title: Immune Variation Project (ImmVar) [CD14]

summary: Gene expression profiling of Monocytes (CD14+CD16-) from human peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from healthy individuals from the Boston area.

overall_design:
Over the course of 18 months, fresh blood samples from healthy participants were collected following a rigorous, standardized set of procedures (SOP). 15ml of blood was collected and used to isolate peripheral blood mononuclear cells (PBMCs). From the PBMCS, cell population of interest, CD14+CD16-, underwent a two-step sorting strategy in order to achieve cell purity >99%. mRNAs from these cells were profiled on Affymetrix GeneChip Human Gene ST 1.0 microarrays. Raw data CEL files were processed using the Robust Multichip Average (RMA) algorithm in Affymetrix PowerTools. To account for non-genetic factors such as batch effects, age, gender, and technical artifacts in gene expression data, we used Principal Component Analysis (PCA). PCs were estimated separately from the gene expression matrix for each population. The optimal numbers of PCs for association analysis were determined based on the PC that resulted in maximum number of cis-eQTLs. This procedure identified 20, 10, and 14 PCs in EU, EA and AA monocytes, respectively.

GSE56034_GSM.ImmVarCD14.*.PC*.txt supplementary files: For each population EU, AA, and EA, individual PC-corrected matrices for samples that have passed both Expression QC and Genotyping QC. These are the same expression matrices that were used for the eQTL association analysis.


title: Novel type of EATL evolving from mucosal γδ-T-cells in a RCD type I patient

status: Public on Apr 02 2014

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

summary:
Enteropathy associated T-cell lymphoma (EATL) is a rare non-Hodgkin lymphoma that may complicate celiac disease and typically occurs in patients with refractoriness to the gluten- free diet. The majority of these patients harbor intra-epithelial lymphocytes (IEL) with an aberrant phenotype in the small intestine which are thus considered as the ‘precursor’ lymphoma cells.
We here report on a case of extra-intestinal EATL that originated from a clonal γδ-IEL population rather than from aberrant IEL. This EATL displayed a distinctive pattern of immunophenotypical, T-cell receptor immunogenetic, and chromosomal aberrancies defining this lymphoma as a novel variant of EATL.

overall_design: sample vs reference

first: R

middle: L

last: van Wanrooij

first: D

last: de Jong

first: A

middle: W

last: Langerak

first: B

last: Ylstra

middle: A

last: Heideman

first: H

middle: F

last: van Essen

middle: J

last: Bontkes

first: C

last: Mulder

first: G

last: Bouma


title: MicroRNA expressions in human hepatocarcinoma cells in response to HBV X protein expression

city: Taichung

first: Wei-Chien

last: Huang

address: 9F, No.6, Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

summary: MicroRNA expression profiling of human Hep3B and HepG2 HCC cells comparing parental cancer cells with stable HBx-transfectants

overall_design: In this study,two pairs of control and HBx-overexpressing HCC cells were used to acquire expression profiles of a total of microRNA.  miRNA microarray analysis was performed with mirVana miRNA Bioarrays V1 (Ambion) according to the manufacturer’s instructions

first: Chia-Jui

last: Yen


title: Decoding the black box of cellulase formation in Hypocrea jecorina by RNA-Seq analysis

status: Public on Apr 01 2014

city: Campinas

first: Gabriela

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

type: Expression profiling by high throughput sequencing

summary: Hypocrea jecorina (anamorph Trichoderma reesei) is one of the most well studied fungi used in biotechnology industry. This fungus is today a paradigm for the comercial scale production of different plant cell wall degrading enzymes, mainly cellulases and hemicellulases. The objective of this study was to analyze the transcriptional profiling of T. reesei grown in presence of cellulose, sophorose and glucose as the carbon source using RNA-seq approach.

overall_design: T. reesei (QM9414) was grown in Mandels-Andreotti medium, supplemented with 1% of cellulose, 2% of glucose or 1mM of sophorose. The cultures were incubated on an orbital shaker (200 rpm) at 28°C for 24, 48 and 72 hours using cellulose as carbon source; for 24 and 48 hours with glucose as the carbon; and 2, 4 and 6 hours with sophorose as the carbon source. In the latter, the mycelium was previously grown on glycerol for 24 hours and then transferred to 20 mL of Mandels-Andreotti medium without peptone. All experiments were performed in three biological replicates. The resultant mycelia were collected by filtration, frozen and stored at -80°C until RNA extraction. After growth, total RNA was isolated from the mycelia using TRIzol® reagent. RNA-seq experiments were performed by LGC Genomics GmbH (Berlin/Germany) using the platform Illumina/HiSeq2000.

first: Lílian

last: dos Santos Castro

first: Amanda

middle: C

last: Campos Antonieto

first: Wellington

middle: R

last: Pedersoli

first: Júlio

last: Bortolossi

first: Vitor

middle: M

last: Faça

first: Nilce

last: Martinez Rossi

first: Antonio

last: Filho

first: Andrei

middle: S

last: Steindorff

first: Rafael

last: Rocha

first: Roberto

last: do Nascimento Silva


title: Transcriptome and Biomineralization Responses of the Pearl Oyster Pinctada fucata to Ocean Acidification and Ocean Warming

status: Public on May 02 2014

city: Beijing

first: Shiguo

last: Li

state: Beijing

address: Tsinghua University

department: School of Life Sciences

country: China

institute: Tsinghua University

summary: To elucidate how does the gene expression profiles of whole transcriptome of P.fucata response to seawater acidification and warming, we have employed microarray as a tool to identify gene responses in these stress.The pearl oysters were added into the tanks with the maintaining conditions of temperature 25 °C and 31 °C, acidity pH7.8 and pH7.5, salinity 33‰ in recirculating seawater. The temperatures and pH values in the studies were near future levels and predicted for 2100 and 2300.

overall_design: Adult Pinctada fucata used in this study were obtained from the Marine Biology Research Station in Leizhou Bay, China. Prior to use, the P. fucata were pre-cultured for one week at 19 ± 0.5 °C, pH 8.1 ± 0.05 and salinity 33±0.5‰ in glass aquaria filled with artificial seawater (Formula Grade A Reef Sea Salt, Formula, Japan). After the acclimation period, the organisms with similar size (6-7 cm length) were assigned to 50 L tanks and subjected to the CO2 and temperature stresses, respectively. The P. fucata were maintained for 72 h in the following conditions: 19 °C, pH 7.8 and salinity 33‰ (group abbreviated as P78); 19 °C, pH 7.5 and salinity 33‰ (P75); 25 °C, pH 8.1 and salinity 33‰ (T25); 31 °C, pH 8.1 and salinity 33‰ (T31). The P. fucata in the pre-culture conditions were used as the control. Each treatment was carried out for three replicates in three independent tanks. Samples from three individuals randomly selected from each tank were pooled together to obtain one biological replicate. The mantle samples were collected and preserved on the hours of 72 after treatments for subsequent studies. All the collected mantles above were snap-frozen in liquid nitrogen, and stored at -80°C.

first: Liping

last: Xie

first: Rongqing

last: Zhang


title: Gene expression analysis of Mycobacterium tuberculosis high-persister (hip) mutants.

status: Public on Apr 07 2014

city: Boston

first: Kim

last: Lewis

state: MA

address: 360 Huntington Ave

country: USA

institute: Northeastern University

summary:
Bacterial persister cells are phenotypic variants of regular cells that are tolerant to antibiotics. High-persister (hip) mutants of Mycobacterium tuberculosis produce 10- to 1,000-fold more persister cells than the wild type strain when challenged with various antibiotics. Comparison of gene expression pattern of the hip mutants may provide clues as to the genetic mechanisms underlying persister formation.
Transcriptome analysis will provide information on what differentiates M. tuberculosis hip strains from regular strains, which will be useful in the development of anti-persister therapy for persister cell eradication.

overall_design: Twelve independent M. tuberculosis hip mutants and the wild type strain were grown to stationary phase in duplicate. To avoid analyzing the drug effect, total RNA was extracted from the cultures prior to the addition of antibiotic for hybridization to Affymetrix microarrays. Data analysis was performed by comparing the hip mutants to the wild type control.

first: Heather

last: Torrey


title: Expression data from transfected BJ fibroblast cell line

status: Public on May 01 2014

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

summary:
Skeletal muscle differentiation is a highly coordinated multistep process in which proliferating mononucleated myoblasts ﬁrst withdraw from the cell cycle, then differentiate into postmitotic mononucleated myocytes, and subsequently fuse into multinucleated myotubes which ﬁnally bundle to form mature muscle ﬁbers. All these processes are controlled by the sequential activation of myogenic regulatory factors, and especially MYOD1 is activated in the early phase to promote the transcription of muscle-specific genes coding for muscle proteins such as alpha-actin, myosin heavy chain and muscle creatine kinase.
We used microarrays to detail the global gene expression changes associated with MYOD1 L122R mutation and identified MYOD1 L122R blocked myogenic differentiation and had a MYC-like transcriptional potential.

overall_design: wild type MYOD1, MYOD1 L122R, MYC, and GFP were introduced into BJ human fibroblast cells by retroviral infection. For retrovirus production, the pcx4 and pBabe vectors system were used.  Retroviruses were obtained by using 293T cells as packaging cells, and were infected into BJ cell lines and selected with 500 μg/ml Zeocin (Invitrogen, Carlsbad, CA, USA). After selection, RNAs were extracted and processed at MSKCC according to procedures recommended by Affymetrix (Santa Clara, CA, USA).

first: Shinji

last: Kohsaka

first: Marc

last: Ladanyi


title: Genome-wide analysis of p53 binding protein

city: Bunkyo-ku

first: Nurmaa

last: Dashzeveg

state: Tokyo

address: 1-5-45 Yushima

department: Molecular Biology

country: Japan

institute: Tokyo Medical and Dental University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Tumor suppressor p53 regulates various role in the cell including cell cycle arrest, DNA repair and apoptosis. Current research achieved to investigate p53 target genes in human osteosarcoma cell line-SaOS2 cell.

overall_design: Examination of p53 binding protein by transfecting flag-tagged wild type p53 into SaOS2 cells.

first: Yoshida

last: Kiyotsugu

first: Zheng-Guang

last: Lu


title: Gene expression profiles of TiPS generated in a defined condition, ES and T cells

status: Public on Mar 26 2014

city: Tokyo

first: Tomohisa

last: Seki

address: 35 Shinanomachi, Shinjuku-ku

institute: Keio University School of Medicine

summary: This experiment was designed to show the similarity among TiPS cells generated in a difined condition and ES cells and the differenced between TiPS cells and T cells.

overall_design: Undifferentiated TiPS cells,ES cells and stimulated T cells were collected. Then, they were applied in this experiment.


title: MiR-155 promotes blood-brain barrier dysfunction in neuroinflammation (part 1)

status: Public on Apr 29 2014

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez-Ramirez

state: California/San Diego

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

summary: Here, we investigated the time-course changes in the pattern of microRNA (miRNA) expression of TNFα and IFNγ-stimulated and unstimulated hCMEC/D3 cells,  an immortalized human cerebral microvascular endothelial cell line.

overall_design: In order to investigate pro-inflammatory cytokine-induced changes in miRNA  levels in hCMEC/D3 cells, we challenged brain endothelial cells with TNFα and IFNγ (100 ng/ml) for 2 h, 6 h and 24 h and determined microRNA expression in cytokine-stimulated and unstimulated cells

first: Dongsheng

last: Wu

first: Gareth

last: Pryce

first: Julie

middle: E

last: Simpson

first: Arie

last: Reijerkerk

first: Josh

last: King-Robson

first: Oliver

last: Kay

first: Helga

last: de Vries

first: Mark

last: Hirst

first: Basil

last: Sharrack

first: David

last: Baker

middle: K

last: Male

first: Gregory

last: Michael

first: Ignacio

last: Romero


title: MiR-155 promotes blood-brain barrier dysfunction in neuroinflammation (part 2)

summary: Over-expression of miR-155 induces changes in the pattern of gene expression of hCMEC/D3 cells. hypothesis tested in the present study was that miR-155 constitute an important regulatory control of the brain endothelial response to inflammatory cytokines.

overall_design: To identify miR-155 target genes in brain endothelim that might be implicated in BBB dysfunction relevant to human disease, we then analysed changes in mRNA expression of hCMEC/D3 cells that overexpress miR-155 and results were contrasted to cells transfected with scrambled miR. To ectopically express miR-155 in hCMEC/D3 cells, 30 nM of pre-miR-155 and the siPORT Amine transfection agent (Applied Biosystems, Warrington, UK) were combined following the manufacturer’s instructions.


title: An atlas of active enhancers across human cell types and tissues

city: Copenhagen N

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

summary: Sequencing of 5' ends of RNA molecules from control and exosome-depleted HeLa-S3 cells.

overall_design: CAGE library construction from RNA extracted from control and exosome-depleted cells.

first: Albin

last: Sandelin

first: Torben

middle: H

last: Jensen

first: Jette

last: Bornholdt

first: Mette

last: Boyd

first: Evgenia

last: Ntini


title: DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

status: Public on Feb 26 2014

city: Tartu

first: Kaie

last: Lokk

address: Riia 23

country: Estonia

institute: University of Tartu

summary:
Background:
DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites.
Results:
Only 2% of the CpGs analyzed are hypermethylated in all 17 tissue specimens; these permanently methylated CpG sites are located predominantly in gene-body regions. In contrast, 15% of the CpGs are hypomethylated in all specimens and are primarily located in regions proximal to transcription start sites. A vast number of tissue-specific differentially methylated regions are identified and considered likely mediators of tissue-specific gene regulatory mechanisms since the hypomethylated regions are closely related to known functions of the corresponding tissue. Finally, a clear inverse correlation is observed between promoter methylation within CpG islands and gene expression data obtained from publicly available databases.
Conclusions:
This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues. Many of the genes corresponding to these differentially methylated regions contribute to tissue-specific functions. Future studies may use these data as a reference to identify markers of perturbed differentiation and disease-related pathogenic mechanisms.

overall_design: DNA methylation analysis of the total 72 tissue samples and controls was performed with the Illumina Infinium HumanMethylation450 BeadChip. The 17 post-mortem human somatic tissues used in this study were collected at the time of autopsy. Controls for unmethylated and methylated DNA were represented, respectively, by whole-genome amplified DNA from subcutaneous adipose tissue (using the GenomiPhi DNA amplification kit; GE Healthcare, Piscataway, NJ, USA) and the universal methylated human DNA standard (Zymo Research). We had two technical and two biological replicates processed by chip technique.

first: Vijayachitra

last: Modhukur

first: Balaji

last: Rajashekar

first: Kaspar

last: Märtens

first: Marina

last: Koltšina

first: Reedik

last: Mägi

first: Raivo

last: Kolde

first: Torbjörn

last: Nilsson

first: Jaak

last: Vilo

first: Andres

last: Salumets

first: Neeme

last: Tõnisson


title: Discovery of PDE7B as a novel effector of GBM growth by computational deconvolution of an in vitro physical coculture system

status: Public on Mar 01 2014

city: Ann Arbor

first: Michael

middle: Dale

last: Brooks

state: Michigan

address: 2800 Plymouth Rd Building 26 Rm 329S

department: Internal Medicine

institute: University of Michigan

summary: Cell-to-cell interactions between tumor cells and their microenvironment are critical determinants of tumor tissue biology and therapeutic responses. Interactions between glioblastoma (GBM) cells and endothelial cells (ECs) establish a purported stem cell niche. We hypothesized that genes that mediate these interactions would be important, particularly as therapeutic targets. Using a novel computational approach to deconvoluting expression data from mixed physical coculture of GBM cells and ECs, we identified upregulation of the cAMP specific phosphodiesterase PDE7B  in GBM cells in response to ECs. We further found that elevated PDE7B expression occurs in most GBM cases and has a negative effect on survival.  PDE7B overexpression resulted in the expansion of a stem-like cell subpopulation, increased tumor aggressiveness,  and increased growth in an intracranial GBM model.  This deconvolution algorithm provides a new tool for cancer biology, and these results identify PDE7B as a therapeutic target in GBM.

overall_design: 3 replicates from U87 monocultures, 3 replicates from HBMEC monocultures, 3 replicates from U87-HBMEC cocultures

middle: D

first: Erin

last: Jackson

first: Nicole

last: Warrington

first: Sara

last: Taylor

first: Diane

last: Mao

first: David

last: Piwnica-Worms

first: Jeffrey

last: Leonard

first: Albert

last: Kim

first: Robi

last: Mitra

first: Joshua

middle: B

last: Rubin


title: Expression and incorporation of microRNA in exosomes released by leukemia cells under room air and hypoxia

status: Public on Feb 20 2014

city: Portland

first: Amiee

middle: Bell

last: Potter

state: OR

address: 3181 SW Sam Jackson Park Rd, Mail Code #L581

department: Integrated Genomics Laboratory

institute: OHSU

summary:
We recently showed that exosomes from primary AML cells and cell lines have potent regulatory capacity and we hypothesized that leukemia cell exosome trafficking might account for the suppression of residual hematopoietic stem and progenitor cells (HSPC) in the leukemic niche.
Here we studied Molm-14 cells in in vitro experiments using purified exosomes under carefully calibrated low-oxygen conditions. This approach revealed the active regulation of stromal- and hematopoietic progenitor cell function. Systematic analysis of AML exosomes identified a panel of differentially enriched hypoxia-responsive miRNAs, including miR-210, -155, and -146a.

overall_design:
We cultured cells under normoxic and hypoxic conditions. Exosomes were released from the parental cells and captured. Total RNA was isolated from both exosomes and cells.

Please note that the sample numbers (in the titles) do differ from pair identification (i.e. pair ID) as the pair is only in reference to the paired-t test and parental vs. released pairs.

first: Jianya

last: Huan

first: Noah

middle: I

last: Hornick

first: Rajani

last: Kaimal

first: John

last: Chevillet

first: Muneesh

last: Tewari

first: Charles

middle: T

last: Roberts Jr

first: Peter

last: Kurre


title: Increased contribution of non-reference alleles in mitochondrial DNA (mtDNA) of Alzheimer's disease (AD) patients

status: Public on Mar 11 2014

city: Ancona

first: Tiziana

last: Casoli

address: Via Birarelli 8

department: Scientific Technological Area

institute: INRCA

summary:
Many observations suggest that mutations of mtDNA could be responsible of the neurodegenerative changes associated with AD.
We examined the signal intensity of the four alleles for each mtDNA nucleotide position (np) in whole blood of AD patients and age-matched controls utilizing a resequencing array, the MitoChip v2.0, and identified 275 statistically different nps which all, with the exception of one, showed an increased contribution of non-reference alleles for AD patients.
PCA and cluster analysis showed that 5 of these nps, characterized by low-level heteroplasmy, could discriminate AD from control subjects with 80% of cases correctly classified.

overall_design: This study included a total of 18 AD patients and 18 age-matched controls. Data acquisition was performed using the Affymetrix Genechip Command Console (AGCC) software and data analysis was carried out with GSEQ 4.1.

first: Giuseppina

last: Di Stefano

first: Patrizia

last: Fattoretti

first: Fiorenzo

last: Conti


title: Immune responses to the in vitro LPS assault engineered in the spaceflight multi-omics study

status: Public on Feb 05 2014

city: Fort Detrick

first: Meskerem

last: Jibitu

address: 568 Doughten Drive

department: Integrative Systems Biology

institute: US Army Center for Environmental Health Research

summary:
Microgravity alters the immune response to in vitro LPS assault engineered in spaceflight: A multi-omics study

Microgravity can facilitate creation of a potent environment for opportunistic infection by augmenting virulence and suppressing the host defense. Presumably, extraterrestrial infection may trigger potentially novel bionetworks different from the terrestrial equivalent, which could only be probed by investigating the host-pathogen relationship with minimum terrestrial bias. Towards this objective, we strategically engineered a cell culture module equipped with a feedback controlled semi-automated platform to expose human endothelial cells to lipopolysaccharide (LPS). The assay was carried out in the STS-135 space shuttle, and a concurrent ground study constituted the baseline. Transcriptomic investigation revealed an immune blunting in microgravity; Lbp, MyD88 and MD-2 failed to encode proteins responsible for early LPS uptake. Longer exposure results implied that there was a delayed response, potentially ineffectual in preventing pathogens from opportunistically modulating the infection network. Lack of recruitment of growth factors and a debilitated apoptosome supported this potential explanation. Certain cytokines, such as IL-6 and IL-8, surged in response to LPS insult in microgravity. Contrasting expressions of B2M, TIMP-1 and VEGRs suggested impaired pro-survival adaptation and healing mechanisms. The susceptibility of oxidative stress and immune regulation to microgravity compelled further investigation of the respective microRNA modulators such as miR-200a and miR-146b. These miRNAs were expressed differently in response to LPS assaults in different gravitational limits. In conclusion, despite a serious drawback attributed to the small sample size, we delineated some of the important aspects of the extraterrestrial etiology; more comprehensive follow up studies are warranted.

Present study though compromised by the small sample size was able to shade lights on several aspects of immunological responses to the endotoxic assault mediated by μG. Implementing the host-pathogen interactions in the spaceflight and subsequently lysing the cells onboard presented the critical distinguishing features of the present study from the past reports.

overall_design: We identified the CCM of Tissue Genesis, Inc., HI as the suitable hardware system to carry out the experiment in the spaceflight. CCM is an automated, feedback controlled module that can concurrently support 24 bioreactors following protocols exclusively programmed for individual bioreactor. For this experiment we use samples EA41, EA 47, EA45, and EA155 that were exposed to LPS for 4 hours. Samples EA123, EA165, EA127, EA126 were exposed to LPS for 8Hrs. Samples EA33, EA 125, EA79 and EA 39 were controls in this experiment.

first: Marti

last: Jett

first: Rasha

last: Hammamieh

first: Allison

last: Hoke

first: Seid

last: Muhie

first: Nabarun

last: Chakraborty

first: Aarti

last: Gautam

first: Stacy

middle: A

last: Miller


title: Discovery of cashmere goat (Capra hircus) microRNAs in skin and hair follicles by Solexa sequencing

status: Public on Jan 31 2014

city: Yangling

first: xiaolong

last: wang

address: Xinong Rd 22

institute: NWAFU

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, the skin tissues were harvested from the three stages of hair follicle cycling (anagen, catagen and telogen) in a fiber-producing goat breed. In total, 63,109,004 raw reads were obtained by Solexa sequencing and 61,125,752 clean reads remained for the small RNA digitalization analysis. This resulted in the identification of 399 conserved miRNAs; among these, 326 miRNAs were expressed in all three follicular cycling stages, whereas 3, 12 and 11 miRNAs were specifically expressed in anagen, catagen, and telogen, respectively. We also identified 172 potential novel miRNAs by Mireap, 36 miRNAs were expressed in all three cycling stages, whereas 23, 29 and 44 miRNAs were specifically expressed in anagen, catagen, and telogen, respectively. Gene Ontology and KEGG pathway analyses indicated that five major biological pathways (Metabolic pathways, Pathways in cancer, MAPK signalling pathway, Endocytosis and Focal adhesion) accounting for 23.08% of target genes among 278 biological functions, indicating that these pathways are likely to play significant roles during hair cycling.

first: Yulin

last: Chen

first: Chao

last: Yuan

first: Xiaolong

last: Wang


title: ChIP-seq of bovine cells (MDBK) to study butyrate-induced histone modification

status: Public on Jan 24 2014

city: Beltsville

first: Congjun

last: Li

state: MD

address: 10300 Baltimore Ave

department: BFGL

institute: ARS, USDA

summary: Utilizing next-generation sequencing technology, combined with ChIP (Chromatin Immunoprecipitation) technology to analyze histone modification (acetylation) induced by butyrate and to map the epigenomic landscape of normal histone H3, H4

overall_design: Cells were treated with 10 mM butyrate for 24 hr, The cells were scraped from the flask and homogenized with ice-cold Dounce homogenizer to release the nuclei.  The collected nuclei were resuspended in digestion buffer and enzymatic shearing was performed. ChIP with anti H3, H4 and acetyl-H3 and acetyl-H4.

first: Robert


title: Chromosomal copy number aberrations in colorectal metastases resemble their primary counterparts and differences are typically non-recurrent.

status: Public on Feb 10 2014

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

summary:
Background & Aims: The metastatic process is complex and remains a major obstacle in the management of colorectal cancer (CRC). To gain a better insight into the biologic events driving the metastatic process we investigated genomic aberrations in a large cohort of matched CRC primaries and distant metastases from various sites.
Methods: In total, 62 primary colorectal cancers, 62 matched normal specimens, and 68 matched metastases (from liver, lung, ovary, omentum, and distant lymph nodes) were analyzed by high resolution array comparative genomic hybridization (array CGH) for DNA copy number changes. Findings were validated using a publicly available dataset consisting of 21 primary tumors and matched liver metastases. Fluorescence in situ hybridization (FISH) was used to confirm some of the DNA copy number changes observed.
Results: Overall patterns of DNA copy number aberrations were highly similar between primary tumors and their metastases, confirming clonality. Additional copy number aberrations in metastasis are rare and rather than recurrent they were sporadic for individual patients. The only recurrent differences between primary tumors and their metastases were two chromosomal regions, 6q21 and 8q24.21 encompassing the MYC oncogene, that coamplified in three metastases of two patients (3.2%). FISH analysis confirmed the high level co-amplification in the metastasis, which were not detected in their primary tumors.
Conclusions: Primary CRC and their metastases show highly similar patterns of DNA copy number changes, additional copy number aberrations in metastasis are rare and recurrences exceptional. These observations are consistent with the hypothesis that the metastatic potential is predestined early in the development of the primary tumor.

overall_design: In total, 62 primary colorectal cancers, 62 matched normal specimens, and 68 matched metastases (liver, lung, ovarian, omentum and distant lymph nodes) were analyzed by high resolution array comparative genomic hybridization (array CGH).

first: Leonie

middle: J

last: Mekenkamp

first: Josien

last: Haan

first: Danielle

last: Israeli

first: Hendrik

middle: F

last: van Essen

first: Jeroen

last: Dijkstra

first: Patricia

last: van Cleef

first: Cornelis

last: Punt

first: Gerrit

last: Meijer

first: Iris

last: Nagtegaal

first: Bauke

last: Ylstra


title: Bisulfite-Seq and RNA-seq profiling of truffle (Tuber melanosporum)

status: Public on Jan 01 2014

city: Taipei

first: Pao-Yang

state: Taiwan

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

type: Methylation profiling by high throughput sequencing

summary: We investigated the ascomycete truffle Tuber melanosporum exploits DNA methylation and transcription to cope with the more than 45,000 repeated elements that are present in its genome. Whole-genome bisulfite sequencing and RNA-sequencing, were performed on different developmental stages of this symbiotic hypogeous fungus -fruitbody (FB), free-living mycelium (FLM), and ectomycorrhiza.

overall_design: Examination of DNA methylation and transcription of truffle in its free living mycelium (FLM), fruit body (FB), and ectomycorrhizal root tips (ECM)

first: Simone

last: Ottonello

first: Matteo

last: Pellegrini

first: Barbara

last: Montanini

first: Artur

last: Jaroszewicz

first: Marco

last: Morselli

first: Wen-Wei

last: Liao


title: Impact of miRNAs modulation on regulatory networks and pathways involved in colon cancer and metastasis development

status: Public on Jan 16 2014

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

institute: University of Padova

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

summary: Originally linked with development and differentiation, the role of microRNAs (miRNAs) in  many important biological processes has emerged and dysregulation of miRNA expression has  been connected with cancer pathogenesis. The association between abnormal expression levels of miRNAs and colon cancer has been mainly demonstrated in primary tumors; more recently, non-overlapping sets of oncomirs, tumour suppressor miRNAs and metastamirs have been associated  with distinct stages of colo-rectal cancer (CRC) progression. In an attempt to identify changes in both miRNA and gene expression levels along the colon mucosa - primary tumor - liver metastasis-  sequence and to classify miRNAs into distinct functional networks according to the expression of  their anti-correlated and differentially expressed target genes, we analyzed a large set of sample-matched miRNA and mRNA expression profiles, including the complete non tumor tissue, primary  carcinoma and liver metastasis sequence from 8 patients. Our study shows that the largest changes  in miRNA and gene expression levels occur in normal mucosa to tumor transition and are almost  stably maintained in the subsequent tumor to metastasis transition. Only a few miRNAs were  differentially expressed between liver metastasis and primary carcinoma; however, miRNA  expression profiles classified better primary tumors and metastases compared to mRNA profiles. By  integration of miRNAs and target genes expression data, we were able to infer regulatory networks  modulated by miRNAs during colorectal tumorigenesis and metastatic process, and associate them  to the affected biological pathways. In particular, we identified a combination of interconnected  miRNAs, up- or down-regulated during tumorigenesis, which are organized into distinct sub-networks, each of which includes several regulatory relationships with differentially expressed  genes. Among them, the relationship between miR-182, up-regulated in colon cancer, and the anti-correlated ENTPD5 gene was identified for the first time and confirmed in an independent set of samples.

platform_organism:
Homo sapiens
synthetic construct

overall_design: We determined miRNA expression profile for 78 samples comprising 23 normal adjacent mucosa (N), 31 primitive colorectal cancer (T) and 24 liver metastases (M), obtained from 45 patients who underwent surgery at University of Padova (Surgery Branch, Department of Oncological and Surgical Sciences) between March 1994 and September 2008. This dataset included 24 samples belonging to 8 patients with matched samples (N, T and M) from the same patients. We also examined the expression profiles for 80 samples, comprising 23 N, 30 T, 27 M, and including 27 per-patient matched samples from 9 patients. Considering both miRNAs and genes expression experiments, we obtained a set of 77 samples (23N, 30T, 24M) with matched miRNAs and genes expression data from the same biological sample, to reconstruct post-transcriptional regulatory networks.

first: Paola

last: Zanovello


title: Lung injury induced by common bile duct ligation in mice

status: Public on Dec 31 2013

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

summary: Liver dysfunction and cirrhosis affect vasculature in several organ systems and cause impairment of organ functions, thereby increasing morbidity and mortality. If a mouse model of hepatopulmonary syndrome (HPS) could be established, greater insight into the genetic basis of the disease would be gained. Our objectives were to establish a mouse model of lung injury after common bile duct ligation (CBDL) and to investigate pulmonary pathogenesis for application in future therapeutic approaches. Balb/c mice were subjected to CBDL. Immunohistochemical analyses and real-time quantitative reverse transcriptional polymerase chain reaction were performed on pulmonary tissues. The presence of HPS markers were detected by western blot and microarray analyses. We observed extensive proliferation of CD31-positive pulmonary vascular endothelial cells 2 weeks after CBDL, and identified 11 up-regulated and 8 down-regulated proteins that were associated with angiogenesis. MMP-9 protein was highly expressed at 3 weeks after CBDL, and less expressed in lungs of the control group. Contrary to our expectation, lung pathology in our mouse model exhibited differences from that of rat models, and the mechanisms responsible for these differences are unknown. This phenomenon may be explained by contrasting processes related to TNF induction of angiogenic signaling pathways in the inflammatory phase; thus, we suggest that our mouse model can be applied to pulmonary pathological analyses in the inflammatory phase, i.e., to systemic inflammatory response syndrome, acute lung injury, and MOD syndrome.

overall_design: After induction of anesthesia, a median abdominal incision was made and the common bile duct was identified. The duct was dissected carefully under a microscope, and doubly ligated with 7-0 Prolene and transected. In the sham operation (control) group, the duct was dissected without common bile duct ligation. Mice were sacrificed at 2 and 3 weeks after surgery. CD31-positive cells were assembled from three mice in each group.

first: Fumiaki

last: Shikata


title: Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays [Omni1-Quad]

city: Philadelphia

first: Daria

last: Babushok

state: PA

address: 3615 Civic Center Blvd, ARC 302

institute: University of Pennsylvania

summary:
To better understand the natural history of bone marrow failure syndromes, we analyzed 124 single nucleotide polymorphism arrays (SNP-A) from a comprehensively characterized cohort of 91 patients who had SNP-A for clinical evaluation of BMFS.
67 samples from 51 patients were genotyped with the Quad610, and 57 samples from 54 patients were genotyped with the Omni1-Quad. This submission includes 55 samples from 54 patients that were genotyped with Omni1-Quad.

overall_design: Illumina Infinium SNP-A genotyping was performed on DNA extracted from bone marrow aspirates using standard manufacturer's protocol

first: Juan

last: Perin

first: Hongbo

last: Xie

first: Jacquelyn

last: Roth

first: Nieves

last: Perdigones

first: Timothy

last: Olson

first: Joshua

last: Cockroft

first: Xiaowu

last: Gai

first: Yimei

last: Li

first: Michele

last: Paessler

first: Hakon

last: Hakonarson

first: Gregory

last: Podsakoff

first: Philip

last: Mason

first: Jaclyn

last: Biegel

first: Monica

last: Bessler


title: Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays

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

overall_design: Refer to individual Series


title: Inducible overexpression analysis of KUODA1 in Arabidopsis seedlings

city: Potsdam

first: Jos

last: Schippers

address: Am Muehlenberg 1

department: Plant Signaling

country: Germany

institute: MPIMP-golm

summary: To identify potenital target genes of the transcription factor KUODA1 (AT5G47390), we performed expression profiling using an estradiol inducible overexpression system.

overall_design: Estradiol-treatment allows for the nuclear translocation of the constitutively expressed chimeric transcription factor XVE and subsequent expression of KUA1 from the LexA promoter. Stable trangenic T3 seedlings were grown for 14 days and either treated with 15 µM estradiol or ethanol (mock) for 4 hours. Two mock and two  estradiol treated samples were used for RNA isolation and hybridization.

first: Dandan

last: Lu

first: Bernd

last: Mueller-Roeber


title: Powdery Mildew- and Salicylic Acid-Induced Gene Expression in Grapevine

status: Public on Jan 10 2014

city: Springfield

first: Laszlo

middle: G

last: Kovacs

state: Missouri

address: 901 S  National Avenue

department: Biology

institute: Missouri State University

summary: Infection by the pathogen grape powdery mildew (Erysiphe necator) causes changes in the transcriptome of its susceptible host Vitis vinifera. Infection triggers the host to synthesize the signaling molecule salicylic acid (SA) which regulates the expression of a broad range of defense-related plant genes. In addition, it is hypothesized that E. necator directly modulates gene expression in V. vinifera via the haustorial complex. This microarray experiment was designed to dissect host transcriptome changes triggered directly by E. necator infection and indirectly through the SA response.  We accomplished this by conducting two separate global leaf transcriptome analyses using the Vitis Affymetrix GeneChip platform: in one, we compared the leaves with fully established PM colonies to healthy reference leaves, in another, we compared healthy leaves with artificially elevated SA levels to healthy reference leaves. Overlaying host transcriptome changes from these two experiments enabled us to glean out V. vinifera genes that modulate their expression in response E. necator in an SA-independent manner.

overall_design: We characterized gene expression profiles in (1) healthy reference leaves, (2) leaves with well-established by E. necator colonies, and (3) healthy leaves in which SA levels were artificially elevated by the presence of methyl salicylate (15 µM) in the atmosphere. Treatments (1) and (2) differed only in the presence E. necator infection, whereas treatments (1) and (3) differed only in SA levels. Consequently, statistical comparisons were made only between signal intensities from treatments (1) and (2) and from treatments (1) and (3). Each treatment was done in three biological repeats, that is, each experiment was repeated three times in 14-day intervals with dedicated biological material (plants were used in a single replicate and not reused in another repeat or treatment). Each biological replicate consisted of 10 potted vines. For RNA extraction, two young leaves were harvested from each of the 10 vines and pooled into a single sample.

first: Patrick

last: Winterhagen

first: Zsofia

last: Toth

first: Balazs

last: Kalapos

first: Yingcai

last: Su

first: Erzsebet

last: Kiss


title: Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays [Illumina Quad610 Beadchip]

first: Daria

last: Babushok

summary:
To better understand the natural history of bone marrow failure syndromes, we analyzed 124 single nucleotide polymorphism arrays (SNP-A) from a comprehensively characterized cohort of 91 patients who had SNP-A for clinical evaluation of BMFS.
67 samples from 51 patients were genotyped with the Quad610, and 57 samples from 54 patients were genotyped with the Omni1-Quad. This submission includes 67 samples from 51 patients that were genotyped with Illumina Quad610 Beadchip.

first: Juan

last: Perin

first: Hongbo

last: Xie

first: Jacquelyn

last: Roth

first: Nieves

last: Perdigones

first: Timothy

last: Olson

first: Joshua

last: Cockroft

first: Xiaowu

last: Gai


title: Novel role of Engrailed 1 as pro-survival transcription factor in basal-like breast cancer and engineering of interference peptides to block its oncogenic function

city: CHAPEL HILL

first: PILAR

last: BLANCAFORT

state: NORTH CAROLINA

address: 4009 MASON FARM RD

department: PHARMACOLOGY

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

summary: Basal-like breast tumors are aggressive cancers associated with high proliferation and metastasis. Currently basal-like breast cancer patients can only be treated with chemotherapy options. However, resistance to chemotherapy often occurs, resulting in recurrence and patient death. Some extremely aggressive basal-like breast cancers are also associated with hypoxia, inflammation and high leukocyte infiltration. Herein we discovered that the neural-specific transcription factor Engrailed 1 (EN1) is exclusively overexpressed in basal-like breast cancers. ShRNA-mediated knockdown of EN1 in basal-like breast cancer cells triggered potent and selective cell death. In contrast, ectopic overexpression of EN1 in normal cells activated survival pathways and conferred resistance to chemotherapeutic agents. Exogenous expression of EN1 cDNA reprogrammed the breast epithelial cells towards a long-lived, neural-like phenotype displaying dopaminergic markers. Gene expression microarrays demonstrated that the EN1 cDNA altered transcription of a high number of inflammatory molecules, notably chemokines and chemokine receptors, which could mediate pro-survival pathways. To block EN1 function, we engineered synthetic interference peptides (iPeps) comprising the EN1-specific sequences mediating essential protein-protein interactions necessary for EN1 function and an N-terminal cell-penetrating peptide/nuclear localization sequence. These EN1-iPeps rapidly mediated a strong apoptotic response in tumor cells overexpressing EN1, with no toxicity to normal or non EN1-expressing cells. Delivery of EN1-iPeps into basal-like cancer cells significantly decreased the IC50 of chemotherapeutic drugs routinely used to treat breast cancer. Lastly, MALDI-TOF mass spectrometry and immunoprecipitation assays demonstrated that EN1-iPeps captured targets involved in transcriptional and post-transcriptional regulation. Importantly, the EN1-iPeps bound the Glutamyl-prolyl tRNA synthetase (EPRS) target, which has been associated with the transcript-specific translational control of inflammatory proteins and activation of amino acid stress pathways. These studies show that EN1 activates intrinsic inflammatory pathways associated with pro-survival in basal-like breast cancer and that peptides targeting EN1 function could potentially be used to combat these lethal forms of breast cancer.

overall_design: reference x sample

first: Adriana

last: Beltran

first: Lee

middle: M

last: Graves

first: Pilar

last: Blancafort


title: Prominin 1/CD133 Endothelium Sustains Growth of Proneural Glioma

city: Rochester

first: Adilia

last: Hormigo

address: 601 Elmwood Avenue, Box 645

institute: University of Rochester Medical Center

summary: As many other tumors, a subset of gliobastoma is thought to be maintained by a restricted population of cancer cells, stem-like cells that express CD133 transmembrane protein. Expression levels of CD133 gene has been linked to a poor prognostic molecular subgroup and is not overexpressed by the PDGF-driven proneural group. Thus, the significance of CD133+ cells for gliomagenesis of the proneural group is undetermined. In addition, the role of the CD133 protein remains elusive and controversial, which results from the difficult isolation of CD133+ cells that has largely relied on the use of antibodies to ill-defined glycosylated epitopes of CD133. Here, we used a knockin lacZ reporter mouse, Prom1lacZ/+, to track Prom1+ cells in the brain and found that Prom1 (prominin1, murine CD133 homologue) is expressed by cells that co-express markers characteristic of neuronal, glial and vascular lineage phenotype. In proneural tumors derived from injection of RCAS-PDGF into the brain of tv-a;Ink4a-Arf-/- Prom1lacZ/+ mice, Prom1+ cells co-express markers for astrocytes and endothelial cells. Therefore, we characterize the tumor propagation in a murine model and found that the mice co-transplanted with Prom1 endothelium and proneural tumor spheres cells had significant tumor burden and vascular proliferation (angiogenesis). Specific genes in Prom1 endothelium are identified that code for endothelial signaling modulators that most likely support proneural tumor progression and can be potential targets for anti-angiogenic therapy.

overall_design: Cells were sorted via FACS to obtain a population of CD31+CD133- cells and a population of CD31+CD133+ cells. Total RNA was extracted from each population and gene expression was assayed on Affymetrix Mouse 430 2.0 arrays with one array per cell population.

first: Bi-Sen

last: Ding

first: Daylon

last: James

first: Rajiv

last: Iyer

first: Ilaria

last: Falciatori

first: Dolores

last: Hambardzumyan

first: Jason

last: Butler

first: Sina

last: Rabbany

first: Adília


title: Expression data from drosophila melanogaster

status: Public on Dec 11 2013

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
Space travel presents unlimited opportunities for exploration and discovery, but requires a more complete understanding of the immunological consequences of long-term exposure to the conditions of spaceflight. To understand these consequences better and to contribute to design of effective countermeasures, we used the Drosophila model to compare innate immune responses to bacteria and fungi in flies that were either raised on earth or in outer space aboard the NASA Space Shuttle Discovery (STS-121).
Microarrays were used to characterize changes in gene expression that occur in response to infection by bacteria and fungus in drosophila that were either hatched and raised in outer space (microgravity) or on earth (normal gravity).

overall_design: Whole Oregon R strain drosophila melanogaster fruit flies either raised on earth or in space that were (1) uninfected, (2) infected with bacteria (Escherichia coli), or (3) infected with fungus (Beauveria bassiana) were used for RNA extraction and hybridization on Affymetrix microarrays.


title: Real- time quantiative PCR analysis of HSC derived from sleep deprived mice

city: Stanford

first: Irv

last: Weissman

address: 265 Campus Dr. West

department: Stem Cell Institute

institute: Stanford University

summary: HSC were derived from mice sleep deprived for 4 hours and compared to mice that slept for 4 hours during the same circadian time.  5 mice were pooled for each sample and bones from femur, tibia and spine were crushed and stained to lineage deplete and enrich for ckit+, sca-1+,Flk-,CD150+, CD34-

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: qpcr miRNA profiling from approximately 50ng total RNA extracted from HSC FACS sorted into Trizol.

first: Ingrid

last: Ibarra

first: Asya

last: Rolls


title: Inhibition of MEK and PI3K alone or in combination alters the transcriptome of the lung during TGFα-induced pulmonary fibrosis

status: Public on Dec 03 2013

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Pulmonary fibrosis is often triggered by an epithelial injury resulting in the formation of fibrotic lesions in the lung, which progress to impair gas exchange and ultimately cause death. Recent clinical trials using drugs that target either inflammation or a specific molecule have failed, suggesting that multiple pathways and cellular processes need to be attenuated for effective reversal of established and progressive fibrosis. Although activation of MAPK and PI3K pathways have been detected in human fibrotic lung samples, the therapeutic benefits of in vivo modulation of the MAPK and PI3K pathways in combination are unknown. Overexpression of TGFα in the lung epithelium of transgenic mice results in the formation of fibrotic lesions similar to those found in human pulmonary fibrosis, and previous work from our group shows that inhibitors of either the MAPK or PI3K pathway can alter the progression of fibrosis. In this study, we sought to determine whether simultaneous inhibition of the MAPK and PI3K signaling pathways is a more effective therapeutic strategy for established and progressive pulmonary fibrosis. Our results showed that inhibiting both pathways had additive effects compared to inhibiting either pathway alone in reducing fibrotic burden, including reducing lung weight, pleural thickness, and total collagen in the lungs of TGFα mice. This study demonstrates that inhibiting MEK and PI3K in combination abolishes proliferative gene changes associated with fibrosis and myfibroblast accumulation and thus may serve as a therapeutic option in the treatment of human fibrotic lung disease where these pathways play a role.

overall_design: mRNA profiles of CCSP/TGFalpha mice treated with vehicle, ARRY, PX-866, ARRY/PX-866

first: Satish

last: Madala

first: Ramakrishna

last: Edukulla

first: Mukta

last: Phatak

first: Stephanie

last: Schmidt

first: Cynthia

last: Davidson

first: Thomas

last: Acciani

middle: R

last: Korfhagen

first: Timothy

last: LeCras

first: Kimberly

last: Wagner

first: William

last: Hardie


title: Expression data from Arabidopsis under simualted acid rain treatments

status: Public on Nov 20 2013

city: Xiamen

first: Tingwu

last: Liu

address: Siming Road 422

institute: Xiamen university

summary:
Acid rain, as a worldwide environmental issue, can cause serious damage to plants. In this study, we provided the first  case study on the systematic responses of arabidopsis (Arabidopsis thaliana (L.) Heynh.) to simulated acid rain (SiAR) by transcriptome  approach.
In this dataset, we include the expression data obtained from Arabidopsis with simulated acid rain treatments for 68 hr, and contrasting with control group in the same time. Totally, 439 differetal expression genes were obtained in our stduy. Form them, 13 genes which dramatically changed their expression were found related to S metabolism.

overall_design: 6 Total samples were analyzed. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen). Preparation of labeled target cRNA was carried out following the technical manual of Arabidopsis Genome GeneChip array (Affymetrix). Double-stranded cDNA was synthesized from 5 μg of template total RNA using the One-Cycle cDNA Synthesis kit (Affymetrix), and biotin labeled cRNA was synthesized using the IVT Labeling kit (Affymetrix). The labeled cRNA was purified with GeneChip Sample Cleanup Module (Affymetrix). The quality and quantity of the cRNA was checked by conducting gel electrophoresis. Twenty micrograms of the purified cRNA of each sample was fragmented and hybridized to arrays for 16 h at 45°C. All arrays were washed and stained automatically by using a fluidics Station 450 (Affymetrix) and scanned by GeneChip® scanner 3000 (Affymetrix). All procedures were performed according to the manufacturer’s protocols (Affymetrix). Normalization and expression estimate computation were calculated from the .CEL output files from the Affymetrix GCOS 1.1 software using RMA implemented in R language using standard settings. Statistical testing for differential expression was performed with logic-t analysis. Functional categories were assigned to genes using the AGI number to search the MIPS database (http://mips.gsf.de/cgi-bin/proj/thal/) and the Arabidopsis Information Resource website, TAIR (http://www.arabidopsis.org/).

first: Hailei

last: Zheng


title: Inference and validation of predictive gene networks from biomedical literature and gene expression data

status: Public on Dec 23 2013

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

summary: Although many methods have been developed for inference of biological networks, the validation of the resulting models has largely remained an unsolved problem. Here we present a framework for quantitative assessment of inferred gene interaction networks using knock-down data from cell line experiments. Using this framework we are able to show that network inference based on integration of prior knowledge derived from the biomedical literature with genomic data significantly improves the quality of inferred networks relative to other approaches. Our results also suggest that cell line experiments can be used to quantitatively assess the quality of networks inferred from tumor samples.

overall_design: Knock-down of eight genes were performed on colorectal cancer cell lines to identify the genes whose expression was significantly affected. These genes were subsequently used to validate the quality of our causal gene interaction network.

first: Catharina

last: Olsen

first: Kathleen

last: Fleming

first: Niall

last: Prendergast

first: Renee

last: Rubio

first: Frank

last: Emmert-Streib

first: Gianluca

last: Bontempi

first: John

last: Quackenbush


title: Psychosocial stress reflected by the PBMC transcriptome in the pig

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary: Unfamiliar individuals (German Landrace pigs) with different aggressiveness were mixed. Subsequently PBMC transcriptome profiles were analysed at postnatal stage (190 dpn)

overall_design: Per psychosocial group 7-8 pigs were collected for expression profiling

first: Eduard

last: Murani

first: Michael

last: Oster


title: miRNA expression profiles of canine mammary cancer cells and macrophages grown in co-culture conditions

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary: miRNA expression in five various canine mammary cancer cell lines grown with macrophages as co-cultures was assessed using Agilent microarrays. We observed significant changes in miRNA expression in comparison to control cells grown as a mono-culture. The changes in the Wnt pathway were most significant.

overall_design: Five cell lines were grown as a co-culture with macrophages for 72 hrs. After that, the cells were sorted out and t-RNA was isolated and hybrydized on Agilent microarrays. The control was RNA isolated from cells grown as a mono-culture.

last: Krol


title: Gene expression signature of EGR3 silencing in M12 human prostate cancer cells

status: Public on Nov 06 2013

city: Irvine

first: Zhenyu

last: Jia

address: 123 Schubert Ct.

department: Statistics

institute: The University of Akron

summary: EGR3 expression is upregulated in human prostate cancer compared to normal prostate tissue and is associated with absence of relapse, while low EGR3 expression in tumors is predicitive of disease relapse (Pio et al., PLOS One 2013; 8(1):e54096). However the function of EGR3 in prostate cancer is unknown. Human prostate cancer cells M12 containing high levels of EGR3 were used for shRNA-mediated silencing of EGR3. Gene expression analysis of EGR3 knockdown cells reveals a role in inflammation and the existence of a crosstalk with the NFkB pathway.

overall_design: The M12 prostate cancer cell line is a tumorigenic derivative of the P69 SV40-T immortalized epithelial cells obtained through serial passages of P69 tumor xenografts in mice (Bae et al., Prostate 1998; 34:275-82). M12 cells were transfected with shRNA scramble plasmid (shSCR) or shEGR3 plasmid and selected with puromycin (1 μg/ml). Single-cell clones were isolated using standard methods. Stably transfected cells (shSCR-M12 and shEGR3-M12) were then maintained in growth medium supplemented with puromycin. Two separate clones (termed cl 2 and cl 3) were studied. Knockdown of EGR3 (50% efficacy on average) was stable over many cell culture passages. Biological duplicates of control cells (scramble shRNA) and of two separate clones of shEGR3 cells (clone 2 and clone 3) were used for the gene expression arrays (i.e. 6 samples).

first: V

last: Baron

first: B

last: Pio

first: Z

first: D

last: Mercola


title: Profiling Methylomic Alterations in Postmortem Prefrontal Cortex Tissues of Individuals with Alcohol Use Disorders

city: Boston

first: Huiping

last: Zhang

state: Massachusetts

address: 72 East Concord Street

department: Psychiatry

institute: Boston University School of Medicine

summary:
Analysis of methylomic alternations related with alcohol use disorders (AUD). The hypothesis is that chronic alcohol consumption might alter genome-wide DNA methylation patterns.
The results suggest that differential DNA methylation might be invovled in neuradaptations to alcohol.

overall_design: Genomic DNA was extraced from postmortem prefrontal cortex tissues of 23 AUD cases and 23 matched controls. Both AUD cases and matched controls are assessed with DSM-IV


title: Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites [S-phase/M-phase synchronized cells]

status: Public on Oct 01 2013

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary: During cell division, transcription factors (TFs) are removed from chromatin twice, during DNA synthesis, and during condensation of chromosomes. How TFs can efficiently find their sites following these stages has been unclear. Here, we have analyzed the binding pattern of expressed TFs in human colorectal cancer cells. We find that binding of TFs is highly clustered, and that the clusters are enriched in binding motifs for several major TF classes. Strikingly, almost all clusters are formed around cohesin, and loss of cohesin decreases both DNA accessibility and binding of TFs to clusters. We show that cohesin remains bound in S phase, holding the nascent sister chromatids together at the TF cluster sites. Furthermore, cohesin remains bound to the cluster sites when TFs are evicted in early M-phase. These results suggest that cohesin binding functions as a cellular memory that promotes re- stablishment of TF clusters after DNA replication and chromatin condensation.

overall_design: Examination of TF binding by ChIP-seq in a CRC cell-line treated with non-targeting siRNA, or siRNA specific to the cohesin subunit RAD21.

first: Jian

last: Yan


title: Genome-wide analysis and comparison of E15 and adult rat lateral ventricular choroid plexus epithelial cells.

status: Public on Sep 16 2013

city: Parkville

first: Shane

last: Liddelow

state: Victoria

address: Level 8 Medical Building, Grattan Street

department: Pharmacology

country: Australia

institute: The University of Melbourne

summary: Transcriptome analysis of lateral ventricular choroid plexus epithelial cells of embryonic day 15 (E15) and adult control Sprague-Dawley rats.

overall_design: We analyzed total RNA extracted from plexus epithelial cells from 6 pooled samples (3 E15, 3 adult) using the Illumina HiSeq 2000 platform.

first: Katarzyna

last: Dziegielewska

first: C

last: Ek

first: Mark

last: Habgood

first: Hannelore

last: Bauer

first: Hans-Christinan

first: Helen

last: Lindsay

first: Matthew

last: Wakefield

first: Jean-Francois

last: Ghersi-Egea

first: Nathalie

last: Strazielle

first: Ingrid

last: Kratzer

first: Kjeld

last: Møllgård

first: Norman

last: Saunders


title: Expression profile of LNCaP prostate cancer cell line treated with DMSO or BP

status: Public on Sep 29 2013

city: Hualien

first: Sheng-Chun

last: Chiu

address: No. 707, Sec. 3, Chung Yang Rd

department: Department of Medical Research

institute: Buddhist TzuChi General Hospital

summary:
N-butylidenephthalide (BP) exhibits its antitumor effect in a variety of cancer cell lines. However, little is known about its effects on prostate cancer. The objective of this study was to obtain additional insights into the mechanisms involved in BP induced cell death in human prostate cancer cells.
To determine the mechanisms of BP-induced growth arrest and cell death in prostate cancer cell lines, we performed a microarray study to identify alterations in gene expression induced by treatment with BP in the LNCaP cells.

overall_design: LNCaP cellss were selected to treated with BP for 3 or 24hr for RNA extraction and hybridization on Affymetrix microarrays.

first: Cheng-Yoong

last: Pang


title: Transcriptomic analysis of SH-SY5Y cells in response to enterovirus type 71 infection

status: Public on Oct 31 2013

city: Beijing

first: li

last: juan

address: East Street Fengtai District

institute: Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

summary: Today, the pathogenesis of human enterovirus type 71 (HEV71) infection in human central neural system remains unclear. HEV71 is the major pathogen of hand-foot-and-mouth disease (HFMD), and has been associated with severe neurological disease and even death in infants and young children. We employed the human whole genome microarray analyze the transcriptome profiling inhuman neuroblastoma cells SH-SY5Y infected with HEV71. The results showed that HEV71 infection lead to altered expression of 161 human mRNAs including 74 up-regulated genes and 87 down-regulated genes. Then we found that the possible roles of the differentially regulated mRNAs in selected pathways including cell cycle/proliferation, apoptosis, and cytokine/chemokine responses by Bioinformatic analysis. Furthermore, we validated the microarray results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about host response to HEV71 infection in human neuroblastoma cells, and this finding will help to understand the pathogenesis of HEV71 infection and virus-host interaction.

overall_design: Total RNA of cells infected with HEV71 was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each pooling RNA sample separately on the GeneChip_ Porcine Genome Array (Affymetrix) at CapitalBio Corporation (Beijing, China) in which GeneChip microarray service was certificated by Affymetrix.

first: LiJuan

last: Xu

first: ChengFeng

last: Qin


title: Gene Expression Changes Between Patent and Fused Cranial Sutures in a Nonsyndromic Craniosynostosis Population

status: Public on Sep 12 2013

city: Portland

first: Amiee

last: Potter

address: 3181 SW Sam Jackson Park Rd, Mail Code #L581

department: Integrated Genomics Laboratory

institute: OHSU

summary: Assaying gene expression in sutural bone fragments from patients diagnosed with non-syndromic craniosynostosis.  Sutural fragments were collected from both the fused and patent cranial suture of infants during cranial vault reconstruction.  Gene expression was compared between the patent and fused sutures using the paired t-test.  The aim was to identify thoses genes significantly differentially expressed in fused suture relative to patent.

overall_design: Total RNA isolated from patent and fused human cranial sutures was assayed. Expression in synostosed suture was compared to patent suture.

first: Jennifer

middle: L

last: Rhodes

first: Rafael

last: Vega

first: Thomas

last: Ridder

first: Rita

last: Shiang


title: Profiling Transcriptomic Alterations in Postmortem Prefrontal Cortex Tissues of Individuals with Alcohol Use Disorders

first: Huiping

last: Zhang

summary:
Analysis of transcriptiomic alternations related with alcohol use disorders (AUDs). The hypothesis is that chronic alcohol consumption might alter genome-wide gene expression patterns.
The results suggest that differential gene expression in the prefrontal cortex is implicated in neuroadaptations to alcohol.

overall_design: Total RNAs were extracted from postmortem prefrontal cortex tissues from 23 AUD cases and 23 matched controls. Both AUD cases and matched controls were assessed with DSM-IV.


title: Transcriptional regulation patterns revealed by high-resolution chromatin immunoprecipitation during cardiac hypertrophy

status: Public on Sep 06 2013

city: Newark

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

summary:
Purpose: To identify the differential transcriptional patterns during postnatal cardiac growth, pressure-induced cardiac hypertrophy and adult mouse hearts
Results: Our data revealed novel transcriptional patterns during cardiac growth conditions. The results showed that most of the essential genes are regulated by promoter clearance of paused RNA pol II, while de novo recruitment is required for regulation of mostly speclaized genes during cardiac growth. We have identified two major modes of gene regulation durign cardiac hypertrophy and four transcriptional growth patterns. The results are published in January 2013 issue of Journal of Biological Chemistry.

overall_design: Methods: Hearts were extracted from 1-2day old C57 mice, from mice subjecetd to Transaortic coarctation or adult mice. The hearts were sent to Active Motif for RNA polII and H3K9ac- ChIP-Seq.

first: Maha

last: Abdellatif


title: Gene expression data in mouse fetal lungs

status: Public on Sep 03 2013

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

summary: Microarray data of mouse postnatal lungs between day 1 and 6 weeks of age. The results provide a general insight into the gene expression profile during the alveolar phase of lung development.

overall_design: We obtained lung tissue of healthy postnatal mice, 4-5 replicates at each time point. Time points were day1, day4, day7, day14, and day 42.

middle: V

first: Namasivayam

last: Ambalavanan

first: Naftali

last: Kaminski


title: The transcription factor IRF4 is essential for T cell receptor affinity mediated metabolic programming and clonal expansion of T cells [RNA-seq]

status: Public on Aug 17 2013

city: Clayton

first: Wei

last: Shi

address: Wellington Rd

institute: Monash University

summary: We demonstrate that transcription factor IRF4 is induced in a T cell receptor (TCR) affinity-dependent manner and functions as a dose-dependent regulator of the metabolic function of activated T cells. IRF4 regulates the expression of key molecules required for aerobic glycolysis of effector T cells, and is essential for clonal expansion and maintenance of effector function of antigen-specific CD8+ T cells.

overall_design: Examination of gene expression profiles in six types of samples

first: Axel

last: Kallies

first: Kevin

last: Man

first: Annie

last: Xin

first: Stephen

last: Nutt

first: Gordon

middle: K

last: Smyth


title: Human cell toxicogenomic analysis links reactive oxygen species to the toxicity of monohaloacetic acid drinking water disinfection byproducts

status: Public on Aug 11 2013

city: Urbana

first: Michael

last: Plewa

state: IL

address: 1101 W Peabody Dr

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

summary: The monohaloacetic acids (monoHAAs) are generated as byproducts during the disinfection of drinking water and are cytotoxic, genotoxic, mutagenic, and teratogenic. Iodoacetic acid (IAA) toxicity was mitigated by antioxidants, suggesting the involvement of oxidative stress. Other monoHAAs may share a similar mode of action. Human oxidative stress and antioxidant defense gene arrays  (SA biosciences) were used to evaluate changes in transcriptome profiles in the human intestinal epithelial cell line FHS 74 INT generated by three compounds, chloroacetic acid (CAA), bromoacetic acid (BAA) and IAA at two time points (30 min and 4 h).

overall_design: Twelve samples were evaluated. Each treated sample was paired with a concurrent negative control (cells treated in medium only).  Three technical repeats were included for each sample and Ct values were calculated from the average of the three repeats. Samples 1,2,and 3 were isolated from  30 min negative controls for CAA, BAA, and IAA respectively.  Samples 4, 5, and 6 were isolated from cells treated for 30 min with CAA, BAA, and IAA respectivley.  Samples 7, 8, and 9 were isolated from 4h negative controls for CAA, BAA, and IAA respectively. Samples 10, 11, and 12 were isolated from cells treated for 4 h with CAA, BAA and IAA respectively. Ct values were normalized against the average of the 5 housekeeping genes included in the array to generate ΔCt values. Fold changes for each gene were calculated as a ratio of 2^-ΔCttest / 2^-ΔCtcontrol.

first: J

last: Pals

first: M

middle: S

last: Attene-Ramos

first: X

last: Menghang

first: E

last: Wagner


title: Dynamic Transcriptional Response of Escherichia coli to Inclusion Body Formation

status: Public on Aug 16 2013

city: Clemson

first: Faraz

last: Baig

state: SC

address: 208 Biosystems Research Complex

department: Bioengineering

institute: Clemson University

summary: DNA microarrays were used to compare the E. coli gene expression response to soluble and insoluble recombinant protein production.  The study objective was to characterize the dynamic transcriptional changes that occur as insoluble recombinant protein is produced

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Recombinant cultures producing VP1GFP and GFPCAT in minimal medium (MM) cultures and VP1GFP in ethanol-treated cultures were analyzed.  A total of 15 samples were collected.  Samples were collected at 5, 20, 40, and 60 minutes post-induction for all induced MM cultures and at 60 minutes post-induction for the induced ethanol-treated cultures.  Samples were collected at time 0 and 60 minutes for the uninduced MM and uninduced ethanol-treated cultures.  Time 0 of the ethanol-treated VP1GFP cultures consisted of six biological replicates, while the remaining 14 samples were conducted in biological replicates.  All biological replicates represent expression data from three independent hybridizations.

first: Lawrence

middle: P

last: Fernando

first: Mary

last: Salazar

first: Rhonda

last: Powell

first: Terri

last: Bruce

first: Sarah

middle: W

last: Harcum


title: The transcription factor IRF4 is essential for T cell receptor affinity mediated metabolic programming and clonal expansion of T cells

first: Wei

last: Shi

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

overall_design: Refer to individual Series


title: miRNA expression in human chondrocyte subtypes

status: Public on Oct 23 2013

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

summary: Frozen blocks of human embryonic limb tissue were sectioned and laser capture microdissected to collect three human chodrocyte tissues - precursor, differentiated and hypertrophic chondrocytes.Total RNA including miRNAs was isolated and analyzed using Applied Biosystems OpenArray® Real-Time PCR system.

overall_design: RT-PCR miRNA expression profiling. miRNA expression from three chondrocyte sub types - precursor, differentiated and hypertrophic  chondrocytes were analyzed using TaqMan® OpenArray® Human MicroRNA Panel.

first: Audrey

last: McAlinden


title: Contribution of the mammary epithelial cell to the immune response during early stages of a bacterial infection to Staphylococcus aureus in goats

status: Public on Aug 31 2013

city: Jouy en josas

first: Pauline

middle: Marie

last: Brenaut

address: Domaine de Vilvert

country: France

institute: INRA

summary: Mastitis is an inflammation of the mammary gland (MG), usually due to bacterial infection. Although considerable attention has been paid to this economically important disease, the early stages of the host response remain poorly defined. In particular, it is unclear how mammary epithelial cells (MEC), a first barrier against pathogens, respond to infection. Indeed, it is difficult to differentiate between the contributions of MEC and infiltrating immune cells to gene expression profiles of mammary tissue during mastitis. The current investigation examines the response of MEC at the early stage of infection using a non invasive RNA sampling method taking advantage of the presence of cytoplasmic crescents contained in milk fat globules. We have recently shown that, in goats, Milk Fat Globules (MFG) provide a unique source of RNA to study the in vivo regulation of gene expression in MEC. This non invasive RNA sampling method was used during the time course of an experimental intra mammary infection (IMI) with S. aureus. Experiments were performed using ovine microarrays (Agilent) to compare gene expression patterns before infection,  at 12h, 18h and 24h post-infection (PI). Furthermore, we combined this approach with laser capture microdissection of MEC isolated from frozen slides of mammary tissue to study some specific genes at the late stage of infection (30h PI). We show that at 18h PI, before the burst of somatic cells in milk, MEC play an important role in the recruitment and activation of inflammatory cells through the IL-8 signaling pathways. Then, at the late stage of infection (30h PI), the contribution of MEC in immune response changes to produce different acute phase proteins, including SAA3, serpin A1 and PTX3. These cells also express factors that contribute directly to fighting infection, such as S100A12. In summary, we demonstrate for the first time  in vivo how MEC orchestrate innate immune response during an IMI with S. aureus in the goat species. We report here new opportunities to assess the dynamics of gene expression in the mammary gland, thus providing significant advances in the understanding of MEC immune capacity. Furthermore, the production of some molecules by MEC, in the early stages of IMI, could provide sensitive biomarkers for early detection and therefore, treatment of mastitis.

overall_design:
Experiments were performed using ovine microarrays (Agilent) to compare gene expression patterns before infection,  at 12h, 18h and 24h post-infection (PI).
20 sample records; mono-colour experimental design

first: P

first: L

last: Lefevre

first: A

last: Rau

first: D

last: Laloe

first: G

last: Pisoni

last: Moroni

first: C

last: Bevilacqua

last: Martin


title: Classification of  Myeloma Using Global MicroRNA Profiling

status: Public on Jul 31 2013

city: London

first: Gareth

last: Morgan

address: 15 Cotswold Road

department: Division of Molecular Pathology

country: United Kingdom

institute: The Institute of Cancer Research

summary: Myeloma is a heterogeneous disease. In this work we used global microRNA profiling to classify clinical samples from UK MRC Myeloma IX, and developed a microRNA-based “outcome classifier” for risk stratification.

overall_design: Global microRNA expression profiling was carried out in 163 newly diagnosed samples from CD138+ cell selection

first: Antonino

last: Neri

first: Ping

last: Wu

first: Luca

last: Agnelli


title: Transcriptome analysis of the D3 mouse embryonic stem cell line in comparison to the MIN6 pancreatic beta-cell insulinoma cell line

status: Public on Jul 23 2013

city: Sydney

first: Chris

last: O'Neill

address: Kolling Institute of Medical Research, Royal North Shore Hospital, Reserve Road, St Leonards

department: Kolling Institute of Medical Research

institute: University of Sydney

summary: Analysis of the transcriptional differences between mouse ES cells from the D3 cell line and transformed beta-cells (MIN6 cell line) as determined by a direct comparative analysis of their transcriptome. The results show that 40% of transcripts were differentially expressed between D3 and MIN6 cells. There is thus a marked difference in the pattern of transcription between the ES cell and beta-cell genomes.

overall_design: Total RNA was extracted from three independent replicates of passage 21 D3 cells and passage 23 MIN6 cells. A whole mouse genome comparison between D3 and MIN6 cells was performed using the Mouse WG-6 v2.0 Expression Beadchip from Illumina.

first: Jennifer

middle: Y

last: Wong

first: Michelle

last: Jack

first: Christopher


title: High-throughput sequencing of PROMPT-enriched samples.

status: Public on Jul 03 2013

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: Sequencing of 5' and 3'ends and RNA-seq of PROMPT and mRNA molecules from control and exosome-depleted cells.

overall_design: CAGE, 3'TAG and RNAseq library construction from RNA extracted from control and exosome-depleted cells.

first: Torben

middle: H

last: Jensen

first: Albin

last: Sandelin

first: Lars

last: Steinmetz

first: Evgenia

last: Ntini


title: The Cytokines Interleukin-1 and Interferon-gamma Differentially Program Beta-glucan–activated Dendritic Cells via IkappaB-zeta Modulation

status: Public on Nov 01 2013

city: Frederick

first: Marco

last: Cardone

address: 1050 Boyles Street

department: CIP

institute: NCI/NIH

summary: To evaluate the DC genome-wide gene expression in response to beta-glucan and its regulation by IL-1 receptor antagonist (IL-1RA) we used a whole genome microarray. The gene expression profiling was performed in DC left untreated or exposed to beta-glucan for 4 and 12 h, in absence or presence of IL-1RA. This strategy allowed the identification of early/immediate and late/secondary genes regulated by beta-glucan in an IL-1-dependent and -independent manner. Human monocyte-derived DC were obtained by a 6/7-d cultures of freshly isolated monocytes with recombinant human IL-4 (10 ng/ml) and GM-CSF (50 ng/ml).

overall_design: Beta-glucan-associated gene expression and its regulation by IL-1RA in human DC was measured in cells left untreated or at 4 and 12 h after exposure to 10 ug/ml of particulate beta-glucan in absence or presence of 2.5 ug/ml of IL-1RA. Five different conditions (Untreated 0h, beta-glucan 4h, IL-1RA + beta-glucan 4h, beta-glucan 12h, and IL-1RA + beta-glucan 12h) were tested using DC from three different donors.

last: Trinchieri

first: M


title: Gene Expression in Whole Blood of Atopic Eczema and Healthy Children at 4 years

status: Public on Jun 29 2013

city: Barcelona

first: M. Carmen

last: López-Sabater

state: Barcelona

address: Av. Joan XXIII S/N

department: Food Science and Nutrition

country: Spain

institute: University of Barcelona

summary:
We studied genes that are related to atopic diseases [i.e., atopic eczema (AE)]. Immunological factors and principal genes involved in the biosynthesis of polyunsaturated fatty acids were included. We analyzed whether expression of genes encoding key enzymes of LC-PUFA synthesis (FADS1, FADS2 and ELOVL5) is associated with circulating LC-PUFA levels and risk of AE in 4-year-old children.
AE (n=20) and non-AE (n=104) children participating in the Sabadell cohort within the INfancia y Medio Ambiente (INMA) Project were included in the present study. RT-PCR with TaqMan Low-Density Array cards was used to measure the expression of these genes.

overall_design: RT-PCR gene expression profile. The samples are described in the sumary. Each sample was measured in duplicate in the same TLDA card and we present the average of each sample.

first: Aida

last: Chisaguano

first: Rosa

last: Montes

first: Teresa

last: Pérez-Berezo

first: Ana

middle: I

last: Castellote

first: Marcela

last: Guerendiain

first: Mariona

last: Bustamante

first: Eva

last: Morales

first: Raquel

last: García-Esteban

first: Jordi

last: Sunyer

first: Angels

last: Franch


title: Expression data from human acute lymphoblastic leukemia cell line SupB15 and its drug resistant subpopulations SupB15-MR

status: Public on Jul 15 2013

city: Manchester

first: jizhong

last: LIU

address: wilmslow road

institute: THE UNIVERSITY OF MANCHESTER

summary:
SupB15 cells are highly sensitive to Mitoxantrone treatment. To obtain drug resistant subpopulations, SupB15 cells were incubated in normal medium or BMSC derived conditioned medium, treated with 10nM of Mitoxantrone for 6 days. SupB15 cells in normal medium could not survive. a small population of SupB15 cells in conditioned medium group survived the treatment and ecpanded, termed as SupB15-MR.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: GeneChip Human Genome U133A 2.0 Array were performed to compare gene expression between SupB15 and SupB15-MR cells

first: Jizhong

last: Liu

first: Vaskar

last: Saha


title: MiR-155 promotes blood-brain barrier dysfunction in neuroinflammation

status: Public on Apr 29 2014

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez-Ramirez

state: California/San Diego

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego


title: Interaction of Wnt signaling with Smad signaling during myogenic differentiation in mouse myoblast cells

status: Public on Jun 21 2013

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Wnt/beta-catenin signaling is involved in various aspects of skeletal muscle development and regeneration. Using C2C12 cells, we examined intracellular signaling and gene transcription during myoblast proliferation and differentiation. The results of the present studies suggest that Wnt signaling is interacting with TGF-beta superfamily signaling through Smad activation.

overall_design: Single analysis for each condition (proliferating C2C12 cells, differentiating C2C12 cells, proliferating Wnt4-overexpressing C2C12 subline cells).

first: Tsutomu

last: Nohno


title: Reduced insulin/IGF-1-like signaling restores germ cell immortality in Caenorhabditis elegans Piwi mutants

status: Public on Jun 01 2013

city: Cambridge

first: Eric

middle: A.

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

institute: University of Cambridge

type: Expression profiling by genome tiling array


title: Transgenerational changes in small RNA profiles of C.elegans mutants lacking PRG-1

summary: An attempt to identify small non-coding RNAs that change with increasing generations after becoming homozygous for the loss of PRG-1

overall_design: Small non-coding RNA (18-30nt) was extracted from animals the indicated number of generations after homozygosity was established

first: Peter

last: Sarkies

first: Matt

last: Simon

first: Shawn

last: Ahmed


title: Histone tail modification profiles of human renal tubule epithelial cells

status: Public on Aug 09 2013

city: Philadelphia

first: Yi-An

last: Ko

state: Pennsylvania

address: 415 curie blvd

department: Genetics & Gene Regulation

institute: UPeenn

summary: To annotate the regulatory elements in the renal tubule epithelial cells, we profiled 6 histone ChIP-seq in the human kidney epithelical cells (HKC8).

overall_design: We pulled down the DNA with specific antibodies of interests against histone tail modifications in the human rebal tubule epithelial cells. The result can be interpretated with ChromHMM for different states.

first: Katalin

last: Susztak


title: Transcription Factor Highly Occupied Target (HOT) Regions of 145 Cell Lines

status: Public on Jan 14 2015

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

type:
Other
Third-party reanalysis

summary:
Purpose: 253 GSM Samples from GSE32970 and GSE29692 was reanalyzed to find the highly occupied target (HOT) regions of 154 cell lines.
Methods: 1. We assigned the binding sites of 542 TFs in 154 cell lines as GSE53962 (Our last submission).  2.We performed a Gaussian kernel density estimation across the genome with a bandwidth of 300 bp, using the centers of each of the TF binding peaks as points. Then, we scanned this density for peaks, and denoted each peak a TF region(Candidate region to find HOT regions).To determine the complexity of the TF region, we summed the Gaussian kernalized distance from the peak to each TF that contributed at least 0.1 to its strength. The TF region around eat peak was derived by finding the maximum distance (in bp) from the peak to a contributing TF, and then adding 150 bp (one half of the bandwidth). Each TF region is centered on the peak, and have a TF complexity value.  3.To define HOT region according to the TF complexity, we required a complexity cutoff for each cell line.To geometrically define the cutoff we first scaled the TF complexity such that the x and y axis were from 0-1. We then found the x axis point for which a line with a slope of 1 was tangent to the curve. We define this point as the cutoff value,TF region whose complexity above this point to be HOT region, and TF region complexity below that point to be lowly occupied target (LOT) regions.
Result: Using the binding sites of 542 TFs in 145 cell lines, we assigned a TF complexity score to each TF region corresponding to the number of distinct TFs bound, resulting in HOT regions of 145 cell lines.

overall_design: TF HOT Regions of 145 Cell Lines. 54 GSM Samples from GSE32970 and 199 GSM Samples from GSE29692 were combined to 154 cell types.

first: Hebing

last: Chen

first: Hao

last: Li


title: Human lung epithelial cells progressed to malignancy through specific oncogenic manipulations

status: Public on Jul 01 2013

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

summary: We have developed cdk4/hTERT-immortalized normal human bronchial epithelial cells (HBECs) to study lung cancer pathogenesis.  By studying the oncogenic effect of common lung cancer alterations (p53, KRAS, and c-MYC) we demonstrate the ability of this model to characterize the stepwise transformation of bronchial epithelial cells to full malignancy.  Using HBECs derived from multiple individuals we found: 1) the combination of five genetic alterations (p53, KRASV12, c-MYC, CDK4 and hTERT) is sufficient for full tumorigenic conversion of HBECs; 2) high levels of KRASV12 are required for full malignant transformation of HBECs, however these levels also stimulate oncogene-induced senescence; 3) RAS-induced senescence is largely bypassed with loss of p53 function; 4) over-expression of c-MYC greatly enhances malignancy but only in the context of sh-p53+KRASV12; 5) HBECs from different individuals vary in their sensitivity to transformation by these oncogenic manipulations; 6) serum-induced epithelial-to-mesenchymal transition (EMT) increases in vivo tumorigenicity; 7) genetically-identical clones of transformed HBECs exhibit pronounced differences in tumor growth, histology, and differentiation as well as sensitivity to standard platinum-based chemotherapies; and 8) an mRNA signature derived from tumorigenic and non-tumorigenic clones is predictive of outcome in lung cancer patients.  Collectively, we demonstrate this HBEC model system can be used to study the effect of oncogenic mutations on malignant progression, oncogene-induced senescence, and EMT along with clinically translatable applications such as development of prognostic signatures and drug response phenotypes.

overall_design: Human bronchial epithelial cells (HBECs) immortalized with cdk4 and hTERT were transformed with p53 knockdown, KrasV12 and cMYC over-expression and profiled on Illumina HumanHT-12 V4.0 expression beadchips. Transformed HBECs were grown in two different growth media: KSFM (defined, serum-free medium) or R10 (RPMI with 10% FBS) as indicated. Clones were isolated from HBECs with sh-p53 + KrasV12 and sh-p53 + KrasV12 + cMYC.

first: Jill

middle: E

last: Larsen

first: John

middle: D

last: Minna


title: A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium

first: zhang

last: jingyu

address: Nanxincun #20

institute: Institute od botany

summary: PARE (parallel analysis of RNA ends) was performed to study the change of uncapped mRNAs before and after cold treatment  in Brachypodium. Different change patterns were identified. We have provided a complete view of uncapped transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants.

overall_design: The uncapped mRNA profiles of 12-day-old Brachypodium seedlings with and without cold treatment  (4 °C for 24 h)  were generated by deep sequencing using Illumina GAIIx

first: Jingyu

last: Zhang


title: A global profiling of  gene expression under cold stress in Brachypodium

summary: RNA-Seq was performed to study the change of gene expression before and after cold treatment  in Brachypodium. Different change patterns were identified. We have provided a complete view of  transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants.

overall_design: The mRNA profiles of 12-day-old Brachypodium seedlings with and without cold treatment  (4 °C for 24 h)  were generated by deep sequencing using  Illumina HiSeq™ 2000.


title: Gene expression profiling of cidofovir treatment and resistance inHeLa, HaCaT, and PHK cells

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Cidofovir is an acyclic nucleoside phosphonate with strong antiviral activity against a broad spectrum of DNA viruses. Although it has previously been shown that cidofovir exerts an antiproliferative effect on HPV positive cells by the induction of apoptosis, the exact mechanism of action remains to be unraveled. In order to study the activity of cidofovir against HPV, gene expression profiling was performed in cidofovir-treated and cidofovir-resistant HeLa, HaCaT, and PHK cells by means of microarrays (HG-U133 Plus 2, Affymetrix).

overall_design: Controls (untreated HeLa, HaCaT, and PHK wild-type cells): 72h of growth. Cidofovir treated (50 µg/ml) HeLa, HaCaT, and PHK cells: 72h of growth. Cidofovir resistant cells (HeLa #52 and HaCaT #51): 72h of growth. All samples were performed in triplicates.

first: Tim

last: De Schutter

first: Dimitrios

last: Topalis

first: Graciela

last: Andrei

first: Robert

last: Snoeck


title: Gene expression profiling of chronic lung disease for the Lung Genomics Research Consortium

status: Public on May 30 2013

city: Pittsburgh

last: Tedrow

state: PA

address: 3471 Fifth Avenue, Suite 1211

department: Internal Medicine

institute: University of Pittsburgh

summary: Microarray data from total RNA extracted from whole lung homogenate from subjects undergoing thoracic surgery. These subjects were diagnosed as being controls or having interstitial lung disease or COPD as determined by clinical history, CT scan, and surgical pathology. There was no intervention, these are cross-sectional data.  All samples are from the Lung Tissue Research Consorium (LTRC and are indexed by their LTRC tissue label).

overall_design: These are 582 total subjects, 254 have interstitial lung disease, 220 have COPD, and 108 are controls, who went for surgery for the investigation of a nodule and have no chronic lung disease by CT or pathology.  Due to the number of samples, multipe batches of arrays were necessary, so 10% of the arrays were picked at random to have replicates throughout each batch to account for possible batch effects.  The feature extracted data was normalized using a pairwise cyclic loess approach, and the probes were collapsed to one probe per gene by selecting the probe with the highest average signal. Each sample is total RNA extracted from flash frozen human whole lung homogenate. Between the two platforms were analyzed. Samples are titled by source (LT=LTRC), 6-digit tissue label, lobe of extraction, and major disease state)

first: Naftali

last: Kaminski

first: Brenda

middle: J

last: Guardela

first: David

middle: A

last: Schwartz


title: Highly pathogenic influenza virus inhibit Inflammatory Responses in Monocytes via Activation of the Rar-Related Orphan Receptor Alpha (RORalpa)

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

summary: Highly pathogenic influenza virus inhibit Inflammatory Responses in Monocytes via Activation of the Rar-Related Orphan Receptor Alpha (RORalpha). Low (PR8) and high pathogenic influenza viruses (FPV and H5N1) were used.

overall_design: Monocytes were infected with low (PR8) and high pathogenic influenza viruses (FPV and H5N1)

first: Judith

last: Friesenhagen


title: Antenatal Blood DNA Methylation Profiles

status: Public on May 24 2013

city: Baltimore

first: Jerry

last: Guintivano

state: MD

address: 720 Rutland Avenue, Ross 1068

institute: Johns Hopkins University

summary: DNA methylation profiles were generating using Illumina HM450 microarrays in a prospective sample blood from the prenatal period of pregnant mood disorder patients who would and would not develop depression post partum.

overall_design: We recruited 54 pregnant women with a history of either Major Depression or Bipolar Disorder (I, II or NOS) and prospectively followed them during pregnancy and after delivery in order to identify genetic and clinical characteristics that precede the development of a postpartum depressive episode. Blood samples profiled were collected at varying time points during pregnancy.

first: Michal

last: Arad

first: Todd

last: Gould

first: Jennifer

last: Payne

first: Zachary

last: Kaminsky