title: Transcriptional profiling of triacylglycerol biosynthesis in rhodococci and identification of a key diacylglyceride O-acyltransferase

status: Public on May 06 2016

city: Berkeley

first: Hiroshi

last: Otani

address: 1 Cyclotron Road

department: DOE Joint Genome Institute

institute: Lawerence Berkeley National Laboratory

summary: Oleaginous microorganisms have considerable potential for biofuel and commodity chemical production. Under nitrogen-limitation, Rhodococcus jostii RHA1 grown on benzoate, an analog of lignin depolymerization products, accumulated triacylglycerols (TAGs) to 55% of its dry weight during transition to stationary phase, with the predominant fatty acids being C16:0 and C17:0. Transcriptomic analyses of RHA1 grown under conditions of N-limitation and N-excess revealed 1,826 dysregulated genes. Genes whose transcripts were more abundant under N-limitation included those involved in ammonium assimilation, benzoate catabolism, fatty acid biosynthesis and the methylmalonyl-CoA pathway. Of the 16 atf genes potentially encoding diacylglycerol O-acyltransferases, atf8 transcripts were the most abundant during N-limitation (~50-fold more abundant than during N-excess). Consistent with Atf8 being a physiological determinant of TAG accumulation, a Δatf8 mutant accumulated 70% less TAG than wild-type RHA1 while atf8 overexpression increased TAG accumulation 20%. Genes encoding type-2 phosphatidic acid phosphatases were not significantly expressed. By contrast, three genes potentially encoding phosphatases of the haloacid dehalogenase superfamily and that cluster with, or are fused with other Kennedy pathway genes were dysregulated. Overall, these findings advance our understanding of TAG metabolism in mycolic acid-containing bacteria and provide a framework to engineer strains for increased TAG production.

overall_design: Transcriptomes of R. jostii RHA1 from nitrogen excess and nitrogen limited cultures were analysed using a Genome Analyzer IIx (Illumina®).

first: Nicolas

last: Seghezzi

first: Sawsan

last: Amara

first: Lindsay

last: Eltis


title: Transcriptome anlaysis of gastrointestinal tract of pre-weaned cavles

status: Public on May 01 2016

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

type: Expression profiling by high throughput sequencing

summary: In order to test the development of gastrointestinal tract (GIT) in pre-weaned cavles, the GIT tissues were collected from day 0, day 7, day 21 and day 42 calves. RNA-seq was used to measure the transcriptome profiles. The RNA-seq analysis revealed the fast development of small intestine and rumen tissue during the first week after birth.

overall_design: The tissues of rumen (RU), mid-jejunum (MJ), distal-jejunum (DJ), ileum (IL) in day 0 (D0), day 7 (D7), day 21 (D21) and day 42 (D42) calves were collected. Their transcriptome profiles were compared to obtain the reginal and temporal differences during the pre-weaned peroid of claves.


title: Differential gene expression profiling of endometrium during the mid-luteal phase of the estrous cycle between repeat breeder and normal fertile cows

status: Public on May 02 2016

city: Tsukuba

first: KENGO

last: HAYASHI

country: Japan

institute: National Institute of Agrobiological Sciences

summary: We investigated differential gene expression profiles of endometrium during the mid-luteal phase of the estrous cycle between repeat breeding (RB) and normally fertilized cows using microarray analysis. Caruncular (CAR) and intercaruncular (ICAR) endometrium of both ipsilateral and contralateral uterine horns to the corpus luteum were collected from RB (inseminated at least three times but not pregnant) and normally fertile cows on Day 15 of the estrous cycle. Global gene expression profiles of these endometrial samples were analyzed with a 15K custom-made oligo-microarray in cattle. Microarray analysis revealed that 405 and 397 genes were differentially expressed in CAR and ICAR of the ipsilateral uterine horn of RB, respectively when compared with normal cows. In contralateral uterine horn, 443 and 257 differentially expressed genes were identified in the CAR and ICAR of RB, respectively when compared with normal cows. In the analysis of whole uterine (combining the above four portions), RB cows showed up-regulation of 37 genes including PRSS2, GSTA3, PIPOX, CNGA1 and IGG1C and down-regulation of 39 genes including CHGA, KRT35, THBS4, CPXM2 and PRF1 compared with normal cows. Our results may suggest that local regulation of molecular mechanisms in each uterine portion contributes to normal uterine physiology.

overall_design: This study was carried out using non-lactating Japanease Black cows in the institute ranch. Repeat breeding (n=4) and normally fertile cows (n=4) were slaughtered on Day 15 of the estrous cycle (the day of estrus was designated as Day 0), and collected endometrial tissues. We collected caruncular and intercaruncular areas in endometrium of both ipsilateral and contralateral uterine horns to the ovary containing the corpus luteum (CL).

first: Keiichiro

last: Kizaki

first: Kengo

last: Hayashi

first: Ryosuke

last: Sakumoto

first: Misa

last: Hosoe

first: Toru

last: Takahashi


title: Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

status: Public on May 17 2016

first: James

middle: Michael

last: Wilkinson

address: Ag/For Building

department: Agriculture, Food, and Nutritional Science

summary: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection of 3rd trimester pregnant pigs can result in transmission of the virus to the fetus and ultimately death in utero or postnatally. Little is known about the immune response to infection at the maternal-fetal interface and in the fetus itself, or the molecular events behind virus transmission and disease progression in the fetus. To investigate these processes, RNA-sequencing of two tissues, uterine endothelium adjacent to the umbilical attachment site and fetal thymus, was performed 21 days post challenge on four groups of fetuses selected from a large PRRSV challenge experiment of pregnant gilts.

overall_design: RNA-seq experiment compared gene expression between four different groups of fetuses (n=12 per group): control (CON-uninfected fetuses from mock inoculated gilts), UNINF (uninfected fetuses from PRRSV-inoculated gilts), INF (infected fetuses from PRRSV-inoculated gilts), and meconium-stained fetuses (MEC-meconium-stained fetuses from PRRSV-inoculated gilts) and investigated two tissues: uterine endometrium (with adherent placental tissue) at the site of umbilical attachment and fetal thymus (96 samples in total). Three contrasts were performed for the differential expression (edgeR) and network (WGCNA) analyses: UNINF v CON, INF v UNINF, and MEC v INF.

first: Jamie

middle: M

first: Andrea

last: Ladinig

first: Hua

last: Bao

first: Paul

last: Stothard

first: Joan

middle: K

last: Lunney

first: Graham

middle: S

last: Plastow

first: John

middle: C

last: Harding


title: RNA-seq analysis of transcriptomes for developing fruits derived from sweet orange varieties

status: Public on Apr 13 2016

city: Beibei

first: Zhi-Liang

last: Zheng

state: Chongqing

address: 15 Ganjuchun

department: Citrus Research Institute

country: China

institute: Southwest University

summary: Transcriptome comparsions and integrated systems analysis were used to identify candidate genes associated with fruit acidity control and gene coexpression subnetworks involved in fruit acid accumulation.

overall_design: mRNA profiles of fruit tissues at two stages (45 days postanthesis (DPA); and 142 DPA) from four varieties with differing fruit acidity.


title: MicroRNAs control mRNA fate by compartmentalizing mRNAs based on 3’UTR length

status: Public on Apr 18 2016

city: reno

first: Wei

last: Yan

state: NV

address: 1664 N. Virginia Street

department: Physiology

country: USA

institute: University of Nevada

summary:
Introduction: we conduct comprehensive transcriptomic profiling analyses on three spermatogenic cell types (pachytene spermatocytes, round and elongating spermatids) purified from adult mouse testes using RNA-seq, and we determined not only the levels of both mRNAs and all known sncRNA species, but their cytoplasmic compartmentalization as well.
Method: Pachytene spermatocytes, round and elongating/elongated spermatids were purified from adult mouse testes using the STA-PUT method. We fractionated the purified spermatogenic cells into RNP, monoribosome, and polyribosome fractions using a continuous sucrose gradient ultracentrifugation method, as described. Large RNAs were isolated using the AquaRNA RNA Purification Kit (Cat#5001MT, Mo Bi Tec, Inc.), whereas small RNAs were prepared by the mirPremier™ microRNA Isolation Kit (Cat#SNC10, Sigma).  Constructions of mRNA and sncRNA libraries were conducted following our published protocols (Refs) and the next-gen sequencing was performed on a Hi-Seq 2000 sequencer with SE50 at the Genomics Microarray Core Facility of the UT Southwestern Medical Center (Dallas, TX).
Result:Bioinformatics analyses revealed miRNAs were mostly enriched in RNPs and RNP-enriched miRNAs preferentially target RNP-enriched mRNAs. More interestingly, we found that miRNAs could distinguish shorter and longer 3’UTR transcript based on the distance between their binding sites and the stop codon.
Conclusions:Overall, our genome-wide transcriptomic and bioinformatics analyses have revealed a highly likely mechanism through which miRNAs shape the haploid male germ cell-specific transcriptome characterized by RNP-enrichment of transcripts with shorter 3’UTRs.

first: Chong

last: Tang

first: Ying

last: Zhang

first: Tian

last: Yu


title: Towards the complete small RNome of Acinetobacter baumannii

status: Public on Mar 30 2016

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

institute: University of South Florida

summary: In recent years, the Gram-negative bacterium Acinetobacter baumannii has garnered considerable attention for its unprecedented capacity to rapidly develop resistance to antibacterial therapeutics. This is coupled with the seemingly epidemic emergence of new hyper-virulent strains. Although strain-specific differences for A. baumannii isolates have been well described, these studies have primarily focused on proteinaceous factors. At present, only limited publications have investigated the presence and role of small regulatory RNA (sRNA) transcripts. Herein, we perform such an analysis, describing the RNA-seq-based identification of 78 A. baumannii sRNAs in the AB5075 background. Together with six previously identified elements, we include each of these in a new genome annotation file, which will serve as a tool to investigate regulatory events in this organism. Our work reveals that the sRNAs display high expression, accounting for >50 % of the 20 most strongly expressed genes. Through conservation analysis we identified six classes of similar sRNAs, with one found to be particularly abundant and homologous to regulatory, C4 antisense RNAs found in bacteriophages. These elements appear to be processed from larger transcripts in an analogous manner to the phage C4 molecule and are putatively controlled by two further sRNAs that are strongly antisense to them. Collectively, this study offers a detailed view of the sRNA content of A. baumannii, exposing sequence and structural conservation amongst these elements, and provides novel insight into the potential evolution, and role, of these understudied regulatory molecules.

overall_design: This study is based on the annotation of novel sRNAs on basis of an Acinetobacter baumannii RNA sequencing dataset.  Each sample was generated by pooling three independent biological replicate RNA preps

first: William

middle: H

last: Broach

first: Mackenzie

last: Lee

first: Lindsey

middle: N

last: Shaw


title: Digital expression profiling highlights a distinct live RNA signature in high-risk Primary Biliary Cholangitis (PBC)

status: Public on Apr 02 2016

city: Newcastle

first: Laura

last: Jardine

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Newcastle University

summary: Using outcome after long term follow-up to define risk at disease presentation high risk (n=9 who went on to require liver transplantation) and low risk (n=7 who responded fully to UDCA) patients were identified and their first liver biopsies retrieved. RNA was successfully extracted and analysed using nanostring® transcriptomics. Patients with progressive disease appear to have a distinct molecular signature.

overall_design: high risk (n=9 who went on to require liver transplantation) and low risk (n=7 who responded fully to UDCA) patient material was processed along with non-diseased control liver (n=8)

first: Claire

last: Hardie

first: Kile

last: Green

last: Jopson

first: Lucy

last: Walker

first: Ben

last: Millar

first: Barbara

last: Innes

first: Jessica

last: Dyson

first: David

last: Jones

last: Brain


title: PDGFRα+ cells in ESC cultures represent the in vitro equivalent of the pre-implantation primitive endoderm precursors

status: Public on Apr 22 2016

city: Palermo

first: Antonio

last: Lo Nigro

address: Via tricomi 5

country: Italy

institute: Ismett

summary: Mouse Embryonic Stem Cells (ESCs) express PDGFRα heterogeneously, fluctuating between a PDGFRα+ (PrE-primed) and a Platelet Endothelial Cell Adhesion Molecule 1 (PECAM1)-positive state (epiblast-primed). The two surface markers can be co-detected on a third subpopulation, expressing epiblast and PrE determinants.

overall_design: Three different subpopulatiosn were sorted based on PECAM1/PDGFRa expression and analyzed by NGS

first: Catherine

last: Verfaillie


title: The microRNAs with potential in predicting lung metastasis of triple negative breast cancer

status: Public on Apr 08 2016

city: Guangzhou

first: Jin

last: Wang

address: No.651 Dongfeng East Road

department: Department of Breast Oncology

institute: Sun Yat-sen University Cancer Center

summary: To identify lung metastasis associated microRNAs in triple negative breast cancer (TNBC), we have employed the commercially available Agilent Human miRNA V19.0 Microarray (Platform GPL19730) as a discovery platform.   In comparison with LM-Normal, 11 microRNAs significantly altered in both LM-Met and LM-Tumor, and then three of them (hsa-miR-21-3p, hsa-miR-21-5p and hsa-miR-211-3p) were excluded, which were also up-regulated in RF-Tumor. Consequently, eight deregulated microRNAs were identified to be putatively involved in process of lung metastasis, especially miR-629-3p, which was most up-regulated in both LM-Met and LM-Tumor. To validate the microarray data, we utilized qRT-PCR to assess expression levels of the eight miRNAs in the same samples.

overall_design: Four TNBC patients with lung metastasis underwent pulmonary lobectomy, and their matched surgical specimens of lung metastases (LM-Met), primary tumors (LM-Tumor) and normal breast tissues (LM-Normal) were obtained. Furthermore, to preclude the unspecific miRNAs in TNBC, primary tumors (RF-Tumor) and corresponding normal breast tissues (RF-Normal) from another four patients with 10-year recurrence-free survival were also collected. The initial 20 samples from the eight patients were prepared for miRNA profiling.   Paired-Sample T Test and Significant Analysis of Microarray (SAM) were used to identify miRNAs with significantly altered expression (fold change > 1.5, p < 0.05). In comparison with Normal, the miRNAs significantly altered in both LM-Met and LM-Tumor, but not in RF-Tumor, was considered as predictive markers for lung metastasis of TNBC.

first: Xiaoming

last: Xie


title: Gene expression signature predicts induction treatment response and clinical outcome in adult Colombian patients with B-acute lymphoblastic leukemia

status: Public on Apr 06 2016

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary:
Background. B-Acute lymphoblastic leukemia (B-ALL) represents a hematologic malignancy with poor clinical outcome and low survival rates in adult patients. Only 61% of Colombian adult patients with ALL achieve complete remission and a median overall survival of less than 11.3 months and event-free survival of 7.34 months. Identification of prognostic factors is crucial for proper treatment strategies and optimal results of therapy. The goal of our study was to determine if gene expression signatures correlate with response to therapy and to evaluate the utility of these as prognostic tools for survival to better predict patient risk prior to therapy.

Methods and findings. This study included 43 adult patients newly diagnosed with B-cell precursor or common B-ALL. Through microarray gene expression profiles, we identified 442 genes differentially expressed between 27 leukemia patients who responded or not to induction chemotherapeutic treatment. Hierarchical analysis with the 99 most differentially expressed genes between the two groups revealed 3 sets of patients that differed in their clinical characteristics, giving these genes high prognostic clinical outcome impact. We validated the expression of 7 genes by RT-PCR in 43 patients, and in addition to finding a correlation with gene expression profiles, we established correlations with good and poor prognosis from the time of diagnosis.

Conclusions. Our study suggests that the response to induction treatment and clinical outcome of patients can be predicted from the onset of the disease and that gene expression profiles can be used to stratify patient risk adequately and accurately. The present study represents the first that shows that gene expression profiling could become a clinically relevant tool for stratification in the early course of disease of Colombian adults B-ALL.

overall_design: Stem cells from bone marrow samples from B-acute lymphoblastic leukemia (B-ALL) patients responding or not to the inductive therapy were isolated by sorting, and the gene expression was compared between the two groups. This submission includes samples from 27 B-ALL patients and 3 healthy individuals.

first: Nataly

last: Cruz-Rodriguez

first: Sandra

last: Quijano

first: Leonardo

middle: J

last: Enciso

first: Paula

middle: L

last: Pinzon

first: Olga

last: Lozano

first: Juan

last: Castillo

first: Li

last: Li

first: Jose

last: Bareño

first: Claudia

last: Cardozo

first: Julio

last: Solano

first: Maria

middle: V

last: Herrera

first: Yennifer

last: Cudris

first: Alba

last: Combita


title: RNA sequencing of Mycobacterium abscessus under infection-relevant conditions

status: Public on Mar 02 2016

city: Dublin

first: Brendan

middle: J.

last: Loftus

address: Conway Institute, University College Dublin

department: School of Medicine & Medical Science

country: Ireland

institute: University College Dublin

summary: RNA sequencing (RNA-seq) of Mycobacterium abscessus in four infection-relevant culture conditions: hypoxic stress, artificial sputum medium, kanamycin-treated medium, and erythromycin-treated medium.

overall_design: Triplicate cultures of M. abscessus were grown in (1) Artificial Sputum media, (2) hypoxic conditions, (3) the presence of kanamycin, and (4) the presence of erythromycin. Triplicate controls were prepared for sample (1) and samples (2-4).

first: Aleksandra

middle: A

last: Miranda-CasoLuengo

first: Adam

last: Dinan


title: Caspase-10 is a negative regulator of caspase-8-mediated cell death with gene inductive properties

status: Public on Apr 20 2016

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Formation of the Death-Inducing Signalling Complex (DISC) initiates the extrinsic apoptotic signalling cascade. Caspase-8 and its regulator cFLIP control death signalling by binding to the receptor via DISC-bound FADD. By elucidating the function of Caspase-10, a close homologue of caspase-8, we unexpectedly found that caspase-10 negatively regulates caspase-8-mediated cell death signalling in the DISC. We demonstrate that caspase-10 inhibits the activation of caspase-8 independent of cFLIP. Furthermore, we show that caspase-8 does not compete with other tandem DED proteins such as cFLIP or caspase-10 in binding via FADD to the receptor as current models suggest. By utilizing caspase-8 knockout cells, we demonstrate that caspase-8 has to be placed upstream of both cFLIP and caspase-10 in the DISC. We further show that DISC formation and/or stability depends on caspase-8 but is independent from its enzymatic activity. Surprisingly, we identified caspase-10 to rewire DISC-signalling to NF-kB activation and cell survival. Our data are consistent with a model in which caspase-10 and cFLIP co-ordinately regulate caspase-8-mediated cell death signalling.

overall_design: Caspase-10 and control shRNA expressing HeLa cells were analysed for gene expression in respect to CD95L stimulation by RNA extraction and hybridization on Affymetrix microarrays. Three indepedent replicates were used for each condition. Untreated cells served as a reference of basal gene expression.

first: Martin

last: Leverkus

first: Sebastian

last: Horn


title: Search for markers for biphenotypic hepatocytes

city: Sapporo

first: Naoki

last: Tanimizu

address: S1, W17, Chuou-ku

institute: Sapporo Medical University

summary: Comparson of Biphenotypic hepatocytes with Mature Hepatocytes

overall_design: Biphenotypic hepatocytes were isolated from DDC-injured liver as Sox9+EpCAM- cells. Gene expression profile of biphenotypic hepatocytes were compared with that of Mature hepatocytes.


title: Expression data from infant ALL with MLL-AF4 rearrangement

status: Public on Mar 22 2016

city: Santander

first: antonio

last: agraz

address: Albert einstein 22

country: Spain

institute: IBBTEC

summary:
MLL-AF4+ blasts from infant B-ALL, CB-derived CD34+CD38-CD19-CD33- HSC, CB-derived CD34+CD19+CD33- B-cell HPCs and CB-derived CD34+CD33+CD19- myeloid HPCs.
We used microarray to estudy gene expression profile comparing ALL vs HSC, HPC and myeloid HPSC.

overall_design: We used highly FACS-purified (purity>98%) MLL-AF4+ blasts from infant B-ALL, CB-derived CD34+CD38-CD19-CD33- HSC, CB-derived CD34+CD19+CD33- B-cell HPCs and CB-derived CD34+CD33+CD19- myeloid HPCs. For each independent sample technical duplicates were always performed. Total RNA was extracted using TRIol reagent, and quantified on a Nanodrop spectrophotometer and Bioanalyzer. High-quality RNA was reverse transcribed and the obtained cDNA was used as a template to synthesize biotinylanted cDNA, then was fragmented and hybridized as duplicates/triplicates to HG-U133 plus2.0 GeneChips (Affymetrix) according to manufacturer's guideline.

first: Michela

last: Bardini

first: Gianni

last: Cazzaniga


title: Comparing regeneration and fibrosis using Acomys and Mus

status: Public on Mar 17 2016

city: Lexington

first: Ashley

last: Seifert

state: Kentucky

address: 675 Rose St.

department: Biology

institute: University of Kentucky

summary: This project is designed to find differentially expressed genes between regeneration and fibrosis in Acomys (regenerator) and Mus (non-regenerator)

sample_organism:
Acomys cahirinus
Mus musculus

platform_organism:
Acomys cahirinus
Mus musculus

overall_design: A 4mm biopsy punch was made in the ears of 15 animals in each species (30 animals total).  Tissue was collected at 5 times points, (D0,D5,D10,D15,D20) post injury from 3 mice of each species.  2 species * 5 time points * 3 animals per time point * triplicate runs per sample * paired-end reads = 180 raw data files

first: Shishir

last: Biswas

first: Jeramiah

last: Smith


title: Gene expression study in WT and NOTCH1 mutated CLL cells.

status: Public on Mar 01 2016

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: D-RT

institute: CRO Aviano

summary: Stabilizing mutations of NOTCH1 have been identified in about 10% of chronic lymphocytic leukemia (CLL) cases at diagnosis, with a higher frequency in unmutated IGHV (IGHV-UM) CLL, chemorefractory CLL and CLL in advanced disease phases. Clinically, the presence of NOTCH1 mutations is an independent predictor of overall survival in CLL and associates with resistance to anti-Cd20 immunotherapy. The Gene Expression Profile was generated to identify the peculiar molecular signatures of NOTCH1 mutated CLL in the context of IGHV-UM CLL.

overall_design: Constitutive gene expression in CLL cells bearing or not NOTCH1 mutation (c.7541_7542delCT). Five samples were selected for each category (WT vs MUT).

first: Federico

last: Pozzo

first: Michele

last: Dal-Bo

first: Valter

last: Gattei


title: Q0990.bdl vs Q0990.Col

status: Public on Feb 26 2016

city: saskatoon

first: daoquan

last: xiang

state: SK

address: 110 Gymnasium Place

institute: NRC Saskatoon

summary: Transcriptional profiling of  Q0990 x bdl vs Q0990 x Col-0 development embryos after 3days and 6 days of fertilization

overall_design:
Two conditional experiments: Q0990 x bdl vs Q0990 x Col-0, and two satges was compared: 3days and 6 days after fertilization. . 4 biological replicates for each experiment.

The submitter states that the Agilent Feature Extraction files have been lost:

the original files was stored in a unrecoverable crashed computer,  because
the Base 2 in my institute is  not in service anymore, so I can not
re-download my file with the Agilent  Feature

first: Daoquan

last: Xiang

first: Dolf

last: Weijers


title: Gene expression profiling of NCI-H292 cells after treatment of TFAP2C-specific siRNA

status: Public on Mar 16 2016

city: Busan

first: BuHyun

last: Youn

address: Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Biological Sciences

country: South Korea

institute: Pusan National University

summary:
Non-small cell lung cancer (NSCLC) remains one of the leading causes of death worldwide, and thus, new molecular targets need to be identified to improve treatment efficacy. Enhanced TFAP2C expression was found in lung cancer patient tissues and lung cancer cell lines, and its overexpression promoted cell proliferation and cell cycle progression.
We conducted microarrays to find the possible downstream effectors regulated by TFAP2C which could play key roles in lung tumorigenesis.

overall_design: Two total RNA samples, extracted from NCI-H292 cells treated with or without TFAP2C siRNA, were analyzed by Affymetrix microarray.

first: JiHoon

last: Kang

first: Wanyeon

last: Kim

first: Sungmin

last: Lee

first: OhJin

last: Kwon

first: Jahyun

last: Chun

first: Beomseok

last: Son

first: EunGi

first: Jae-Myung

first: HyeSook


title: Frontal Cortex Transcriptome Analysis of Mice Exposed to Electronic Cigarettes During Early Life Stages

status: Public on Feb 01 2016

city: Tuxedo

first: Dana

last: Lauterstein

state: NY

address: 57 Old Forge Rd

department: Environmental Medicine

institute: New York University

summary:
Our study demonstrated that e-cigarettes, both with and without nicotine, induced sex-dependent gene expression change.
This RNA-seq study examined the expression profiles of brain frontal cortex samples from mice exposed to classic tobacco flavored blu™ e-cigarettes during gestation and lactation.

overall_design: Brains were extracted and sectioned from ~1-month-old male and female offspring the week following exposure, RNA was isolated and purified from frontal cotrex tissues, and gene expression profiles were analyzed by RNA Sequencing.

first: Catherine

last: Klein

first: Judith

last: Zelikoff


title: Substitutional Analysis on Influenza PeB Binding

status: Public on Feb 27 2016

city: Potsdam

first: Henry

last: Memczak

address: Karl Liebknecht Straße 24/25

institute: University of Potsdam

summary: In search for peptides with higher or special binding affinity and for further understanding of the mode of action, a full substitutional analysis of peptide PeB using microarrays was performed. Thus, 152 PeB mutant variants were generated. In each of them, the full-length sequence was preserved except for only one amino acid from the eight loop-forming amino acids of the original PeB peptide (ARDFYDYDVFYYAMD) which was substituted with the 19 remaining natural amino acids. To assess binding, influenza material was labeled with a protein reacting fluorophore.

overall_design: Microarray-based substitutional analysis of peptide PeB was performed using a PepStar® peptide library spotted on glass slides by JPT Peptide Technologies. The slides were used without additional treatment. For the labeling of proteins with a fluorescent dye, Dyomics DY-634 (λex = 635 nm, λem = 654 nm, Fluoro-spin 634 Kit (emp Biotech) was used, according to the manufacturer´s instructions. The following materials were labeled: NewYork H3N2, Aichi H3N2, Victoria H3N2 and California H1N1. Labeled analytes were incubated several hours or overnight at indicated concentrations using Femtotip buffer (FTP)30 (20 mM Tris, 30% glycerol, 3% polyvinylpyrrolidon 90, 0.1% Tween 20, pH 8.4) for dilution. The slides were washed twice in FTP and twice in ultrapure water and subsequently dried under a stream of nitrogen. Experiments were performed in triplicates using glycans (2,3'-/2,6'-sialyllactose) and proteins (Anti-H1/Anti-H3 antibodies, fetuin) as positive and negative controls.

first: Walter

middle: F

last: Stoecklein


title: Expression data of human vascular smooth muscle cells (hVSMC) in response to n-LDL and ox-LDL.

status: Public on Feb 09 2016

city: México City

first: Juan

middle: Pablo

last: Reyes-Grajeda

state: DF

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México,

department: Proteomics and transciptomics

country: Mexico

institute: National Instiutute of Genomic Medicine

summary:
Early transcriptomic response to n-LDL and ox-LDL in human vascular smooth muscle cells (hVSMC).
We used microarrays with the aim of assessing early molecular changes that induce a response in the VSMC using native and oxidized low-density lipoprotein (n-LDL and ox-LDL).

overall_design: For each LDL internalization experiment, three biological replicates were used and the samples pooled with the aim of obtain three technical replicates (three arrays for condition).

middle: P


title: Signaling networks of developing hair follicles

city: New York

first: Michael

last: Rendl

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

summary: The hair follicle (HF) is a complex miniorgan that serves as an ideal model system to study stem cell (SC) interactions with the niche during growth and regeneration. Dermal papilla (DP) cells are required for activating SCs during the adult hair cycle, but the signal exchange between niche and SC precursors/transit amplifying progenitor cells (TACs) that regulates HF morphogenetic growth is largely unknown. Here we use six transgenic reporters to isolate 14 major skin and HF cell populations. With next-generation RNA sequencing we characterize their transcriptomes and define unique molecular signatures. SC precursors, TACs and the DP niche express a plethora of known and novel ligands and receptors. Signaling interaction network analysis reveals a birds-eye view of pathways implicated in epithelial-mesenchymal interactions. Using a systematic tissue-wide approach this work provides a comprehensive platform, linked to an interactive online database, to identify and further explore the SC/TAC/niche crosstalk regulating HF growth.

overall_design: FACS was used to isolate specific cell types from P5 mouse back skin

first: Amélie

last: Rezza

first: Zichen

last: Wang


title: Differential induction of apoptosis, IFN signaling and phagocytosis in macrophages infected with a panel of attenuated and non-attenuated poxviruses

status: Public on Mar 14 2016

city: Madrid

first: Susana

last: Guerra

address: Calle del Arzobispo Morcillo, 4

department: Department of Preventive Medicine

institute: Universidad Autónoma de Madrid

summary: Similarities as well as differences were found in macrophages infected with different virus strains, particularly at the expression level of immunomodulatory genes, but infection with MVA was particularly efficient in triggering changes in gene expression associated with increased activation of innate immunity.

overall_design: Two-condition experiment, uninfected vs. infected cells. Biological replicates: 6 control replicates, 3 infected replicates.

first: Sandra

last: Royo

first: Bruno

last: Sainz Jr.

first: Enrique

last: Hernández-Jiménez

first: Hugh

last: Reyburn

first: Eduardo

last: López-Collazo


title: Expression data between WT and G3/4 Terc KO mouse ESCs during differentiation

status: Public on Jan 29 2016

city: Tian Jin

first: Yu

last: Yin

address: 94 Wei Jin Road

institute: Nankai University

summary:
Mammalian telomeres are formed by tandem repeats of the TTAGGG sequence, and shorten with each round of cell division in the absence of telomerase. Telomere shortening and dysfunction has been implicated in the pathology of several age-related diseases and premature ageing syndromes. Telomerase is important for telomere length maintenance. Telomerase RNA component, also known as TERC, is a component of telomerase. Terc knockout leads to telomerase deficiency and telomere shortening. Heterozygous telomerase-deficient (Terc+/-) mice were housed and bred for homozygous generation. ESC lines were generated with high efficiency from wild-type (WT, Terc+/+), heterozygous (Het, Terc+/-) and early- to late-generation (G1, G3 and G4) Terc-/- mouse blastocysts. Telomeres were shorter in Terc+/- ES cells than in WT ES cells, and further shortened from G1 to G4 Terc-/- ES cells. We took advantage of ES cell lines with various telomere lengths to investigate roles of telomere length on differentiation capacity of ES cells. We found that telomere length, but not telomerase activity, is required for differentiation of ES cells into epidermis.
We performed microarray analysis to investigate differential gene expression profile at genome-wide levels between WT and G3/G4 Terc-/- (KO) mouse ES cells and during differentiation in vitro of WT and G4 Terc-/- mouse ES cells.

overall_design: We sought to find out the differentiated expressed genes between WT and G3/4 Terc KO ESCs during differentiation. WT or G3/4 Terc KO cells were selected at different stages (D0, D8 and D15) during ESCs differentiation for RNA extraction and hybridization on Affymetrix microarrays.

last: Liu

first: Fang

first: Lin


title: Transcriptome-wide regulation of pre-mRNA splicing and expression by the RNA-binding protein Quaking during monocyte to macrophage differentiation

status: Public on Jan 04 2016

city: Santa Cruz

first: Lily

last: Shiue

state: CA

address: 1156 High Street

department: MCD Biology

institute: UCSC

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

overall_design: Refer to individual Series


title: Transcriptome-wide regulation of pre-mRNA splicing and expression by the RNA-binding protein Quaking during monocyte to macrophage differentiation [Microarray]

summary:
Expression levels of the RNA-binding protein Quaking (QKI) are low in monocytes of early, human atherosclerotic lesions, but abundant in macrophages of advanced plaques. Specific depletion of QKI protein impaired monocyte adhesion, migration, differentiation into macrophages, and foam cell formation in vitro and in vivo. RNA-seq and microarray analysis of human monocyte and macrophage transcriptomes, including those of a unique QKI haploinsufficient patient, revealed striking changes in QKI-dependent mRNA levels and splicing of RNA transcripts.
Microarray analysis of gene expression and splicing in THP-1 cells transfected with shRNAs, with or without PMA treatment to induce differentiation.

overall_design: 12 total samples were analyzed: THP-1 monocytic cell line transfected with QKI or control shRNAs; samples taken at day 0 or day 3 of PMA-induced differentiation into macrophages.

first: Ruben

middle: G

last: de Bruin

first: Manuel

last: Ares Jr

first: Anton

last: van Zonneveld

first: Eric

last: van der Veer


title: Expression by CD133+ cells isolated from the adult human exocrine pancreas

status: Public on Jan 15 2016

city: St. Petersburg

first: Michael

last: Shamblott

state: FL

address: 601 4th St South, CRI 3005

department: Pediatrics

institute: University of South Florida Health

summary: Expression from CD133+ cells isolated from adult human exocrine tissue was compared to a CD133-depleted cell population

overall_design: Islet-depleted exocrine tissue from three independent adult human cadaveric pancreata were cultured for four days in Miami media 1A. Following trypsinization, cells were isolated using anti-CD133 immunomagnetic beads to >95% CD133+.  CD133-negative cells were further depleted of CD133+ cells to <1% CD133+.

first: Danielle

last: Gomez


title: Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum

status: Public on Jan 26 2016

city: Pretoria

first: Stanford

last: Kwenda

state: Gauteng

address: Lunnon Road, Hilcrest

department: Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within the adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress response. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 63 sRNAs were differentially expressed with 57 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST (e-value < 0.001) showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. A large number of these sRNAs is starvation-induced, suggesting their role in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens.

overall_design: sRNA profiles from P. atrosepticum SCRI1043 cells existing under growth-promoting and starvation conditions were generated using Strand-specific RNA sequencing

first: Vladimir

last: Gorshkov

first: Enrico

last: Rubagotti

first: Paul

last: Birch

first: Lucy

last: Moleleki


title: Leukemia-associated activating mutation of Flt3 expands dendritic cells and alters T cell responses

status: Public on Jan 28 2016

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: One of the most common genetic alterations in acute myeloid leukemia is the internal tandem duplication (ITD) in the FLT3 receptor for cytokine FLT3 ligand (FLT3L). The constitutively active FLT3-ITD promotes the expansion of transformed progenitors, but also has pleiotropic effects on normal hematopoiesis. We analyzed the effect of FLT3-ITD on dendritic cells (DCs), which express FLT3 and can be expanded by FLT3L administration. We report that young pre-leukemic mice with the Flt3ITD knock-in allele manifest an expansion of all DCs including classical (cDCs) and plasmacytoid (pDCs). The expansion originated in DC progenitors, occurred in a cell-intrinsic manner and was further enhanced in Flt3ITD/ITD mice. The mutation caused the downregulation of Flt3 on the surface of DCs and reduced their responsiveness to Flt3L. Flt3ITD mice showed enhanced capacity to support T cell proliferation, including a cell-extrinsic expansion of regulatory T cells (Tregs). Accordingly, these mice restricted alloreactive T cell responses during graft-versus-host reaction, but failed to control autoimmunity in the absence of Tregs. Thus, the FLT3-ITD mutation directly affects DC development, thereby indirectly modulating T cell homeostasis and supporting Treg expansion. This effect of FLT3-ITD may subvert immunosurveillance and promote leukemogenesis in a cell-extrinsic manner.

overall_design: Sorted splenic dendritic cell subsets from either Flt3+/+ or Flt3ITD/+ mice were sequenced for mRNA profiling. For each subset per genotype contains 2-3 replicates, all from independent experiments.

first: Boris

last: Reizis


title: Transcriptome-wide regulation of pre-mRNA splicing and expression by the RNA-binding protein Quaking during monocyte to macrophage differentiation [RNA-Seq]

summary: Expression levels of the RNA-binding protein Quaking (QKI) are low in monocytes of early, human atherosclerotic lesions, but abundant in macrophages of advanced plaques. Specific depletion of QKI protein impaired monocyte adhesion, migration, differentiation into macrophages, and foam cell formation in vitro and in vivo. RNA-seq and microarray analysis of human monocyte and macrophage transcriptomes, including those of a unique QKI haploinsufficient patient, revealed striking changes in QKI-dependent mRNA levels and splicing of RNA transcripts.

overall_design: RNA-seq analysis of primary monocytes and macrophages from a  QKI haploinsufficient patient and their (control) sibling.


title: Genome-wide maps of chromatin state in drug sensitive and resistance Lewis lung carcinoma isograft mouse model

status: Public on Jan 20 2016

city: Shanghai

first: Jiejun

last: Shi

address: No.1239, Siping Road

institute: Tongji University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We investigated histone modifications in regulation of gene expression using chromatin immunoprecipitation (ChIP) sequencing in samples from drug-sensitive vs. resistant murine lung cancer isografts. Histone modification fluctuation was analyzed in both genome wide scale and individual genes. The data showed that both chromatin status of gene promoter and transcription profile were altered by drug-resistance. Promoter activity of most low CG promoter (LCP) and high CG promoter (HCP) related genes were increased in drug resistant samples. These LCP genes were enriched in hematopoietic cell differentiation and angiogenesis-related pathways. In contrast, the HCP genes were prone to tumorigenesis, like the p53 pathway. Further analysis revealed that the key regulators during hematopoietic cell development in the thymus branch and bone marrow branch were regulated in opposite ways, which may contribute to blood cell differentiation.

overall_design: LLC-R and LLC-NR cells were subcutaneously inoculated into the right flanks of C57BL/6J mice to allow tumor isografts to grow to an approximate size of 500 mm3 and then tumor isograft tissues were dissected and used for further study. Tissue sections of each isograft were prepared and formaldehyde was then inactivated. Tissue homogenate were then harvested for extraction of nuclei and digested with micrococcal nuclease. Each of different histone modification antibodies (i.e. H3K4me3,H3K27me3,H3K36me3,H3K9ac) were used to immunoprecipitate the above RNase-digested chromatin.The resulted DNA fragments were sequenced using an Illumina HiSeq instrument.

first: Cizhong

last: Jiang

first: Jianmin

last: Fang


title: Deficits in histone acetylation and methylation are restricted to specific loci in Huntington's disease models

status: Public on Dec 31 2015

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

institute: Instituto de Neurociencias (UMH-CSIC)

summary: The present study extends the analysis initiated in a previous report in the popular HD transgenic mouse strain N171-82Q (82Q) (Valor et al., 2013), to other diverse mHtt-expressing animal and cellular models. We show that bulk histone hypoacetylation is not a general rule. Moreover, examination of other histone post-traslational modifications led to a detailed study of the trimethylation of lysine 4 of histone H3 (H3K4me3), which is tightly associated with active genes (Lopez-Atalaya et al., 2013), by combining both single-gene and genome-wide approaches. Comparison of the 82Q and another animal model, the R6/1 strain, revealed that changes in the levels of bulk H3K4me3 may be correlated with the degree of methylation impairment for specific genes. Yet, these changes are restricted to few genomic positions. In any case, and reminiscent of the situation with histone acetylation (Valor et al., 2013; McFarland et al., 2012), deficits in histone H3 methylation do not follow a straight relationship with transcriptional dysregulation.

overall_design: Genome-wide profiling by high throughput sequencing of H3K4me3 in the adult hippocampus of N171-82Q (HD) and their wild-type littermates mice (WT). Chromatin immunoprecipitation (ChIP) was carried out using pooled whole hippocampal tissue from 3 mice. DNA libraries (HD, WT, input) were constructed and single-end sequenced (1x50bp) in HiSeq 2500 platform (Illumina).

first: Jose

last: Lopez-Atalaya

first: Luis

last: Valor


title: Chip-chip of Sir3 and of Sir2, and ChAP-chip of AAR from budding yeast cells

city: MIAOLI COUNTY

first: GUNN-GUANG

last: LIOU

state: TAIWAN

address: 35 KEYAN ROAD, JHUNAN TOWN

department: INSTITUTE OF MOLECULAR AND GENOMIC MEDICINE

country: Taiwan

institute: NATIONAL HEALTH RESEARCH INSTITUTES

type: Genome binding/occupancy profiling by genome tiling array

summary:
O-acetyl-ADP-ribose (AAR) is a small metabolic molecule that is generated during NAD-dependent deacetylation by Sir2. Sir2 regulates gene expression, DNA repair, and genome stability.
chromatin affinity-precipitation (ChAP) method was used to detect the chromatin fragments at which small molecules interact with binding partners.
Chromatin immunoprecipitation of Sir3  and of Sir2, respectively, applied with tilling array chip (ChIP on chip of Sir3 and of Sir2, respectively) and Chromatin affinity-precipitation of AAR applied with tilling array chip (ChAP on chip of AAR ) analysis demonstrated that an extended spreading of Sir3 and of AAR, but not Sir2 in Saccharomyces cerevisiae Ysa1 deleted cells compared with those in wild type cells

overall_design: Comparison the distributions of Sir3, of Sir2 and of AAR on silent heterochromatin of Ysa1 deletion cells vs those of wild type cells

first: Gunn-Guang

last: Liou

first: Shu-Yun

last: Tung


title: The impact of oxygen availability on yeast survival in stationary phase.

status: Public on Jan 01 2016

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: Saccharomyces cerevisiae is currently widely used as a model to study chronological aging of metazoan cells. Chronological aging is typically studied in aerobic stationary phase (SP) cultures, i.e. the final stage of batch cultures in which growth is arrested due to exogenous carbon source exhaustion. Survival of yeast cells in SP defines their chronological lifespan (CLS). S. cerevisiae SP cultures have strongly contributed to the understanding of cellular mechanisms involved in aging and indicated a key role for oxygen. Oxygen is the natural starting point for reactive oxygen species (ROS) that may both have malignant and beneficial effects on aging. In addition, oxygen allows yeast to grow on ethanol and organic acids formed during the initial respiro-fermentative growth phase on glucose. This post-diauxic phase is hallmarked by reduced growth rates, increased expression of genes involved in SP survival, and increased stress resistance.    To date, the role of oxygen and respiration in aging has mostly been studied using respiratory deficient mutants, and respiration repressing agents. However, genetic or chemical interventions may result in unwanted side effects that influence survival in SP. We therefore followed a different approach to evaluate the impact of oxygen availability on yeast robustness in SP, i.e. its CLS and stress resistance, by using the capability of S. cerevisiae to grow under anaerobic conditions.   A thorough physiological comparison of strictly anaerobic and aerobic SP cultures revealed that the presence of oxygen during growth and aging of S. cerevisiae strongly affects its energetic status, longevity and stress tolerance in a positive way. Combining the physiological data with genome-wide expression analysis revealed that the oxygen-dependent diauxic growth phase enabled the full induction of robustness in S. cerevisiae, and points to appropriate pre-conditioning of cells as a crucial factor to survive starvation. These findings highlight the importance of exogenous energy availability in the conditions leading to growth arrest, and bring new insight on the role of oxygen in the aging of eukaryotes.

overall_design: The goal of the present study is to evaluate the impact of oxygen availability on yeast longevity. More specifically, the questions addressed are whether the presence of a ‘conditioning’ post-diauxic phase and the ability to utilize efficiently reserves,  characteristics of aerobicity, affects yeast survival during stationary phase. To this end, S. cerevisiae was cultivated in well controlled bioreactors under the presence or absence of oxygen. S. cerevisiae’s response to oxygen availability was monitored by an in-depth physiological analysis combined with genome wide expression analysis.

first: Markus

last: Bisschops

first: Tim

last: Vos

first: Ruben

last: Martinez

first: Pilar

last: de le Torre

first: Pascale

last: Daran-Lapujade

first: Jack

middle: T

last: Pronk


title: Gene Expression Human Preimplantation Embryos

status: Public on Dec 25 2015

city: Iowa City

first: Bradley

last: Van Voorhis

state: IA

address: 200 Hawkins Drive

department: Div. of Reproductive Endocrinology

institute: Univ. of Iowa

summary:
Differential gene expression in preimplantation embryos has been documented, but few focused studies have been done to compare differential expression in human embryos after embryonic genome activation and specifically how they relate to blastocyst development. We hypothesized that blastocyst stage embryos would differentially express genes in pathways important in cell division, mobilization, and processes important in embryo implantation including endometrial apposition, adhesion, and invasion. We analyzed gene expression in 6 preimplantation human embryos.
Embryos studied were previously cryopreserved, supernumerary human embryos donated by couples who completed their family building through in vitro fertilization and had given specific consent for use in research. Embryos cryopreserved at the pronuclear stage were thawed and cultured to cleavage (Day 3) or blastocyst (Day 5) stage. Differential gene expression was first obtained through Affymetrix gene expression microarrays and then validated both in silico using the Gene Expression Omnibus and in vitro with RT-qPCR. Compared to cleavage stage embryos, blastocyst stage embryos differentially expressed 51 genes (p < 0.001), with overrepresentation in amoebiasis pathways and pathways in cancer.

overall_design: Human embryos studied were previously cryopreserved, supernumerary human embryos donated by couples who completed their family building through in vitro fertilization and had given specific consent for use in research. Human embryos cryopreserved at the pronuclear stage were thawed and cultured to cleavage (Day 3) or blastocyst (Day 5) stage. Differential gene expression was first obtained through Affymetrix gene expression microarrays (3 individual cleavage stage embryos, and 3 individual blastocyst stage embryos). These findings were then validated both in silico using the Gene Expression Omnibus and in vitro with RT-qPCR on a new set of human embryos.

first: Erika

last: Munch


title: High-resolution genomic profiling of male breast cancer reveals differences hidden behind the similarities with female breast cancer.

city: Lund

first: Ida

last: Johansson

address: Department of Oncology Clinical Sciences Lund University BMC C13

department: Oncology

country: Sweden

institute: Lund University

type: Genome variation profiling by genome tiling array

summary:
Male breast cancer (MBC) is extremely rare and poorly characterized on the molecular level. Using high-resolution genomic data, we aimed to characterize MBC by genomic imbalances and to compare it with female breast cancer (FBC), and further to investigate whether the genomic profiles hold any prognostic infor- mation. Fifty-six fresh frozen MBC tumors were analyzed using high-resolution tiling BAC arrays. Significant regions in common between cases were assessed using Genomic Identification of Significant Targets in Cancer (GISTIC) analysis. A publicly available genomic data set of 359 FBC tumors was used for reference purposes. The data revealed a broad pattern of aberrations, confirming that MBC is a heterogeneous tumor type. Genomic gains were more common in MBC than in FBC and often involved whole chromosome arms, while losses of genomic material were less frequent. The most common aberrations were similar between the genders, but high-level amplifications were more common in FBC. We identified two genomic subgroups among MBCs; male-complex and male-simple. The male-complex subgroup displayed striking similarities with the previously reported luminal-complex FBC sub- group, while the male-simple subgroup seems to represent a new subgroup of breast cancer occurring only in men. There are many similarities between FBC and MBC with respect to genomic imbalances, but there are also distinct differ- ences as revealed by high-resolution genomic profiling. MBC can be divided into two comprehensive genomic subgroups, which may be of prognostic value. The male- simple subgroup appears notably different from any geno- mic subgroup so far defined in FBC.
Male breast cancer (MBC) is extremely rare and poorly characterized on the molecular level. Using high-resolution genomic data, we aimed to characterize MBC by genomic imbalances and to compare it with female breast cancer (FBC), and further to investigate whether the genomic profiles hold any prognostic infor- mation. Fifty-six fresh frozen MBC tumors were analyzed using high-resolution tiling BAC arrays. Significant regions in common between cases were assessed using Genomic Identification of Significant Targets in Cancer (GISTIC) analysis. A publicly available genomic data set of 359 FBC tumors was used for reference purposes. The data revealed a broad pattern of aberrations, confirming that MBC is a heterogeneous tumor type. Genomic gains were more common in MBC than in FBC and often involved whole chromosome arms, while losses of genomic material were less frequent. The most common aberrations were similar between the genders, but high-level amplifications were more common in FBC. We identified two genomic subgroups among MBCs; male-complex and male-simple. The male-complex subgroup displayed striking similarities with the previously reported luminal-complex FBC sub- group, while the male-simple subgroup seems to represent a new subgroup of breast cancer occurring only in men. There are many similarities between FBC and MBC with respect to genomic imbalances, but there are also distinct differ- ences as revealed by high-resolution genomic profiling. MBC can be divided into two comprehensive genomic subgroups, which may be of prognostic value. The male- simple subgroup appears notably different from any geno- mic subgroup so far defined in FBC.

overall_design: Tumor cellularity was determined on H&E-stained sections and only tumors with high tumor cell content were included. DNA was extracted from fresh frozen tissue using a modification of a back-extraction protocol from the organic phase of the Qiagen Lipid mini RNA kit (Qiagen, Valencia, CA) as follows: 1 M Tris-buffer containing 4 M Guanidine Thiocyanate and 50 mM Sodium Citrate, followed by glycogen precipitation. DNA quality was assessed with a BioAnalyzer. Sufficient good quality DNA from 56 fresh frozen MBC tumors was available for high-resolution tiling BAC aCGH. BAC arrays, containing about 32,000 BAC clones mapped to the UCSC Human Genome build 17, were produced at the SCIBLU Genomics Resource Center, Lund University, Sweden. The aCGH data were normalized using PopLowess. Circular binary segmentation (CBS) was used for breakpoint analysis with an a of 0.01 and segments containing at least four probes were used in subsequent analyses.

first: Cecila

last: Nilsson

first: Pontus

last: Berglund

first: Carina

last: Strand

first: Göran

last: Jönsson

first: Johan

last: Staaf

last: Ringnér

first: Heli

last: Nevanlinna

first: Rosa

middle: B

last: Barkardottir

first: Åke

last: Borg

first: Håkan

last: Olsson

first: Lena

last: Luts

first: Marie-Louise

last: Fjällskog

first: Ingrid

last: Hedenfalk


title: Identification of copy number variations by array comparative genomic hybridization in multi-ethnic multiple myeloma patients

city: Kuala Lumpur

first: Ivyna

middle: PN

last: Bong

state: Kuala Lumpur

address: Jalan Pahang

department: Cancer Research Centre

country: Malaysia

institute: Institute for Medical Research

summary: The aim of this study is to identify copy number variations in multiple myeloma patients from the 3 major ethnic groups (Malays, Chinese and Indians) in Malaysia. Identification of common chromosomal aberrations and their degree of penetrance is possible by comparing the microarray data across all the samples under studied.

overall_design: 63 multiple myeloma samples were analyzed. Each sample was compared against normal control (match with patient's race and gender), which was pooled from ten healthy individuals.

first: I

first: C

last: Ng

first: K

middle: M

last: Chang

first: Z

last: Zakaria


title: Relative spatial homogeneity revealed by transcriptional profiling of multi-region medulloblastoma samples

city: Toronto

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

institute: The Hospital for Sick Children

summary: Affymetrix Human Gene 1.1 ST Array profiling of 52 primary, multi-region medulloblastoma samples.

overall_design: Total RNA was extracted from primary medulloblastoma samples and hybridized to Affymetrix Human Gene 1.1 ST Arrays (24-Array Plates) according to the manufacturer's instructions.

first: Florence

last: Cavalli

first: Marco

last: Marra

first: Michael

middle: D

last: Taylor


title: Small molecule-induced bioenergetic reprogramming directs prostate cancer inhibition via UPR signaling

status: Public on Dec 16 2015

city: La Jolla

first: Roy

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: We previously identified SMIP004 (N-(4-butyl-2-methyl-phenyl) acetamide), as a novel inducer of cancer-cell selective apoptosis of human prostate cancer cells. SMIP004 decreased the levels of positive cell cycle regulators, such as cyclin A, CDK4 and SKP2 while upregulating cyclin-dependent kinase inhibitors p27 and p21, resulting in G1 arrest and inhibition of colony formation in soft agar. However, the mechanism of SMIP004-induced cancer cell selective apoptosis remained unknown. We used profiling to unravel a SMIP004-induced pro-apoptotic pathway, which initiates with bioenergetic reprogramming at the level of mitochondria. SMIP004 causes downregulation of aerobic glycolysis, rapid upregulation of components of the mitochondrial electron transport chain, and oxidative stress. The latter, in turn, elicits cell cycle arrest by rapidly targeting cyclin D1 for proteasomal degradation, drives transcriptional downregulation of the androgen receptor, and activates pro-apoptotic signaling through the unfolded protein response and MAPK activation. Finally SMIP004 was found to potently inhibit the growth of prostate and breast cancer xenografts in mice.

overall_design: There are two biological replicates SMIP004Rep1 and SMIP004Rep2 and two technical replicates for each biological replicates (SMIP004 Rep1_1 and SMIP004 Rep1_2).  Total RNA from cells treated with 40 uM SMIP004 for 24 h, vehicle or positive controls (Roscovitine, 20uM, Campthotecin 500 nMM, Bortezomib 50 nM) was obtained using the RNeasy Mini Kit. The drug treated and control samples were compared.

first: Elizabeth

last: Rico-Bautista

first: Dieter

last: Wolf


title: Disrupting SUMOylation potentiates transactivation function and ameliorates polyglutamine AR-mediated disease

status: Public on Dec 21 2015

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: Our findings demonstrate beneficial effects of enhancing transactivation function of the ligand-activated polyQ AR and indicate that the SUMOylation pathway may provide new targets for therapeutic intervention.

overall_design: We mutated conserved lysines in the polyQ AR that are targeted by SUMO, a modification that inhibits AR transactivation function.

first: Andrew

last: Lieberman


title: Expression profiling of primary glioma samples

status: Public on Oct 30 2015

city: Beijing

first: Xiaolong

last: Fan

state: Beijing

address: No. 19, XinJieKouWai St., HaiDian District

department: School of Life Sciences

institute: Beijing Normal University

summary:
Background: Signaling by receptor tyrosine kinases (RTK) is frequently dysregulated in gliomas. Inter-individual variability in the causes for dysregulated RTK signaling may have hampered the efficacy of targeted therapies. Using gene expression modules around key regulators in the RAS-RAF-MEK-MAPK cascade and in the phosphatidylinositol 3-kinase-AKT pathways, we developed a “RMPA” clustering scheme to distinguish gliomas with varying extents of RTK signaling.
Results: We identified gene modules consistently co-expressed with NF1 (NF1-M), Sprouty (SPRY-M) and PTEN (PTEN-M) in gliomas. Their signatures enabled robust clustering of adult diffuse gliomas of WHO grades II-IV into RMPAhigh and RMPAlow phenotypes in a morphology-independent manner.  In five independent data sets from three continents containing more than 1500 adult diffuse gliomas, RMPAhigh gliomas were associated with poor prognosis while RMPAlow gliomas were not. The RMPAhigh and RMPAlow glioma subtypes showed distinct levels of the activities of RAS-RAF-MEK-MAPK cascade and PI3K-AKT pathway and harbored unique sets of genomic alterations in the RTK signaling-related genes.  The RMPAhigh gliomas contained large numbers of immature vessel cells and tumor associated macrophages and both cell types expressed high levels of pro-angiogenic RTKs including MET, VEGFR1, KDR, EPHB4 and NRP1.
Conclusion: Inter-glioma variability in RTK signaling activities can be defined using the RMPA clustering scheme. The combined signatures of NF1-M, SPRY-M and PTEN-M reflect RTK signaling activity both in the glioma cells and in the glioma microenvironment. Our data show that RTK signaling in the glioma microenvironment may play a pivotal role in glioma progression.

overall_design: Transcriptome data from 22 fresh gliomas (2 astrocytoma II, 1 oligodendrocytoma II, 7 oligoastrocytoma II, 4 anaplastic oligoastrocytoma III and 8 GBM) were obtained using Affymetrix Human Gene 1.0 ST Array. Unsupervised hierarchical clustering of the expression data for the SPRY-M, NF1-M and PTEN-M was performed on these transcriptome data to identify samples with RMPAhigh or RMPAlow signature.

first: Tao

last: Jiang


title: Expression data from Pseudomonas aeruginosa wild type and ∆anr grown as biofilms on ∆F508 cystic fibrosis bronchial epithelial cells (CFBEs)

status: Public on Nov 15 2015

city: Hanover

first: Deborah

last: Hogan

state: NH

address: Vail Building Rm 208

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

summary: The transcription factor Anr regulates the response to low oxygen in P. aeruginosa and is inhibited by oxygen. We used microarrys to compare gene expression in P. aeruginosa PAO1 wild-type with an isogenic anr mutant in order to determine which transcripts are affected by Anr. We grew P. aeruginosa cells as biofilms on CFBE cells in order to model cystic fibrosis airways infections.

overall_design: Pseudomonas aeruginosa biofilms grown on CFBEs. Wild-type PAO1 and a ∆anr mutant. Three biological replicates of each strain were analyzed.

first: John

middle: H

last: Hammond


title: DNA methylation response of hematopoietic stem cells to recombinant lentiviral vector infection

status: Public on Sep 11 2015

city: Evry

first: Daniel

last: Stockholm

address: 1bis rue de l'Internationale

department: R&D

country: France

institute: Genethon - EPHE

type: Methylation profiling by genome tiling array

summary:
Human cord blood CD34+ cells respond to the infection with LV by modifying the methylation profile of a large number of CpG sites in their genome.
Different vector preparations vary in their capacity to trigger a response; some induce sporadic modifications only while others trigger a strong response that systematically includes de novo methylation of the same 4126 CpG-s corresponding to 1059 genes

overall_design: Illumina Infinium 450K arrays were performed according to the manufacturer's directions on bisulfite converted gDNA extracted from CD34+ cells from cord blood. CpG methylation profiling on Illumina Infinium 450K arrays was performed.

first: Tamas

last: Aranyi

first: Roseline

last: Yao

first: Catherine

last: Poinsignon

first: Thibaut

last: Wiart

first: Guillaume

last: Corre

first: Jorg

last: Tost

first: Nizar

last: Touleimat

first: Anne

last: Galy

first: Andras

last: Paldi


title: expression profiles in the chicken PSM differentiation at Stage 12HH chicken embryo

status: Public on Dec 09 2015

city: BOSTON

first: Masayuki

last: Oginuma

state: MASSACHUSETTS

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: To examine global gene expression profile of chicken early paraxial mesoderm differentiation, we microdissected stage 12HH chicken PSM regions into 20 pieces (10 pieces both left-right PSM), including the tail bud, the PSM and somites. We create microarray series using these fragments.

overall_design:
Duplicated 10 fragmented tissues from stage 12 chicken PSM regions.
contributor: IGBMC microarray facility

first: Philippe

last: Moncuquet

first: Olivier

last: Pourquie


title: Sternal cartilage microarray (WT vs. TIMPless)

status: Public on Aug 31 2015

first: Rama

last: Khokha

state: ON

address: 101 College St.

country: Canada

institute: Ontario Cancer Institute

summary: Timps are natural metalloproteinase inhibitors that direct the cell microenvironment in health and disease, yet the essential requirement of this gene family in mammals is unknown. We generated quadruple Timp deficient mice lacking Timp1, Timp2, Timp3 and Timp4 (TIMPless) and found that Timp function is essential for postnatal lifespan, lung form and function and skeletogenesis. TIMPless mice survive embryogenesis but develop pervasive skeletal aberrations characterized by axial cartilage overgrowth and growth plate closure in long bones. We performed microarray analysis to identify signaling pathways affected by the loss of the entire Timp family in sternal cartilage.

overall_design: Cartilage, excluding the xiphoid process, was macrodissected from the sternums of 4-week old WT and TIMPless mice (n=6/genotype).

first: Alison

last: Aiken

first: Yu-Jia

last: Shiah


title: Relative spatial heterogeneity revealed by transcriptional profiling of multi-region high-grade glioma samples

first: Marc

last: Remke

summary: Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array profiling of 20 primary, multi-region high-grade glioma samples.

overall_design: Total RNA was extracted from primary high-grade glioma samples and hybridized to GeneChip® Human Genome U133 Plus 2.0 Array according to the manufacturer's instructions.

first: Florence

last: Cavalli

first: Marco

last: Marra

first: Michael

last: Taylor


title: Systems analyses reveal shared and diverse attributes of Oct4 regulation in pluripotent cells

status: Public on Aug 07 2015

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary: We combine a genome-scale RNAi screen in mouse epiblast stem cells (EpiSCs) with genetic interaction, protein localization and “protein-level dependency” studies – a systematic technique that uncovers post-transcriptional regulation – to delineate the network of factors that control the expression of Oct4, a key regulator of pluripotency. Our data signify that there are similarities, but also fundamental differences in Oct4 regulation in EpiSCs vs. embryonic stem cells (ESCs). Through multiparametric data analyses we predict that Tox4 is associating with the Paf1C complex, which maintains cell identity in both cell types and validate that this protein-protein interaction exists in ESCs and EpiSCs. We also identify numerous knockdowns that increase Oct4 expression in EpiSCs, indicating that, in stark contrast to ESCs, Oct4 is under active repressive control in EpiSCs. These studies provide a framework for better understanding pluripotency and for dissecting the molecular events that govern the transition from the pre-implantation to the post-implantation state.

overall_design: RNA-seq of Tox4 knockdown in mouse EpiSCs

first: Li

last: Ding

first: Frank

last: Buchholz


title: Physical and functional CSL-p53 interactions underlie control of cancer stromal cell evolution

status: Public on Aug 24 2015

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

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

overall_design: Refer to individual Series


title: Wheat: Control vs. Pathogen-infected

status: Public on Aug 06 2015

first: Xiuliang

last: Zhu

address: Zhongguancun street 12#

institute: The Chinese Academy of Agricultural Sciences

summary: Differentially expressed kinase genes in Rhizoctonia cerealis resistant wheat lines CI12633/Shanhongmai compared with the susceptible wheat line Wenmai 6 via Agilent Wheat Gene Expression Microarray assay. Goal was to identify the kinase genes whose expression was higher in CI12633/Shanhongmai compared with the susceptible wheat line Wenmai 6

overall_design: CI12633/Shanhongmai vs. Wenmai 6

first: Zengyan

last: Zhang


title: Physical and functional CSL-p53 interactions underlie control of cancer stromal cell evolution [ChIP-seq]

summary: Senescence of stromal fibroblasts has been linked to establishment of cancer associated fibroblasts (CAF) and aging-associated increase of tumors. However, in clinically occurring carcinomas, density and proliferation of CAFs are frequently increased rather than decreased. We previously showed that genetic deletion or down-modulation of the canonical Notch effector CSL/RBP-Jκ in skin dermal fibroblasts is sufficient for CAF activation with consequent development of multifocal keratinocyte tumors. We now show that CSL deletion or knockdown induces senescence of primary fibroblasts derived from dermis, oral mucosa, breast and lung. CSL functions in these cells as a constitutive direct repressor of multiple senescence- and CAF-effector genes. At the same time, it physically interacts with p53, repressing its activity, and p53 activation provides a failsafe mechanism against compromised CSL function. Concomitant loss of CSL and p53 overcomes fibroblast senescence, enhances expression of CAF effector genes and, in vivo, promotes tumour and stromal cell expansion. Together, the findings support a CAF activation/stromal evolution model under convergent CSL/p53 control.

overall_design: Examination of genome-wide CSL binding sites in primary human dermal fibroblasts usinf two different antibodies against CSL

first: Maria

last: Procopio

first: Karine

last: Lefort

first: Ugo

last: Ala

first: Paolo

last: Provero


title: Transcriptome Kinetics of 1[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl] imidazole (CDDO-Im) in Human Umbilical Vein Endothelial Cells (HUVEC): Mechanism of Action of Cytoprotection

status: Public on Aug 01 2015

city: JBSA FT SAM HOUSTON

first: Phillip

middle: Dalton

last: Bowman

state: TX

address: 3698 CHAMBERS PASS STE B

department: DCR

institute: US Army Institute of Surgical Research

summary: This study evaluated temporal gene expression profiles to better characterize the early transcriptional events and their relationship to the dynamics of the cytoprotective response in human umbilical vein endothelial cells (HUVEC) to CDDO-.

overall_design: Time-course gene expression profiling was performed on HUVEC treated with CDDO-Im for 0.5, 1, 3, 6, and 24 hours.

first: James

last: Bynum

first: Xinyu

last: Wang

first: Salomon

last: Stavchansky


title: Comparative transcriptomic analysis of Arabidopsis plants treated with short oligogalacturonides and mock

status: Public on Jun 05 2015

city: Helsinki

first: Martin

last: Broberg

address: Viikinkaari 5D

department: Biosciences

country: Finland

institute: University of Helsinki

summary: The importance of oligogalacturonides for plant defence and growth has been described extensively in litterature. However, much of previous global transcriptome analyses for plants treated with oligogalacturonides have focused on long (>10 galacturonosyl residues) oligogalacturonides. This study focuses on the transcriptomic impact that trimeric oligogalacturonides and a mixture of oligogalacturonides have on plant transcriptomes and overall biology.

overall_design: Arabidopsis seedling were grown on liquid 1/2 MS medium in 12-well culture plates in vitro for 12 days.  12 seedlings were cultured per well, and three wells were combined per biological replicate. The seedling plants were treated either with 1/2 MS medium (mock), 1/2 MS with trimeric oligogalacturonides (trimers) and a mixture of 1/2 MS and oligogalacturonides (short OG-mix) with a degree of polymerization of 2-20 for 3 hours. RNA was extracted from the seedlings, three biological replicates per treatment, and sequenced using the SOLiD 5500XL platform.

first: Pär

last: Davidsson

first: Tarja

last: Kariola

first: Veronica

last: Witick

first: Nina

last: Sipari

first: Pekka

last: Heino

first: Minna

last: Pirhonen

first: E

last: Palva


title: Cigarette smoke silences innate lymphoid cell function in the lung, facilitating an IL-33-dependent, exacerbated Th-1 response to infection

status: Public on Jun 01 2015

city: Gaithersburg

first: Zheng

last: Liu

address: One Medimmune Way

institute: Medimmune LLC

summary: Using gene expression profiling to examine how IL33 treatment affect gene expression in lung tissues of mice

overall_design: Mice were exposure to cigarette smoke or room air and treated with intranasal IL-33 or PBS, the lung tissues then subjected to microarray analysis to examine the gene expression profiles

first: Jennifer

last: Kearley

first: Jonathan

middle: S

last: Silver

first: Caroline

last: Sanden

first: Aaron

last: Berlin

first: Natalie

last: White

first: Michiko

last: Mori

first: Tuyet-Hang

last: Pham

first: Christine

middle: K

last: Ward

first: Gerard

middle: J

last: Criner

first: Nathaniel

last: Marchetti

first: Tomas

last: Mustelin

first: Jonas

last: Erjefalt

first: Roland

last: Kolbeck

first: Alison

last: Humbles


title: Metabolic imbalance caused by loss of malic enzymes in the legume endosymbiont Sinorhizobium meliloti

status: Public on Jul 25 2015

city: Hamilton

first: Turlough

last: Finan

state: Ontario

address: 1280 Main Street West

department: Biology

institute: McMaster University

summary: Malic enzymes decarboxylate the tricarboxylic acid (TCA) cycle intermediate malate to the glycolytic end-product pyruvate and are well positioned to regulate metabolic flux in central carbon metabolism.  The bacterium Sinorhizobium meliloti has a NAD(P)-malic enzyme (DME) and a NADP-malic enzyme (TME) and DME is required for symbiotic N2-fixation.  To help understand the role of these enzymes, we examined growth, metabolic and transcriptional consequences resulting from the deletion of these enzymes.  Few effects were observed upon growth with glucose, whereas growth with the gluconeogenic substrate, succinate, resulted in transcriptional and metabolic effects particularly in the dme mutant strains.  When grown with succinate, DME mutant cells accumulated hexose sugar phosphates and trehalose, while TME mutants accumulated putrescine.  Succinate-grown DME mutant cells also showed increased transcription of genes for gluconeogenesis and for pathways such as amino acid and fatty acid synthesis that divert metabolites away from the TCA cycle.  These data suggested that, DME is required to regulate the levels of TCA cycle intermediates and that the activity of TME is insufficient to prevent the accumulation of TCA cycle intermediates in cells utilizing succinate as carbon source.  Consistent with this, in short-1-3 hour incubations with succinate, dme mutant cells excreted large amounts of malate whereas little malate was excreted from tme or wild-type cells.   These results support the suggestion that DME is required for N2-fixation in alfalfa because it is required for synthesis of pyruvate and acetyl-CoA and the rapid metabolism of C4-dicarboxylates supplied by the plant.

overall_design: RNA expression was measured for S. meliloti in exponential phase grown in MOPS (morpholinpropanesulfonic acid) buffered minimal media under 2 growth conditions: 1) 15 mM succinate, 2) 15 mM glucose; using wild type cells as well as dme and tme mutant strains (6 experiments, 2 replicates: total 12 samples)

first: Ye

last: Zhang

first: Laura

last: Smallbone

first: George

last: diCenzo

first: Richard

last: Morton


title: Bcl11b maintains quiescent mammary repopulating units

status: Public on Mar 30 2015

city: Palo Alto

first: Shang

last: Cai

address: 915 Campus Dr.

institute: Stanford University

summary: This gene expression microarray analysis is to test how induced Bcl11b expression affect the overall gene expression profile of Comma D Beta Cells in the progenitor (sca1+) and differentiated (Sca1-) population. Comma D beta Cell line was cultured DMEM F12+2% FBS+1% PSA+5ug/ml insulin+10ng/ml EGF in 175 cm2 culture flask overnight, followed by 100ng/ml Doxycycline treatment for 1 day. Then, cells were trypsinized and subjected for flow sorting of Sca1+ and Sca- population. RNA was then extracted and subjected to microarray gene expression analysis.

overall_design: Sca1+ and Sca1- cells in the presence or absence of Doxycycline.

first: Michael

last: Clarke


title: Cardiac gene expression profiling of neonatal Salvador mutant mice

status: Public on May 12 2015

city: Houston

first: Todd

middle: Ryan

last: Heallen

state: Texas

address: One Baylor Plaza

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine

summary: In this study, we identified a number of genes whose expression are regulated by the Hippo tumor suppressor pathway. To disrupt Hippo signaling in the mouse heart, we inactivated the single mammalian Salv ortholog using a Salv conditional null allele and the Nkx2.5 cre allele that directs cardiac cre activity. Total RNA from P8-stage hearts were used for expression profiling.

overall_design: Genes transcriptionally regulated by the Hippo pathway during cardiogenesis were identifed through expression profiling in Salvador mutant (Salv CKO) neontate hearts. Total RNA from postnatal day 8 (P8)-stage hearts was purified to generate biological replicate samples (2 control and 2 Salv CKO) and generate expression profiles. 3 technical replicates were used for each sample.

middle: R


title: Comparison of Osx+ cells and Ocn+ cells in the bone marrow.

status: Public on Apr 10 2015

city: Boston

first: Vionnie

middle: W. C.

last: Yu

state: MA

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital/Harvard University

summary: We performed gene expression microarray comparing Osx-mCherry cells and Ocn-Topaz cells isolated from the OsxCre-mCherry;OcnCre-Topaz double transgenic mice by flow cytometry.

overall_design: In the OsxCre-mCherry;OcnCre-Topaz mouse model, Osx+ cells were labeled red, Ocn+ cells were green, and Osx+Ocn+ cells were yellow within the same animal. This system allows isolation of osteolineage subsets within the same animal by flow cytometry.

middle: W

first: Francesca

last: Ferraro

first: Stephania

last: Lymperi

first: David

last: Scadden


title: Tissue-specific transcriptomics, chromosomal localization, and phylogeny of chemosensory and odorant binding proteins from the red flour beetle Tribolium castaneum reveal subgroup specificities for olfaction or more general functions

status: Public on Mar 01 2015

city: Göttingen

first: Georg

last: Oberhofer

state: Lower Saxony

address: Justus von Liebig Weg 11

department: Developmental Biology

institute: University Göttingen

summary: Chemoreception is based on the senses of smell and taste that are crucial for animals to find new food sources, shelter, and mates. The initial step in olfaction involves the translocation of odorants from the periphery through the aqueous lymph of the olfactory sensilla to the odorant receptors by chemosensory proteins (CSPs) or odorant binding proteins (OBPs).To better understand the roles of CSPs and OBPs in a coleopteran pest species, the red flour beetle Tribolium castaneum (Coleoptera, Tenebrionidae), we performed transcriptome analyses of male and female antennae, heads, mouthparts, legs, and bodies, which revealed that all 20 CSPs and 49 of the 50 previously annotated OBPs are transcribed. Only six of the 20 CSP are significantly transcriptionally enriched in the main chemosensory tissues (antenna and/or mouthparts), whereas of the OBPs all eight members of the antenna binding proteins II (ABPII) subgroup, 18 of the 20 classic OBP subgroup, the C+OBP, and only five of the 21 C-OBPs show increased chemosensory tissue expression. By MALDI-TOF-TOF MS protein fingerprinting, we confirmed three CSPs, four ABPIIs, three classic OBPs, and four C-OBPs in the antennae.Most of the classic OBPs and all ABPIIs are involved in chemoreception. A few are also present in other tissues like odoriferous glands and testes and may be involved in release or transfer of chemical signals. The majority of the CSPs as well as the C-OBPs are not enriched in antennae or mouthparts, suggesting a more general role in the transport of hydrophobic molecules.

overall_design: RNAseq data obtained from different body parts of adult males and females, as well as larvae

first: Ernst

middle: A

last: Wimmer

first: Stefan

last: Dippel


title: Genomic DNA hybridization of Pseudomonas aeruginosa strains PAO1 and PA14

first: Deborah

last: Hogan

summary: Genomic DNA from Pseudomonas aeruginosa strains PAO1 and PA14

overall_design: Pseudomonas aeruginosa genomic DNA was isolated, fragmented and hybridized to Affymetrix Pseudomonas GeneChips.

first: John

last: Hammond


title: Chordoma Cell Lines Characterization

status: Public on May 05 2015

city: Ulm

first: Adrian

last: von Witzleben

address: Albert-Einstein-Allee 23

institute: Institute of Pathology

summary: mRNA Expression of established chordoma cell lines for characterization.

overall_design: Comparative analysis

first: Thomas

middle: F

last: Barth


title: Identification of Arabidopsis thaliana PRR9 regulated clock components and circadian outputs through genome-wide binding sites analysis

status: Public on Dec 03 2015

city: East Lansing

first: Tiffany

middle: L

last: Liu

state: Michigan

address: 3260 Molecular Plant Sciences Building

department: Plant Biology

institute: Michigan State University

summary: We identified genome-wide PRR9 targets by conducting chromatin immunoprecipitation followed by high-throughput sequencing.

overall_design:
Plants were grown in cycling 12 h light/12 h dark for two weeks before harvesting at ZT4.  The four samples include the immunoprecipitated and input control for prr9-1 PRR9::HA-PRR9 CCR2::LUC #109 (HA9) and the prr9-1 (s9c) parental control.

PRR5 PRR7 and TOC1 raw data available from the following Series:
PRR5: GSE36361
TOC1: GSE35952
PRR7: GSE49282 (GSM1196649 and GSM1196650)

first: Linsey

last: Newton

first: Eva

last: Farre


title: The role of DNA methylation on the organization of the cancer epigenome

status: Public on Feb 06 2015

city: Los Angeles

first: Fides

last: Lay

state: CA

address: 615 Charles E Young Drive South, BSRB 457

department: MCDB

institute: UCLA

type: Methylation profiling by high throughput sequencing

summary: We assess global chromatin accessibility following high salt wash

overall_design: Simultaneous genome-wide mapping of DNA methylation and nucleosome occupancy of K562 cells

first: Yaping

first: Ben

last: Berman

first: Peter

last: Jones


title: Transcriptome analysis of kidney cancer

status: Public on Feb 05 2015

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: The aim of this research was to explore activation/deactivation of signaling pathways during cancerogenesis.

overall_design: Tissue samples from malignant tumors were obtained from patients who had undergone surgery. Samples were formain fixed and embedded in paraffin. Tumors were evaluated by a pathologist to confirm the diagnosis and estimate the tumor cell numbers. All tumor samples used in this study contained at least 80% tumor cells.

middle: V

first: Alexander

last: Aliper

first: Andrey

last: Golubov

first: Olga

last: Kovalchuk

first: Anton

last: Abuzdin


title: Quantitative Analysis of Wild Type and Dicer1-ifKO Hippocampal Transcriptomes (mRNA and small RNA) Through Next Generation Sequencing (mRNA-Seq).

status: Public on Feb 04 2015

city: Sant Joan d'Alacant

first: Angel

last: Barco

address: Av. Santiago Ramón y Cajal

institute: Instituto de Neurociencias (UMH-CSIC)

summary:
Methods: CaMKIIa-creERT2 (Erdmann et al., 2007) and Dicer1f/f (Harfe et al., 2005) were crossed to produce inducible forebrain-restricted Dicer1 knockout mice (Dicer-ifKO) mice. Hippocampal mRNA profiles of 3-month-old wild-type (WT) and (Dicer-ifKO) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. Each sample included total RNA isolated from the hippocampus of 3 mice. In total, 12 mice per genotype were used. The sequence reads that passed quality filters were mapped to reference genome (GRCm38/mm10) using Bowtie 2 (2.0.5) and TopHat (2.0.6). SAM/BAM files were further processed with Samtools (0.1.18). Read count quantitations were obtained using Seqmonk (0.26.0). Normalization of read counts and differential expression analysis between genotypes was carried out using DESeq2 R package from Bioconductor (Release 2.13). qRT–PCR validation was performed using SYBR Green assays.
Results: We mapped about 13-14 million sequence reads per sample to the mouse genome (build GRCm38/mm10) and quantified 76,938 annotated transcripts. DESeq2 R package was used to normalize the counts and perform the differential expression. Differential analysis output was filtered by FDR threshold (padj < 0.1). This approach led us to identify 641 gene isoforms, corresponding to 314 genes that were differentially regulated in the mouse hippocampus upon Dicer ablation.
Conclusions: We extend here the characterization of inducible forebrain-restricted Dicer1 mutants confirming the initial memory improvement. Moreover, we describe several novel phenotypes associated with early Dicer loss in the mature brain including an exacerbated response to seizures, increased CA1 neuron excitability, a pronounced weight gain and enhanced induction of immediate early genes (IEGs) in relevant neuronal nuclei. To identify candidate genes that could explain these phenotypes, we conducted two complementary genomic screens for the miRNAs primarily affected and their targets. Overall, our results explain both the initial and late consequences of Dicer loss in excitatory neurons and indicate that Dicer and the miRNA system play a critical role regulating neuronal homeostasis and responsiveness.

overall_design: Hippocampal mRNA profiles of 3-month-old wild-type (WT) and Dicer-ifKO (3 weeks upon tamoxifen administration) male mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. Each sample included total RNA isolated from the hippocampus of 3 mice. In total, 12 mice per genotype were used.

first: Jose

middle: P

last: LOPEZ-ATALAYA

last: BARCO


title: Drug effects on hippocampal microRNA profiles after traumatic brain injury

status: Public on Jan 08 2015

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

country: USA

institute: GenUs BioSystems, Inc.

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

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

overall_design: Refer to individual Series


title: Quantitative Analysis of Wild Type and Dicer1-ifKO Hippocampal Transcriptomes (mRNA and small RNA) Through Next Generation Sequencing (smallRNA-Seq).

state: Alicante

summary:
Methods: CaMKIIa-creERT2 (Erdmann et al., 2007) and Dicer1f/f (Harfe et al., 2005) were crossed to produce inducible forebrain-restricted Dicer1 knockout mice (Dicer-ifKO) mice. Hippocampal small RNA profiles of 3-month-old wild-type (WT) and (Dicer-ifKO) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. Each sample included total RNA isolated from the hippocampus of 3 mice. In total, 12 mice per genotype were used. After trimming of the adapter sequences and masking for low-complexity or low-quality sequence, the inserts were sorted in separated files according to their lengths. The reads in which no match of the adapter sequences is found were discarded. Inserts of length 18-50 were pooled together and mapped to reference genome (GRCm38/mm10) using Burrows-Wheeler Alignment Tool (BWA) v.0.5.9. We used BWA to map the inserts with a maximum of 2 mismatches. Inserts mapping to several positions on the reference sequences with the same mapping quality were attributed at random to one of the position with a mapping quality of 0. Files were further processed using Samtools v.0.1.18 to get binary files (BAM). Read count quantitations were obtained using Seqmonk (0.26.0). We counted reads that mapped to annotated features (miRNAs, 2035; miscRNA, 491; mRNA 76938; rRNA, 341; snoRNA, 1602; snRNA, 1431; tRNAs, 26248; tRNA, 22). The DESeq2 R package from Bioconductor was used to normalize the counts and perform the differential expression analysis.
Results: We mapped about 17-22 million sequence reads per sample to the mouse genome (build GRCm38/mm10) and quantified 109,108 annotated features. DESeq2 R package was used to normalize the counts and perform the differential expression. Differential analysis output was filtered by FDR threshold (padj < 0.1). This approach led us to identify 119 annotated features (including 96 miRNAs) that were differentially regulated in the mouse hippocampus upon Dicer ablation.
Conclusions: We extend here the characterization of inducible forebrain-restricted Dicer1 mutants confirming the initial memory improvement. Moreover, we describe several novel phenotypes associated with early Dicer loss in the mature brain including an exacerbated response to seizures, increased CA1 neuron excitability, a pronounced weight gain and enhanced induction of immediate early genes (IEGs) in relevant neuronal nuclei. To identify candidate genes that could explain these phenotypes, we conducted two complementary genomic screens for the miRNAs primarily affected and their targets. Overall, our results explain both the initial and late consequences of Dicer loss in excitatory neurons and indicate that Dicer and the miRNA system play a critical role regulating neuronal homeostasis and responsiveness.

overall_design: Hippocampal small RNA profiles of 3-month-old wild-type (WT) and Dicer-ifKO (3 weeks upon tamoxifen administration) male mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. Each sample included total RNA isolated from the hippocampus of 3 mice. In total, 12 mice per genotype were used.


title: SNP-based LOH of hepatocellular carcinoma (HCC)

status: Public on Feb 28 2015

city: Guangzhou

first: Guo-liang

last: Huang

address: 651 Dongfeng East Road

department: Cancer Center

country: China

institute: Sun Yat-Sen University

summary: High frequency of loss of heterozygosity (LOH) at locus D4S2964 was found in hepatocellular carcinoma (HCC) by our previous studies and others’. The present study was designed to explore genes around the locus affected by LOH and their clinical implications. 440 SNPs located at 49 genes around D4S2964 were selected from NCBI website for the SNPs microarray fabrication. LOH of these SNPs markers in 112 cases of HCC tissues and paired adjacent liver tissues were investigated by the SNP microarray. A map of LOH of SNPs in genes around D4S2964 was constructed.

overall_design: 112 pairs of HCC tissues and corresponding non-tumor tissues was genotyped. LOH and its clinical implication was analyzed.

first: Guo-Liang

first: Hui-Yun

last: Wang


title: miRNA expression of whole hippocampus 24hr post-injury in rat

summary: Traumatic brain injury dysregulates microRNA expression in the brain. We hypothesized that injury-induced epigenetic changes contribute to neurodegeneration and learning and memory deficits after TBI. These changes may provide a mechanistic explanation for neuropsychiatric comorbidities in TBI patients. Our objective is to compare and contrast the effects of several neuroprotective drugs (JM6, PMI-006 and E33-estrogen) on the TBI-induced changes in microRNA expression in the hippocampus, a region of the brain that is critical for learning and memory. We will also study if different neuroprotective drugs have similar effects on common microRNAs which may cooperatively regulate a common set of gene targets.

overall_design:
3 biological samples each of Naïve, Sham control, TBI and TBI plus JM6, TI plus PMI-006, and TBI plus E33 rat hippocampi were obtained 24 hr post-sham injury or TBI, stored in RNA later and sent to GenUs Biosystems for microRNA microarray analysis.

[Support/contributor]  The Moody Project for Translational Traumatic Brain Injury Research

first: Helen

last: Hellmich

first: Deborah

last: Boone

first: Harris

last: Weisz

middle: T

first: Karen

middle: E

last: Torres


title: Quantitative Analysis of Wild Type and Dicer1-ifKO Hippocampal Transcriptomes (mRNA and small RNA) Through Next Generation Sequencing.


title: Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize

status: Public on Jan 01 2015

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: Maize is highly sensitive to short term flooding and submergence. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18W and M162W) and sensitive (B97 and B73) genotypes were identified. Transcriptome analysis was performed on these inbreds to provide genome level insights into the molecular responses to submergence.

overall_design: RNA deep sequencing of shoot tissue from four inbreds (B73, B97, Mo18W and M162W) in three conditions 24h control (non-submerged), 24h submerged and 72h submerged.

first: Harkamal

last: Walia