middle: E

last: Eisinger

first: Laurel

last: Kelnhofer

first: Emily

last: Jobe


title: Transcriptomic profiling of cardiac biopsies from mice subjected to ischemic preconditioning

status: Public on Jun 24 2016

city: Lund

first: Olof

last: Gidlof

address: Solvegatan 19

country: Sweden

institute: Lund University

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

summary: Microarray profiling of cardiac biopsies from the area at at risk and remote myocardium of mice subjected to ischemic preconditioning.

overall_design: Mice were subjected to ischemic preconditioning (IPC) through reversible ligation of the left coronary artery or a sham procedure. The procedure consisted of 4 minutes of ischemia followed by 4 minutes of reperfusion, repeated 4 times and then followed by a 30 minute reperfusion period. Biopsies were taken from the area at risk (AAR) and remote myocardium (RM) from two IPC mice and two sham control mice.


title: NALP3 inflammasome up-regulation and CASP1 cleavage of the glucocorticoid receptor causes glucocorticoid resistance in leukemia cells [HumanMethylation450 Somatic]

status: Public on Mar 24 2015

city: Memphis

first: Steven

middle: William

last: Paugh

state: TN

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences Department

institute: St. Jude Children's Research Hospital

summary: Glucocorticoids are universally used in the treatment of acute lymphoblastic leukemia (ALL), and glucocorticoid resistance in leukemia cells confers a poor prognosis.  To elucidate mechanisms of glucocorticoid resistance, we determined the prednisolone sensitivity of primary leukemia cells from 444 newly diagnosed ALL patients and found significantly higher expression of caspase 1 (CASP1) and its activator NLRP3 in glucocorticoid resistant leukemia cells, due to significantly lower somatic methylation of CASP1 and NLRP3 promoters.  Over-expression of CASP1 resulted in cleavage of the glucocorticoid receptor, diminished glucocorticoid-induced transcriptional response and increased glucocorticoid resistance. Knockdown or inhibition of CASP1 significantly increased glucocorticoid receptor levels and mitigated glucocorticoid resistance in CASP1 overexpressing ALL.  Our findings establish a new mechanism by which the NLRP3/CASP1 inflammasome modulates cellular levels of the glucocorticoid receptor and diminishes cell sensitivity to glucocorticoids. The broad impact on glucocorticoid transcriptional response suggests this mechanism could also modify glucocorticoid effects in other diseases.

overall_design: DNA methylation profiling

middle: W

first: Wenjian

last: Yang

first: William

last: Evans


title: Transcriptional profile of human white adipocytes (hMADS cells) after white-to-brown conversion

status: Public on Dec 19 2016

city: Toulouse cedex 4

first: Nathalie

last: Viguerie

address: 1 avenue Jean Poulhès BP 84225

department: Institute of Metabolic and Cardiovascular Diseases, UMR1048

country: France

institute: INSERM-Université Paul Sabatier

summary: This study aimed at determining the transcriptional changes associated with the white-to-brown conversion of human mesenchymal adipose-derived stem cells firstly differentiated into white adipocytes (in the presence of rosiglitazone from day 2 to day 9). White differentiation was completed within 14 days, and PPARg (rosiglitazone) or PPARa (GW7647) agonists were added to the medium for 4 additional days to induce the brown phenotype. Cells were harvested at day 18 and processed for microarray experiments (Agilent).

overall_design: All samples were co-hybridized with a reference pool of RNA from hMADS cells at D9 of differentiation. Four samples of each condition (control, rosiglitazone- and GW7647-treated cells) obtained in 4 independent experiments were used.

first: Valentin

last: Barquissau


title: NALP3 inflammasome up-regulation and CASP1 cleavage of the glucocorticoid receptor causes glucocorticoid resistance in leukemia cells [HG-U133A]

overall_design: Gene expression profiling


title: miRNA expression profile in intestinal ischemia reperfusion of adult mice

status: Public on Jun 25 2016

city: Dalian

first: Xiaofeng

last: Tian

address: Zhongshan Road NO.467

department: General Surgery

institute: The Second Hospital of Dalian Medical University

summary: Intestinal ischemia/reperfusion (I/R) contributes to tissue damage, cellular apoptosis, systemic inflammatory responses, and even multiple organ dysfunction syndrome, however, underlying mechanisms remain unkown. In this report, we provide a comprehensive assessment of the expression of 1177 miRNAs on intestine tissues from mice suffering from sham and intestinal I/R. We find that 57 miRNA are up-regulated and 74 are down-regulated significantly. MiRNAs may be integral modulators of intestinal inflammation and enterocyte apoptosis associated with I/R and represent novel targets for future therapeutics.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In the study, we profiled miRNA expression in the intestine from mice of 3 sham group and 3 intestinal ischemia/reperfusion group.

first: Jihong

last: Yao

first: Zhenlu

last: Li

first: Guangzhi

first: Guo

last: Zuo

first: Dongcheng

last: Feng

first: Yang

first: Wei

last: Xu

first: Huirong

last: Jing


title: Real-time quantitative PCR analysis of murine splenic chemokines and cytokines [chemokines & receptors assay]

first: Chong

last: Wu

summary: C57BL/6 mice were subjected to sham surgery or orthotopic Hepa1-6 hepatic tumor inoculation. Spleen tissues from mice subjected to sham surgery (control mice), mice bearing a 2-week orthotopic hepatoma, and mice bearing a 4-week othotopic hepatoma were collected. Total RNA was extracted from the spleen tissues,and we used the RT² Profiler PCR array-mouse chemokines & receptors (SABioscience) array panel to quantitate gene expression of chemokine and receptor genes from the spleens.

first: Limin

last: Zheng


title: NALP3 inflammasome up-regulation and CASP1 cleavage of the glucocorticoid receptor causes glucocorticoid resistance in leukemia cells [HumanMethylation450 Germline]


title: Pioneering activity of the C-terminal domain of EBF1 shapes the chromatin landscape for B cell programming

status: Public on May 06 2016

first: Senthilkumar

last: Ramamoorthy

type: Methylation profiling by high throughput sequencing


title: NALP3 inflammasome up-regulation and CASP1 cleavage of the glucocorticoid receptor causes glucocorticoid resistance in leukemia cells [ChIP-Seq]

first: Steven

overall_design: Duplicate treatments of two conditions (wild type and CASP1) including input controls


title: NALP3 inflammasome up-regulation and CASP1 cleavage of the glucocorticoid receptor causes glucocorticoid resistance in leukemia cells [HumanMethylation27]

first: Wenjian


title: NALP3 inflammasome up-regulation and CASP1 cleavage of the glucocorticoid receptor causes glucocorticoid resistance in leukemia cells [HG-U133_Plus_2]

first: William


title: NALP3 inflammasome up-regulation and CASP1 cleavage of the glucocorticoid receptor causes glucocorticoid resistance in leukemia cells [cell line Nalm6]

overall_design: Two by two treatment in quadruplicate


title: Gene expression analysis in developmentally arrested root nodules formed by Sinorhizobium meliloti and Medicago truncatula

status: Public on Jun 01 2015

city: Stanford

first: Melanie

middle: J

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

summary: The bacterium, Sinorhizobium meliloti, interacts symbiotically with leguminous plants such as Medicago truncatula to form nitrogen-fixing root nodules. During symbiosis, plant and bacterial cells differentiate in a coordinated manner, resulting in specialized plant cells that contain nitrogen-fixing bacteroids. Medicago nodules are organized in structurally distinct tissue zones, representing different stages of bacterial and plant differentiation. We used laser-capture microdissection (LCM) to analyze bacterial and plant gene expression in four root nodule regions. In parallel, we analyzed gene expression in nodules formed by wild type bacteria on six plant mutants with nitrogen fixation deficiencies (dnf). We found that bacteroid metabolism is drastically remodeled during bacteroid differentiation. Many processes required for bacterial growth are down-regulated in the nitrogen fixation zone. The overall transcriptional changes are similar to those occurring during nutrient limitation by the stringent response. We also observed differential expression of bacterial genes involved in nitrogen fixation, cell envelope homeostasis, cell division, stress response and polyamine biosynthesis at distinct stages of nodule development. In M. truncatula we observed the differential regulation of several host processes that may trigger bacteroid differentiation and control bacterial infection. We analyzed plant and bacterial gene expression simultaneously, which allowed us to correlate processes in both organisms.

sample_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: We harvested root nodules from nitrogen fixation deficient Medicago truncatula mutants dnf1, dnf2, dnf3, dnf4, dnf5, dnf7 and two wild type lines M. truncatula  [Gaertn.] cv Jemalong and A-17 21 days after inoculation with Sinorhizobium meliloti CL150. For each of three replicates we harvested root nodules from 9-17 plants. In order to identify symbiotically regulated genes we carried out pairwise comparisons between the samples and used hierarchical clustering to group genes with similar expression profiles.

first: Claus

last: Lang

first: Sharon

middle: R

last: Long


title: Gene expression data of ovarian cancer from Singapore

status: Public on Jan 10 2016

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

institute: National University of Singapore

summary: A collection of 100 ovarian cancer sample gene expression data from Singapore.

overall_design: Frozen archival epithelial ovarian cancer tumors samples from Department of Obstetrics & Gynecology, National University of Singapore dated from 2006 to 2014 were collected and subjected to microarray analysis.

first: Ruby

middle: Y

last: Huang

first: Jieru

last: Ye

first: Jeffrey

last: Low

first: Mahesh

last: Choolani

first: Jean

middle: P

last: Thiery

first: Tuan

middle: Z


title: NALP3 inflammasome up-regulation and CASP1 cleavage of the glucocorticoid receptor causes glucocorticoid resistance in leukemia cells

last: Paugh


title: Sexual Dimorphism in the Th17 Signature of Ankylosing Spondylitis

status: Public on Oct 07 2015

city: Toronto

first: Eric

last: Gracey

state: ON

address: 60 Leonard Ave

department: Immunology

country: Canada

institute: University of Toronto

summary: Male AS patients have an elevated Th17 cell frequency vs. female AS patients (Gracey et al, Arthritis and Rheumatology, 2015). This analysis was performed to further examine differences between male and female AS patients

overall_design: AS patients were compared to healthy controls (HC). For sex-specific anaylsis, three groups were compared: F-HC vs. M-HC, M-AS vs. M-HC and F-AS vs. F-HC. A one way ANOVA was performed to identify genes differentially regulated in male and female AS patients

first: Robert

middle: D

last: Inman


title: Comparative in situ gene expression profile of starry-sky tumor-associated macrophages and germinal centre macrophages

status: Public on Dec 20 2014

city: Edinburgh

first: Christopher

last: Gregory

address: 47 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

summary: Cells undergoing apoptosis are known to modulate their tissue microenvironments. By acting on phagocytes, notably macrophages, apoptotic cells inhibit immunological and inflammatory responses and promote trophic signaling pathways. Paradoxically because of their potential to cause death of tumor cells and thereby militate against malignant disease progression, both apoptosis and tumor-associated macrophages (TAM) are often associated with poor prognosis in cancer. In order to better understand the influence of tumor cell apoptosis and in particular its effect on TAM, we investigated global gene expression signatures of undisturbed TAM engaged in engulfment of apoptotic tumor cells. We studied a xenograft model of an aggressive ‘starry-sky’ non-Hodgkin’s lymphoma, Burkitt’s lymphoma (BL), in which apoptotic tumor cells are common and frequently observed in association with the starry-sky TAM  (SS-TAM, so called because they appear histologically as ‘stars’ in a ‘sky’ of tumor cells) that accumulate in these tumors. We used a BL cell line (BL2) whose cells phenotypically resemble the tumor biopsy cells from which the line was derived including the capacity to undergo apoptosis constitutively. BL xenografts in SCID mice closely recapitulated the starry-sky histological picture of the human lymphoma. Due to the high sensitivity of macrophages to their environments, we adopted laser-capture microdissection of individual SS-TAM in BL xenografts in order to obtain unbiased in situ transcriptional profiles of these cells, which we compared specifically with those of similarly-captured macrophages, the tingible-body macrophages from normal germinal centers (GCM). The rationale for this comparison was based upon BL being a germinal center malignancy and tingible-body macrophages being regarded as normal equivalents of SS-TAM.

overall_design: Gene expression profiles of SS-TAM from BL2 xenograft tumors were compared to splenic GCM profiles. Three mice from each group were analysed. RNA was isolated from 1000 captured macrophages from each mouse and global gene expression signatures were obtained using Affymetrix Mouse Gene 1.0 GeneChip arrays.

first: Sofia

last: Petrova

first: Catriona

middle: A

last: Ford

first: Jorine

last: Voss

first: Tom

last: Freeman

first: Donald

last: Dunbar


title: Cytogenomic profiling of breast cancer brain metastases reveals potential for repurposing targeted therapeutics

status: Public on Dec 31 2014

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

summary:
Comparative genomic hybridization analysis for detection of copy number variation for cancer genes in breast cancer mestastatic brain tumors
DNA was isolated and analyzed in a two-color experiment using Cancer CGH+SNP 180Kx4 arrays from Agilent and Agilent SureScan system: Cy5-labeled specimen DNA and Cy3-labeled reference Agilent (female) reference DNA

overall_design: 10 metastatic brain tumor specimens originating from breast cancer were analyzed (6 of which were only fresh frozen treated and 4 specimens were divided to run both fresh frozen and formalin fixed parafin embeded counterparts), also investigated were 4 matched primary breast cancer specimens (FFPE treated).


title: small RNA analysis in human platelets stored in blood bank

status: Public on Sep 30 2014

city: Rio de Janeiro

first: Daniel

last: Carvalho

state: Rio de Janeiro

address: Caixa Postal 26820

country: Brazil

institute: GenOne Biotetechnologies

type: Non-coding RNA profiling by high throughput sequencing

summary: Human platelets collected from healthy donors according to standard international protocols were pooled and stored at 4ºC during 7 days. The small RNA population changes across the days were evaluated by NGS aproach.

overall_design: The smallRNA population was evaluated at fresh platelets and after 1 day, 2 days, 3 days, 4 days, 5 days and 7 days of storage at 4ºC.

first: Rommel

last: Rodríguez Burbano

first: Caroline

last: Moreira Nunes


title: Medial prefrontal cortex: genes linked to bipolar disorder and schizophrenia have altered expression in the highly social maternal phenotype

status: Public on Feb 28 2014

first: Xinyu

last: Zhao

summary: The transition to motherhood involves CNS changes that modify sociability and affective state.  However, these changes also put females at risk for postpartum depression and psychosis, which impairs parenting abilities and adversely affects children.  Thus, changes in expression and interactions in a core subset of genes may be critical for emergence of a healthy maternal phenotype, but inappropriate changes of the same genes could put women at risk for postpartum disorders.  This study evaluated microarray gene expression changes in medial prefrontal cortex (mPFC), a region implicated in both maternal behavior and psychiatric disorders.  Postpartum mice were compared to virgin controls housed with females and isolated for identical durations.  Using the Modular Single-set Enrichment Test (MSET), we found that the genetic landscape of maternal mPFC bears statistical similarity to gene databases associated with schizophrenia (5 of 5 sets) and bipolar disorder (BPD, 3 of 3 sets).  In contrast to previous studies of maternal lateral septum and medial preoptic area, enrichment of autism and depression-linked genes was not significant (2 of 9 sets, 0 of 4 sets).  Among genes linked to multiple disorders were fatty acid binding protein 7 (Fabp7), glutamate metabotropic receptor 3 (Grm3), platelet derived growth factor, beta polypeptide (Pdgfrb), and nuclear receptor subfamily 1, group D, member 1 (Nr1d1).  RT-qPCR confirmed these gene changes as well as FMS-like tyrosine kinase 1 (Flt1) and proenkephalin (Penk).  Systems-level methods revealed involvement of developmental gene networks in establishing the maternal phenotype and indirectly suggested a role for numerous microRNAs and transcription factors in mediating expression changes.  Together, this study suggests that a subset of genes involved in shaping the healthy maternal brain may also be dysregulated in mental health disorders and put females at risk for postpartum psychosis with aspects of schizophrenia and BPD.

overall_design: In total, 10 total RNA samples derived from micropunched medial prefrontal cortex were used for microarray analysis: 5 samples from lactating maternal mice (maternal) and 5 samples from age-matched virgin mice (virgin).  All samples are biological replicates.

first: Brian

last: Eisinger

first: Terri

last: Driessen

first: Changjiu

first: Stephen

last: Gammie


title: Ablation of coactivator Med1 regulates bulge keratinocyte stem cells and accelerates epidermal regeneration after injury [skin wound]

status: Public on Jan 01 2014

city: San Francisco

first: Yuko

last: Oda

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

summary: Transcriptional coactivator Mediator complex facilitates transcription of various transcription factors. Previously, we have generated Med1 conditional null mice, where a critical subunit of Mediator, Med1, is removed from keratinocytes. Here we present evidence that ablation of Med1 accelerated epidermal regeneration after injury. As bulge keratinocyte stem cells are important contributors to regenerate epidermis, we first analyzed properties of stem cells in Med1 null mice. BrdU long retaining analysis revealed that deletion of Med1 still maintained quiescence of bulge keratinocyte stem cells, despite of general hyperplasia observed in Med1 deficient keratinocytes. Gene expression analysis demonstrated that a series of niche matrix proteins decreased in Med1 deficient keratinocytes. In contrast, the expression of stem cell marker Sox9 was not altered, suggesting stem cells are present but activated because of abnormal niche surrounding stem cells. In addition, Med1 deletion suppressed injury induced inflammatory reaction, which indirectly regulates epidermal regeneration.  We also indicated that TGFβ1 significantly decreased in both bulge and epidermal keratinocytes upon Med1 deletion. Our study demonstrates that coactivator Med1 has a critical role to maintain bulge stem cells and epidermal regeneration presumably through regulation in TGFβ signaling.

overall_design: n=3 WT and KO (each sample contain RNA isolated from wounded or nonwounded skins excised from 3 mice)

first: Lizhi

last: Hu

first: Thai

last: Nguyen

first: Frankie

last: Fong

last: Bikle


title: Ablation of coactivator Med1 regulates bulge keratinocyte stem cells and accelerates epidermal regeneration after injury [10wk skin]

overall_design: n=4 WT and KO (each sample contain RNA from one mouse)


title: Epigenetic and transcriptional control in hematopoietic development and lineage differentiation

status: Public on Jul 28 2014

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

summary: Hematopoiesis is a well-established model system to study molecular mechanisms of lineage-specific differentiation. Key transcription factors (TFs), such as PU.1, NF-E2 and GATA1 are implicated in crucial aspects of distinct hematopoietic lineages. How TFs collaborate with histone modificatons and how they affect the chromatin status remains to be elucidated. Chromatin-Immunoprecipitation followed by next-generation sequencing (ChIP-seq) has been proven to be an excellent tool to study chromatin modifications genome-wide. In this study, ChIP-seq was used to investigate the H3K4me2 landscape at enhancers during hematopoietic differentiation, starting from the hematopoietic stem cell (HSC) up to the fully differentiated erythrocyte, megakaryocyte or granulocyte. Although cell morphology and gene expression profiles differ extensively in committed erythrocytes, megakaryocytes and granulocytes, the genomic landscape of H3K4me2 is surprisingly alike across the three cell types. Granulocytes, in particular, seem to display an ‘erythocyte-like’ chromatin pattern. Similar results were observed for another chromatin mark, H3K27ac. Unexpectedly, the common progenitors of erythrocytes and granulocytes do not display a similar chromatin pattern, excluding the idea that the H3K4me2 mark is placed early on during differentiation. These results also suggest that the chromatin state is probably not the determining factor for lineage differentiation, but that rather lineage specific TF binding is important. In agreement with this, mature megakaryocytes loose the H3K4me2 mark surrounding erythrocyte-specific genes. This might be explained because megakaryocytes and erythrocytes both express the lineage specific TFs GATA1 and NF-E2. Altogether, we show that committed granulocytes and erythrocytes display similar H3K4me2 and H3K27ac patterns, and that those marks alone cannot predict which genes will be expressed eventually.

overall_design: Genomic ChIP-Seq on key transcription factors and histone modification marks in hematopoiesis

first: Annouck

last: Luyten

first: Ramesh

last: Shivdasani

first: X

middle: S

last: Liu


title: Ablation of coactivator Med1 regulates bulge keratinocyte stem cells and accelerates epidermal regeneration after injury [10wk keratinocyte]

overall_design: n=3 WT and KO (each group contains keratinocytes isolated from adult skins excised from 2 mice)

middle: C


title: Effects of mixed exercise training on gene expression in human skeletal muscle

status: Public on Dec 24 2013

city: Wageningen

first: Milene

last: Catoire

address: Bomenweg 2

department: Human Nutrition

country: Netherlands

institute: Wageningen University

summary: Background: Exercise has a positive effect on overall health. This study was performed to get an overview of the effects of mixed exercise training on skeletal muscl

overall_design: 18 middle-aged men performed 12 weeks of exercise training (2x endurance training and 1x resistance training), muscle biopsies were taken at baseline and 3 days after the last training session

first: Milène

first: Marco

last: Mensink

first: Patricht

last: Schrauwen

first: Sander

last: Kersten


title: Microarray analysis of male strobili in fertile and sterile male strobili of Cryptomeria japonica

status: Public on Jul 30 2013

city: Tsukuba

first: Norihiro

last: Futamura

state: Ibaraki

address: 1 Matsunosato

institute: Forestry and Forest Products Research Institute (FFPRI)

type: Expression profiling by genome tiling array

summary:
Investigation of comprehensive gene expression level changes in male strobili of sterile mutant, compared to the fertile plant. We designed a new custum array derived from ESTs of Cryptomeria japonica for this study.
Male strobili of C. japonica were collected from Toyama 1 half-sib F2 pedigree. Toyama 1 male-sterile mutant was first reported in Saito, M. , H. Taira, and Y. Furuta (Journal of Forest Research 3(3):167-173).

overall_design: Microarray studies using both individual samples and pooled samples were performed. Total RNA was extracted from male strobili at four developmental stages derived from each seven fertile and male-sterile trees as individual samples. Pooled RNA samples were prepared from four to eight different fertile and sterile plants at three developmental stages.

first: Kenji

last: Shinohara


title: Ablation of coactivator Med1 regulates bulge keratinocyte stem cells and accelerates epidermal regeneration after injury.

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

overall_design: Refer to individual Series

first: Daniel


title: Genome-wide expression profiling in bone marrow-derived macrophage (BMM) cells upon RANKL treatment

status: Public on Jul 30 2014

city: Los Angeles

first: Kyunghwan

last: Kim

state: California

address: 1450 Biggy Street NRT6517

department: Biochemistry and Molecular Biology

institute: University of Southern California

summary: To screen for altered gene expression during osteoclastogenesis, RANKL-treated BMM cells were subjected to gene expression profiling.

overall_design: BMM cells were treated with M-CSF and RANKL for 0, 1, 2 and 3 days. Total RNA was isolated and analyzed by gene expression microarray using the MouseRef-8 v2.0 Expression BeadChip.

last: An

first: Wange

last: Lu

first: Woojin


title: Expression data from post mortem Alzheimer's disease brains

status: Public on Apr 17 2013

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

summary:
To identify molecular pathological alterations in AD brains, we performed interspecies comparative microarray analyses using RNAs prepared from postmortem human brain tissues donated for the Hisayama study and hippocampal RNAs from the triple-transgenic mouse model of AD (3xTg-AD)
Three-way ANOVA of microarray data from frontal cortex, temporal cortex and hippocampus with presence/absence of AD and vascular dementia, and sex, as factors revealed that the gene expression profile is most significantly altered in the hippocampi of AD brains. Comparative analyses of the brains of AD patients and a mouse model of AD showed that genes involved in non-insulin dependent DM and obesity were significantly altered in both, as were genes related to psychiatric disorders and Alzheimer’s disease.

overall_design: We prepared RNA samples from the gray matter of frontal and temporal cortices and hippocampi derived from 88 postmortem brains, among which 26 cases were pathologically diagnosed as having AD or an AD-like disorder. High-quality RNA (RIN≧6.9) samples were subjected to microarray analysis using the Affymetrix Human Gene 1.0 ST platform, and only those results that passed examinations for quality assurance and quality control of the Human Gene 1.0 ST arrays were retrieved. In total, we obtained gene expression profiles from the following samples: 33 frontal cortex samples, among which 15 were from AD patients; 29 temporal cortex samples, among which 10 were from AD patients; 18 hippocampus samples, among which 8 were from AD patients

first: Masaaki

last: Hokama

first: Nona

last: Abolhassani


title: Expression data of TAGLN-overexpressing RKO human colon cancer cells

status: Public on Jul 18 2013

city: Guangzhou

first: Ying

last: Lin

state: Guangdong

address: 107 West Yanjiang Road

department: Gastroenterology and Hepatology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen Univeristy

summary:
Transgelin was the top-ranked marker of metastatic potential identified in the comparison of node-positive colorectal cancer (CRC) versus node-negative CRC in our previous study. Transgelin is localized in the nucleus of cultured CRC cells and microRNA-mediated knockdown of TAGLN (the gene encoding transgelin) expression modulates the expression of genes involved in the epithelial-to-mesenchymal transition.
We performed gene expression profiling on control and transgelin-overexpressing RKO cells using Affymetrix microarray technology.

overall_design: The plasmid carrying TAGLN was generated using the pcDNA6.2/EmGFP-Bsd/V5-DEST vector (Invitrogen, Carlsbad, CA) and the pDONR221-TAGLN-mut plasmid from a previous study by an LR recombination reaction (http://www.invitrogen.com). After lipofectamine-mediated transfection of the TAGLN-carrying plasmid or the vector-only control plasmid, stable transfectants were selected and cultured in medium containing 25 μg/ml blasticidin followed by RNA extraction and hybridization on Affymetrix microarrays. Six samples were obtained from three independent experiments (technical replicates).

first: Yuan-yuan

last: Fang

first: Hui-min

last: Zhou


title: Expression data from control and Ascorbic Acid (AA) stimulated Mc-3T3-E1 osteoblasts

status: Public on May 02 2012

first: Noushin

last: Nabavi

address: 1265 Military Trail

summary:
Despite advances in investigating functional aspects of osteoblast (OB) differentiation, especially studies on how bone proteins are deposited and mineralized, there has been little research on the intracellular trafficking of bone proteins during OB differentiation.  Collagen synthesis and secretion is markedly upregulated upon Ascorbic Acid (AA) stimulation.  Understanding the mechanism by which collagen is mobilized in specialized OB cells is important for both basic cell biology and diseases involving defects in bone secretion and deposition.  RabGTPases are major regulators on protein trafficking throughout the cell.  In this study, we identified the Rab GTPases that are upregulated during 5-day AA differentiation of OBs using microarray analysis, namely Rab1, Rab3d and Rab27b.
We used microarrays to detail the global programme of gene expression underlying procollagen production and trafficking and identified up-regulated genes during this process.

overall_design: Control Mc3T3-E1 cells and 5 day Ascorbic Acid stimulated cells were processed for RNA extraction and hybridization on Affymetrix microarrays.

first: Rene

last: Harrison


title: Genome-wide analysis of   transcription factor PfNF-YB in Plasmodium falciparum.

status: Public on Jul 16 2013

city: Sao Paulo

first: Wania

middle: Rezende

last: Lima

state: Sao Paulo

address: Rua Matão, travessa 14, n 321

department: Physiology

institute: University of São Paulo

type: Genome binding/occupancy profiling by genome tiling array

summary: PfNF-YB is a transcription factor of Plasmodium falciparum and is known as a CCAAT-box-binding subunit B. PfNF-YB belongs to NF-Y complex family that is conserved from yeast to human. PfNF-YB is highly expressed in schizont stage and co-localized at the nucleus in mature form during intraerythrocytic stage. We found that melatonin and cAMP second messenger can modulate the PfNF-YB expression in P. falciparum. To better understand the function of PfNF-YB in P. falciparum we proposed to perform chromatin immunoprecipitation (ChIP) of PfNF-YB together with chromatin profiling by ChIP-on-chip analysis. The results showed that PfNF-YB binds to CCAAT of several genes in schizont stage.

overall_design: comparison of PfNF-YB vs control beads and IgG

first: David

last: Martins-Jr

first: Kleber

last: Parreira

first: Anthony

last: Holder

first: Ronaldo

middle: F

last: Hashimoto

first: Célia

last: S Garcia


title: Extension of Life-span with Enhanced Energy Expenditure by a Modulator of NAD-metabolism in Aged Mice

status: Public on May 01 2011

city: Daejeon

first: JeongSook

last: Lee

address: 335 Gwahangno

department: Biological science

country: South Korea

institute: KAIST

summary: Analysis of treatment at gene expression level in aged mice. Results provide important information of the response of drug modifying NAD metabolism which has been implicated in anti-aging effect of calorie restriction in aging process.

overall_design: Total RNA obtained from skeletal muscles and brain (cortex) subjected to calorie restriction or β-lapachone treatment compared to untreated control.

first: Jeongsook

first: Ahhyung

last: Park

first: Seonmi

last: Jo

first: Sanghee

first: Myungkyu

first: Sangku

last: Yoo

first: Sukjin

last: Yang

first: Youngil

last: Yeom

first: Taehwan

last: Kwak

first: Jinman

last: Kim

first: Daesoo


title: Hepatic molecular alterations more than muscle's differentiate obese hyperphagic mice from those prolonged fed with the high-fat diet

status: Public on May 01 2013

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary:
Although mitochondrial dysfunctions are implicated in the pathogenesis of obesity, the molecular mechanisms underlying obesity-related metabolic abnormalities are still not well established. To acquire a comprehensive picture of mitochondrial molecular changes within metabolically active tissues, we focused on hepatic and muscle whole cellular transcriptome and mitochondrial proteome alterations in 16 and 48 weeks old high fat diet (HFD)-feed wild type C57BL/6J and hyperphagic, genetically modified mice with leptin dysfunction (ob/ob and db/db).
On transcriptome level, the most discriminative hepatic alterations distinguished between genetically modified and wild type mice, and between overnight fasted and non-fasted mice, while the muscle transcriptional alterations related mainly to the fasting state. The fractions of uniquely different proteins were consistently higher in hyperphagic than in HFD-fed mice and in fasted than non-fasted mice . The liver samples revealed overall higher number of differentially expressed RNAs and proteins than muscle samples. Differentially expressed genes and proteins in the liver, but not in the muscle, could be assigned to several Gene Ontology terms, including oxidation-reduction and several metabolic processes. Thus, altered expression of genes and proteins accompanied the state of obesity and was quantitatively different in the liver and muscle.
Our parallel microarray- and quantitative mitochondrial mass spectrometry-based study performed on hepatic and muscle samples identified a higher number of differentially expressed proteins than any other studies investigating obesity-related proteomes. However, even with our integrated transcriptomic and proteomic approach still many details and dynamics of a chain of metabolic events leading to obesity-related mitochondrial dysfunctions remain unresolved .

overall_design: 48 samples each of liver and muscle (total samples: 96). Samples splitted equally according to 3 criterions: age (24 young/24 old), fasting status (24 fasted/24 non fasted), and strain+diet (12 each: B6.V-Lep ob/J+D12450B, B6.BKS(D)-Lep rdb/J+D12450B, C57BL/6J+D12450B, C57BL/6J+D12492). Overall 3 replicates for each strain+diet/age/fasting_status combination. Low fat diet = D12450B; high fat diet = D12492.

first: Monika

last: Nesteruk

first: Ewa

last: Hennig

first: Michal

last: Mikula

first: Jakub

last: Karczmarski

first: Artur

last: Dzwonek

first: Tymon

last: Rubel

first: Agnieszka

last: Paziewska

first: Marek

last: Woszczynski

first: Joanna

last: Ledwon

first: Michalina

last: Dabrowska

first: Bozena

last: Walewska-Zielecka

first: Kazimiera

last: Pysniak

last: Dadlez

first: Jerzy

last: Ostrowski


title: Large Scale Expression Changes of Genes Related to Neuronal Signaling and Developmental Processes Found in Lateral Septum of Postpartum Outbred Mice

status: Public on Mar 26 2013

city: Madison

first: Xinyu

last: Zhao

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

summary: Coordinated gene expression changes across the CNS help to produce the mammalian maternal phenotype.  Lateral septum (LS) is a brain region critically involved with aspects of maternal care, and we recently examined gene expression of whole septum (LS and medial septum) in selectively bred maternal mice.  Here, we expand on the prior study by 1) conducting microarray analysis solely on LS in virgin and postpartum mice, 2) using outbred mice, and 3) evaluating the role of sensory input on gene expression changes.  Large scale changes in genes related to neuronal signaling were identified, including nine GABAA receptor subunits (p<0.05).  Subunits α4 and δ were downregulated in maternal LS, likely reflecting a reduction in the extrasynaptic, neurosteroid-sensitive α4/δ containing receptor subtype.  Conversely, subunits ε and θ were increased in maternal LS.  Sixteen K+ channel related genes showed altered expression, as did dopamine receptors Drd1a and Drd2 (both downregulated), hypocretin receptor 1 (Hcrtr1), kappa opioid receptor 1 (Oprk1), and transient receptor potential channel 4 (Trpc4).  Expression of a large number of genes linked to developmental processes or cell differentiation were also altered in postpartum LS, including chemokine (C-X-C) motif ligand 12 (Cxcl12), fatty acid binding protein 7 (Fabp7), plasma membrane proteolipid (Pllp), and suppressor of cytokine signaling 2 (Socs2).  Additional genes that are linked to anxiety, such as glutathione reductase (Gsr), exhibited altered expression.  Pathway analysis also identified changes in genes related to cyclic nucleotide metabolism, chromatin structure, and the Ras gene family.  The sensory presence of pups was found to contribute to the altered expression of a subset of genes across all categories.  This study suggests that both large changes in neuronal signaling and the possible terminal differentiation of neuronal and/or glial cells play important roles in producing the maternal state.

overall_design: In total, 18 total RNA samples derived from microdissected lateral septum were used for microarray analysis: 6 samples from lactating maternal mice (maternal), 6 samples from maternal mice that have had their pups removed (pups removed), and 6 samples from age-matched virgin mice (virgin).  All samples are biological replicates.

first: Brian

last: Eisinger

first: Changjiu

first: Terri

middle: M

last: Driessen

first: Charles

last: Saul

first: Stephen

last: Gammie


title: Genome-wide profiling of whole blood from healthy adult volunteers before and after receiving non-live vaccines including seasonal influenza or pneumococcal vaccine or placebo (saline) injections

status: Public on Apr 19 2013

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research


title: Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire (RNA-seq)

status: Public on Jan 17 2013

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: According to current models, transcription factors (TFs) activated by extracellular stimuli operate in the context of a pre-established enhancer repertoire induced and maintained by lineage-specific TFs. Here, we uncovered the existence of latent enhancers, defined as regions of the genome that in terminally differentiated cells are poorly accessible and lack the histone marks characteristic of enhancers, but readily acquire these features in response to extracellular cues. Stimulation of resting macrophages caused simultaneous binding of stimulus-activated TFs and lineage-determining TFs to these regions, enabling deposition of enhancer-specific features. Once unveiled, these enhancers did not return to a latent state even when stimulation ceased; instead, they persisted and mediated a faster and stronger response upon restimulation. We suggest that stimulus-specific expansion of the available cis-regulatory repertoire provides an epigenomic memory of the exposure to environmental agents.

overall_design: Poly(A) fraction of the total mRNA of resting and stimulated murine bone marrow derived macrophages was extracted and subjected to by multiparallel sequencing. Experiments carried out in untreated cells as well as in cells treated for 4hrs (IFNg, IL4, TNFa, TGFb1, IL1b, MALP2, CpG)

first: Renato

last: Ostuni

first: Viviana

last: Piccolo

first: Sara

last: Polletti

first: Serena

last: Ghisletti

first: Gioacchino

last: Natoli


title: Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire (ChIP-seq)

overall_design: Chromatin immunoprecipitations of H3 lysine 4 mono-methylated, H3 lysine 27 acetylated, H3 lysine 4 tri-methylated, the transcription factors PU.1, Stat1, Stat6 and JunB and the total RNA polymerase II followed by multiparallel sequencing performed in murine bone marrow-derived macrophages (BMDMs). Experiments were carried out in untreated cells as well as in cells treated for 4hrs (lipopolysaccharide (LPS), IFNg, IL4, TNFa, TGFb1, IL1b, MALP2, CpG) and 24hrs (LPS). Same experiments were carried out in Stat1 KO (BMDM stimulated with IFNg) and Stat6 KO (BMDM stimulated with IL4) backgrounds. In case of IL4 an independent time-course was performed considering 15', 30', 1hrs, 2hrs and 4hrs after treatment while for IFNg we considered 30', 1hrs and 2hrs after treatment. For washout experiments, IP against H3 lysine 4 mono-methylated was performed 24hrs and 72hrs after stimulation as well as 48 hours after washout of the stimulus (24hrs).


title: Porcine IVM GDNF

status: Public on Nov 09 2012

city: Guelph

first: Derek

last: Toms

state: Ontario

address: 50 Stone Road East

department: Animal and Poultry Science

institute: University of Guelph

summary: Treatment of oocytes derived from large (4-6 mm; LG) or small (>3 mm; SM) follicles with glial cell line-derived neurotrophic factor (GDNF) during in vitro maturation.

overall_design: Four-condition experiment, SM and LG oocytes, each with and without GDNF. Biological replicates: 9 per condition, independently collected. Pools of three replicates per array.

last: Tsoi

first: Michael

last: Dyck

first: Julang

last: Li


title: Histone H3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells

status: Public on Feb 10 2009

first: Wei

last: Xie

address: 611 Young Dr. East, Boyer Hall Rm 332, UCLA

institute: UCLA

summary: Lysine 56 acetylation in the helical core of histone H3 opens yeast chromatin and enables histone gene transcription, DNA replication, DNA repair, and prevents epigenetic silencing. While K56Ac is globally abundant in yeast and flies its presence has been uncertain in mammals. We show here using mass spectrometry and genome wide analyses that K56Ac is present in human embryonic stem cells (hESCs) overlapping strongly at active and inactive promoters with the binding of the key regulators of pluripotency NANOG, SOX2 and OCT4. This includes also the canonical histone gene promoters and those for the hESC-specific microRNAs. K56Ac then relocates to developmental genes upon cellular differentiation. Thus K56Ac state more accurately reflects the epigenetic differences between hESCs and somatic cells than other active histone marks such as H3 K4 tri-methylation and K9 acetylation. These results suggest that K56Ac is involved in the human core transcriptional network of pluripotency.

overall_design: Genome wide location analysis ChIP-chip was performed in two human embryonic stem cell lines (HSF1 and HSF6) and two somatic cell lines (ARPE and BJ), for each of the following histone modifications: H3 K56Ac, H3 K9Ac, H3 K4me3 and H3 K27me3.

first: Chunying

last: Song

first: Nicolas

middle: L

last: Young

first: Adam

last: Sperling

first: Feng

last: Xu

first: Rupa

last: Sridharan

first: Anne

last: Conway

first: Benjamin

last: Garcia

first: Kathrin

last: Plath

first: Amander

middle: T

last: Clark

last: Grunstein


title: Genome-wide profiling of whole blood from healthy adult volunteers before and after receiving non-live vaccines including seasonal influenza or pneumococcal vaccine or placebo (saline) injections II

status: Public on Jul 10 2013

first: Damien

last: Chaussabel

summary: The objective of this study is to: 1) Characterize the immune responsiveness to administration of non-live vaccines in three cohorts of healthy adult subjects through the analysis of blood leukocytes transcriptional profiles. 2) Validate whole blood transcriptional profiles generated from standard 3mL blood draws versus 200uL blood draws obtained by finger stick. 3) Discover potential biomarkers for immune-responsiveness to non-live vaccines.

overall_design: A total of 621 blood samples were collected either by venipuncture (387) or finger prick (234) from four groups of healthy adults receiving either, 2009/10 seasonal influenza or 23-valent pneumococcal vaccine or placebo (saline) injections. Subjects were recruited in 3 cohorts with 4-7 individuals per group; cohort 3 was recruited for validation of the systemic day 1 immune signature in response to seasonal influenza and pneumococcal vaccination.  From each subject, peripheral blood was drawn into Tempus tubes (Applied Biosystems) or obtained by finger prick into micro capillaries and then transferred into tempus reagent to lyse blood cells and stabilize RNA before storing at -80ºC until mRNA extraction.  The training set for transcriptional profiling of blood obtained by venipuncture was performed in cohort 1 which included 6 healthy adult individuals receiving seasonal influenza vaccine, 6 healthy adult individuals receiving pneumococcal vaccine, and 6 healthy adult individuals receiving placebo (saline injections). The test set for transcriptional profiling of blood obtained by venipuncture was performed in cohort 2 which included 6 healthy adult individuals receiving seasonal influenza vaccine, 6 healthy adult individuals receiving pneumococcal vaccine, and 6 healthy adult individuals receiving placebo (saline injections). The validation set for confirming systemic day 1 transcriptome immune signature in response to seasonal influenza and pneumococcal vaccination was performed in cohort 3 which included 6 healthy adult individuals receiving seasonal influenza vaccine and 4 healthy adult individuals receiving pneumococcal vaccine.  The training set for transcriptional profiling of blood obtained by finger prick was performed in cohort 2 and the test set in cohort 1.


title: Human airway epithelial cell response to LPS and house dust mite antigen

status: Public on Oct 01 2009

city: RTP

first: John

last: Tomfohr

state: NC

address: 111 T.W. Alexander Dr. P.O. Box 12233

institute: NIEHS

summary:
Allergic asthmatic, allergy only, asthma only (no allergy), and non-allergic non-asthmatic (control) subjects underwent bronchoscopy with instillation of saline, lipopolysaccharide (LPS), and house dust mite antigen in separate subsegmental bronchi. Airway epithelial cells were collected four hours later (three samples per subject). RNA was extracted from these cells for microarray analysis.
Keywords: gene expression arrays (two-dye: sample against common "universal" reference RNA)

overall_design:
There are four main phenotypic groups:
1. control (no allergy or asthma)
2. allergy only (no asthma)
3. asthma only (no allergy)
4. allergy and asthma
and three exposures: saline, house dust mite antigen (HDM), and LPS. Samples from the different exposures were all collected at the same time: four hours after instillation. The hybridizations were carried out in two main "batches": samples in batch 1 were processed in mid 2004, samples in batch 2 about a year later in 2005. There is a clear "batch effect": differences between expression profiles from the two batches (likely caused by technical differences between hybridization and scanning methods). This should be considered when analyzing the data.

first: J

last: Sundy

first: K

last: Foss

first: E

last: McElvania-Tekippe

first: I

last: Yang

first: D

last: Schwartz


title: Transcriptional profiling of turkey muscle satellite cells transfected with DAP-siRNA during proliferation and differentiation

status: Public on Jun 01 2012

city: East Lansing

first: Kelly

last: Sporer

state: MI

address: 3365 Anthony Hall

department: Food Science and Human Nutrition

institute: Michigan State University

summary: In this study, we directly compared turkey muscle satellite cell gene expression between satellite cells with the gene Death-Associated Protein (DAP) knocked down by siRNA transfection and those transfected with a lipofectamine control using our 6K Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray (GPL9788).  The DAP gene was previously identified as differentially expressed by genetic line and during development of turkey skeletal muscle (Sporer et al., 2011). Gene expression changes were investigated in satellite cells after 72 h of proliferation and after 48 h of differentiation. We identified novel candidate genes and pathways as playing potentially crucial roles in the DAP-mediated attenuation of the normal processes of proliferation and differentiation in turkey satellite cells previously identified by Velleman et al. (submitted).

overall_design: This experiment was designed to investigate the role of DAP expression in turkey satellite cells during two crucial processes in muscle development: proliferation and differentiation.  Satellite cells were isolated from 7-week-old turkeys from the RBC2 line.  Cells were transfected with either DAP siRNA or a lipofectamine control; DAP expression was knocked down by over 50% with siRNA transfection (Velleman et al., submitted).  Satellite cells were then induced to proliferate for 72h or differentiate for 48h; culture plates from each stage (n=4) were frozen until RNA extraction.   Microarrays directly compared the DAP-knockdown to control from each of 4 culture plates and utilized a dye swap to equal 8 arrays for each of the cell developmental stages, proliferation and differentiation, and 16 arrays for the overall experiment investigating the role of DAP expression in satellite cell development and function.  Hybridizations were performed in random order.

first: Sandra

middle: G

last: Velleman

first: Robert

last: Tempelman

first: Gale

last: Strasburg


title: CD109 plays a role in osteoclastogenesis.

status: Public on Jan 29 2013

city: Toroto

first: Maayan

last: Inger

address: Fitzgerald Building 150 College Street, Room 221

institute: University of Toronto

summary: The primary aim of this project was to identify novel factors, in particular the cell-surface protein CD109, which regulate osteoclastogenesis. Microarray analysis was performed comparing two pre-osteoclast cell lines generated from the RAW 264.7 osteoclast cell line: one that has the capacity to fuse forming large multinucleated cells and one that does not fuse. It was found that CD109 was up-regulated by > 17-fold in the osteoclast forming cell line when compared to the cell line that does not fuse.

overall_design: H10 (osteoclastogenic cell line) and C8 (non osteoclastogenic cell line) cells were plated for two days in 60 mm tissue culture dishes at a density of 0.5 x 10^6  in a culture medium consisting of 8 ml of Dulbecco's Modified Eagle Medium (DMEM, Life Technologies, Grand Island, NY, USA) supplemented with 10% Fetal Bovine Serum (FBS) and 10% antibiotics (164 IU/mL of penicillin G, 50 mg/ml of gentamicin, and 0.25 mg/ml of fungizone) as well as purified recombinant RANKL (60ng/ml). Following two days of culture, total RNA was extracted from the  H10 and C8 cells (Qiagen RNeasy Minikit, Germantown, MD, USA) and the concentration of extracted RNA was measured (using a nanodrop method). Experiment was done in triplicates

first: Yongqiang

last: Wang

first: Howard

last: Tenenbaum

first: Michael

last: Glogauer


title: Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire

first: Iros

last: Barozzi

overall_design: Refer to individual Series


title: Profiling FACS Sorted Calvarial Osteoblast Cultures: Day 7 (pOBCol3.6GFP) and Day 17 (pOBCol2.3GFP)

status: Public on Apr 20 2005

city: Farmington

first: Baikang

last: Pei

state: CT

institute: University of Connecticut

summary:
This study compares a comprehensive microarray analysis of unsorted mCOB cultures at two level of cell differentiation with cells that are more homogeneous for a level of cellular differentiation.
It demonstrates the loss of information and in some cases misinformation that occurs when a heterogeneous population of cells are used for a microarray study.
Keywords: other

first: Ivo

last: Kalajzic

first: Ada

last: Staal

first: Wen-Pen

first: Yuli

last: Wu

first: Susan

middle: E

last: Johnson

first: Jean

middle: H

last: Feyen

first: Winfried

last: Krueger

first: Peter

last: Maye

first: Fang

last: Yu

first: Yifang

last: Zhao

first: Lynn

last: Kuo

first: Rishi

last: Gupta

first: Luke

last: Achenie

first: Hsin-Wei

first: Dong-Guk

last: Shin

first: David

last: Rowe


title: Whole blood expression profiling of obese diet-sensitive, obese diet-resistant and lean human subjects

status: Public on Nov 05 2009

city: Durham

first: SUJOY

last: GHOSH

address: 700 George Street

institute: North Carolina Central University

summary: We have carried out whole-genome expression profiling of whole blood from obese subjects, defined as obese diet-sensitive and obese diet-resistant, and well matched lean individuals. The diet-sensitive or diet-resistant status refers to the different rates of weight loss observed in the two groups on a low-calorie diet regimen. Bioinformatic analysis revealed alterations in transcription in key pathways that are consistent with impaired capacity for fatty acid oxidation driven mitochondrial ATP synthesis in obese subjects who are resistant to weight loss.

overall_design: A total of 80 samples are analyzed. This consists of 20 lean subjects studied at one timepoint and 20 obese subjects (10 diet-sensitive and 10 diet-resistant) studied at 3 timepoints during caloric restriction (day of entry into program, week 3 into the program and week 6 into the program)

first: Sujoy

last: Ghosh

first: Robert

last: Dent

first: MaryEllen

last: Harper

first: Shelby

last: Gorman

first: Joan

last: Stuart

first: Ruth

last: McPherson


title: RNA duplex map in living cells reveals higher order transcriptome structure

status: Public on Apr 04 2016

city: Stanford

first: Zhipeng

last: Lu

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

summary: RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here we develop PARIS, a method based on reversible psoralen-crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher order architectures, and RNA:RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures, and discovered conserved long-range and alternative structures. XIST, a lncRNA essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cells are crosslinked with AMT and RNA is extracted from cells by RNase digestion. Crosslinked RNA fragments are selected from total RNA by 2D gel electrophoresis. Purified crosslinked RNA duplexes are proximity ligated and crosslinking is reversed. Then the chimeric RNA molecules are converted into cDNA libraries for high-throughput sequencing.