title: Gene expression profiling of MeCP2 deficient zebrafish embryos

status: Public on Jul 21 2015

city: Singapore

first: Wan Ying

last: Leong

address: 8 College Road

institute: DUKE-NUS Graduate Medical School

summary: Investigation of whole genome gene expression level changes in mecp2 morphant zebrafish embryos as compared to wild-type strain.

overall_design: In order to explore the targets of transcription factor Mecp2 in zebrafish, we knockdown Mecp2 using morpholino targeting splice junction. Wild-type and mecp2 morphant embryos were collected and analyzed at 24hpf. Gene expression profiles of Mecp2 morphant embryos were compared to gene expression profiles of wild type embryos using Nimblegen whole transcriptome zebrafish microarrays.

first: Wan-Ying


title: MicroRNA expression profiling of tamoxifen sensitive and resistant ER+ breast cancer cell lines

status: Public on Aug 01 2015

city: Odence

first: Henrik

last: Ditzel

address: J.B. Winsløws Vej 25

country: Denmark

institute: University of Southern Denmark

summary: Tamoxifen is an effective anti-estrogen treatment for patients with estrogen receptor-positive (ER+) breast cancer. However, about 30% of such patients receiving tamoxifen as an adjuvant therapy experience recurrence within 15 years, and most patients with advanced disease eventually develop resistance to tamoxifen. To elucidate the underlying molecular mechanisms of tamoxifen resistance, we performed a systematic analysis of miRNA-mediated gene regulation in three clinically-relevant tamoxifen-resistant human breast cancer cell lines (TamRs) compared to their parental tamoxifen-sensitive MCF-7/S0.5 cell line. Alterations in the expression of 131 miRNAs in tamoxifen-resistant vs. parental cell lines were identified, 22 of which were common to all TamRs using both sequencing and LNA-based quantitative PCR technologies.

overall_design: ER+ and tamoxifen sensitive breast cancer cell line (MCF-7/S0.5) and its derived tamoxifen resistant clones: TAMR-1, TAMR-4 and TAMR-8 were miRNA expression profiled in triplicates of each using Exiqon's miRCURY LNA based microRNA Ready-to-use PCR, Human panel I+II, V2.R (Exiqon, product number 203608).

first: Tejal

last: Joshi

first: Daniel

last: Elias

first: Jan

last: Stenvang

first: Fei

last: Teng

first: Maria

middle: B

last: Lyng

first: Anne

middle: E

last: Lykkesfeldt

first: Nils

last: Brunner

first: Jun

last: Wang

first: Ramneek

last: Gupta

first: Christopher

middle: T

last: Workman


title: Gene expression profile in the cochlear tissue of Cmah-null mouse

status: Public on Jul 10 2015

city: Seoul

first: Deug-Nam

last: Kwon

address: 1 hwayang-dong, Kwangjin-gu

country: South Korea

institute: Konkuk University

summary: CMP-Neu5Ac hydroxylase (Cmah) disruption caused several abnormalities and diseases including hearing loss in old age. However, underling molecular mechanisms that give rise to age-related hearing loss (AHL) in Cmah-null mouse are still obscure.  To identify differential gene expression profiles associated with Cmah disruption, we performed microarray analysis using Illumina MouseRef-8 v2 Expression BeadChip, using the cochlear tissues from a control mouse and a Cmah-null mouse.

overall_design: Total RNA was extracted and purified from the cochlear tissues  of WT and Cmah-null mice using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer’s protocol. The RNA quality was verified using an Agilent Bioanalyzer 2100 (Agilent Technologies; Palo Alto, CA, USA) using the RNA 6000 Pico Assay. Generation of double-stranded cDNA, preparation and labeling of cRNA, hybridization to Mouse Ref-8 v2.0 Expression BeadChip (Illumina, Inc.; San Diego, CA, USA), washing, and scanning were all performed according to the standard Illumina protocol. Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner.

first: Jin-Hoi

last: Kim


title: Expresssion data from reovirus treated breast cancer cell lines

status: Public on Jun 13 2015

city: Calgary

first: Don

last: Morris

address: 1331, 29th Street, NW

department: Oncology

country: Canada

institute: Tom Baker Cancer Centre

summary:
Reovirus mediated cell death of breast cancer is orchestrated via apoptotic cell death pathways
We used inhouse microarrays to detail the global programme of gene expression following reovirus treatment

overall_design: Breast cancer cell lines were treated with reovirus for 12 and 24 hours and RNA was extracted.  Microarray was performed in inhouse (University of Calgary miroarray facility) chips.

first: Chandini

last: Thirukkumaran


title: A food deprivation affects the miRNome in the lactating goat mammary gland

status: Public on Jul 01 2015

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

country: France

institute: INRA

type: Non-coding RNA profiling by high throughput sequencing

summary: Nutrition affects milk composition influencing its nutritional properties. Nutrition also modifies the expression of mammary genes, whose regulation is not completely known. MicroRNAs (miRNA) are small non-coding RNA that work as important post-transcriptional gene expression regulators by targeting messenger RNAs. Our goal was to characterize miRNA whose expression is regulated by nutrition in the lactating goat mammary gland, and which may give clues to decipher the regulations of milk components biosynthesis and secretion. Using high-throughput sequencing technology, miRNomes of the lactating mammary gland have been established from 4 goats fed ad libitum and 6 goats food deprived during 48h. Food deprivation affected the expression of 30 miRNA (padj<0.1), 16 were downregulated and 14 were upregulated. Prediction tools Diana-microT suggests a potential role of several nutriregulated miRNA in the lipid metabolism. Among putative targets 19 differently expressed genes (DEG) previously identified in the same sample, were found. Functions of these 19 DEG revealed their involvement in tissue remodeling. This study constitutes the first evidence of nutriregulated miRNA in the ruminant mammary gland. The characterization of these 30 miRNA could contribute to a better understanding of genes regulations in the mammary gland in response to nutrition.

overall_design: MicroRNA profiles of mammary glands from 10 Alpine goats at the peak of lactation (48 ± 2 days post-partum) generated by a HiSeq 2500 using Illumina Solexa technic.

first: Lenha

last: Mobuchon

first: Sandrine

last: Le Guillou

first: Denis

last: Laloë

last: de la Foye

first: Fabienne

last: Le Provost

first: Christine

last: Leroux


title: Dynamics of tolerant potato-potato virus Y interaction

status: Public on Aug 06 2015

city: Ljubljana

first: Ziva

last: Ramsak

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.

overall_design: 2 genotypes, mock and virus inoculated plants, inoculated (1-7dpi) and non-inoculated (1-11 dpi) leaves; one-colour design

first: Tjaša

last: Stare

first: Živa

last: Ramšak

first: Katja

first: Kristina

last: Gruden


title: Transcriptome study of the covS-regulation of a Group A Streptococcus pyogenes M23ND

status: Public on Aug 05 2015

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

country: USA

institute: University of Notre Dame

type: Expression profiling by high throughput sequencing

summary: We investigated the covS-regulation of S. pyogenes in a hypervirulent M23 strain using RNA-sequencing. The differential gene expression comparison between the covS- mutant and isogenic wild type covS+ identified altered expression of 349 (18%) genes, including a broad spectrum of virulence genes and diverse metabolic genes. The data showed that the strain achieved hypervirulence by enhancing the expression of genes responsible for invasiveness and antiphagocytosis (i.e., hasABC), by abrogating the expression of toxic genes (i.e., speB), and by compromising gene products with dispensable functions (i.e., sfb1). Meanwhile, we found that covS also regulated diverse kinds of metabolic genes that maximized nutrient utilization and energy metabolism during growth and dissemination. From constructing a genome-scale metabolic model, we identified fourteen non-redundant metabolic gene modules, which constitute unique sources for specific nutrients. These genes were probably essential for pathogen growth and virulence. In general, this study provided quantitative transcriptomic signatures of the covS regulation in a hypervirulent S. pyogenes strain and addressed major aspects of the covS-modulated virulent mechanisms.

overall_design: Examination of expression profiling of covS- mutant strain and isogenic wild type covS+ at different growth stages.

first: Zhong

last: Liang

first: Jeffrey

middle: A

last: Mayfield

first: Victoria

last: Ploplis

first: Francis

middle: J

last: Castellino


title: Expression data from rat organotypic hippocampal slices lentivirally infected with shRNF10 or scramble construct

status: Public on Jun 20 2015

city: Milan

first: Nico

last: Mitro

state: MI

address: Via Balzaretti 9

department: Pharmacological and biomolecular sciences

country: Italy

institute: Università degli studi di Milano

summary:
RNF10 is a synapse-to-nucleus protein messsenger regulating NMDAR-dependent gene trascription. We have charaterized the impact of the absence of RNF10 on structural synaptic plasticity.
In this dataset we included expression data from homogenates of DIV14 rat organotypic hippocampal slices lentivirally infected with shRNF10 or scramble construct

overall_design: 8 total samples were analyzed (4 shRNF10 and 4 scramble).

first: Margarita

middle: C

last: Dinamarca

first: Francesca

last: Guzzetti

first: Anna

last: Karpova

first: Dmitry

last: Lim

first: Stefano

last: Musardo

first: Manuela

last: Mellone

first: Elena

last: Marcello

first: Adeline

last: Burguière

first: Antonio

last: Caldarelli

first: Armando

last: Genazzani

first: Julie

last: Perroy

first: Laurent

last: Fagni

first: Pier

middle: L

last: Canonico

first: Michael

middle: R

last: Kreutz

first: Fabrizio

last: Gardoni

first: Monica

last: Di Luca


title: Molecular expression profile reveals potential biomarkers and therapeutic targets incanine endometrial lesions

status: Public on Jul 11 2015

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

summary: Cystic endometrial hyperplasia (CEH), mucometra, and pyometra are common uterine diseases in intact dogs, with pyometra being a life threatening disease. This study aimed to determine the gene expression profile of these conditions, in addition to potential biomarkers for closed-cervix pyometra, the most severe condition

overall_design: Total RNA was extracted from 69 fresh endometrium samples collected from 21 healthy female dogs during diestrus, 16 CEH, 15 mucometra and 17 pyometra (eight open and nine closed-cervix). Global gene expression was detected using the Affymetrix Canine Gene 1.0 ST Array

first: Rolando

last: Villacis


title: Epigenome analysis of angiogenin impact on bladder cancer

status: Public on Jun 03 2015

city: Honolulu

first: Rafael

last: Peres

state: HI

address: 701 Ilalo Street, #354

department: Clinical and Translational Research

institute: University Of Hawaii Cancer Center

summary: We investigated if Overexpression of ANG in UROtsaANG and RT112Scr could cause epigenetic changes, comparing to UROtsaEmpty and RT112KD-ANG, respectively . The alteration of genome-wide DNA methylation in these cells was analyzed using Illumina whole genome methylation array. Specifically, methylated DNAs with 5-mC were amplified using nonbiased conditions, labeled and hybridized to a BeadChip array covering over >450,000 methylation sites. ANG expression was noted to be associated with a change in global DNA methylation levels compared to control cells

overall_design: Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip. The bisulfite treatment, microarray service and analysis of the array were provided by Macrogen Inc. (Seoul, South Korea).

first: R

first: C

last: Rosser


title: Transcriptional profile of Synechococcus in the dark or light with or without photosynthesis inhibitors

status: Public on Jun 01 2015

city: Tokyo

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

country: Japan

institute: Waseda University

summary:
In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, dramatically reduces the transcription rate in the dark (dark repression), and its cellular functions enormously depend on light as an energy source through photosynthetic activity. Here, we employed high-density oligonucleotide arrays to investigate comprehensive profiles of genome-wide Synechococcus gene expression when illuminated or dark-acclimated cells are treated with photosynthesis inhibitors DCMU or DBMIB. In addition, we added rifampicin to the DBMIB-treated cells in the dark, and analyzed genome-wide expression profiles.
Treatment with DCMU or DBMIB under illuminated condition mimicked dark-repression-like genome-wide transcription profiles. Addition of DBMIB under dark condition largely attenuated dark-repression and kept relatively large amount of transcripts, this high-transcripts level still kept when rifampicin was additionally administered.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design:
Wild type (WT) strain was analyzed under illuminated or dark condition with or without inhibitors using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: a duplicate experiments (except for light 0min samples, quadruplicate experiments) in WT under light, dark, light+DCMU, light+DBMIB, dark+DBMIB, and dark+DBMIB+rifampicin conditions. Samples were cultivated at 30min or 60min after addition of the stimuli (the timing at which each stimuli was added is ZT 12h) from Synechococcus elongatus PCC 7942 (WT strain).
timecourse data (0~60 min under dark or light condition with or without DCMU, DBMIB and rifampicin) from Synechococcus elongatus PCC 7942 (WT) strains

first: Sotaro

last: Takano


title: Genome wide 5hmC patterns in the mouse liver, embryonic fibroblasts and induced pluripontent stem cells.

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

type: Methylation profiling by high throughput sequencing

summary: We carry out hydroxymethyl DNA immunoprecipitation (hmeDIP) prior to sequencing on the Ion Proton semiconductor sequencing platform to demonstate the strategy as an alternative method to Illumina sequencing.

overall_design: Genome 5hmC patterns were generate on the Ion Proton seqencer. 2x mouse liver, 1x MEF, 1x iPSC datasets generated

middle: P

first: Angie

last: Fawkes

first: Raffaele

last: Ottaviano

first: Jennifer

middle: M

last: Hunter

first: Richard

last: Clark

first: Audrey

last: Coutts

first: Lee

last: Murphy

last: Meehan


title: A YAP/TAZ-Regulated Molecular Signature is Associated with Oral Squamous Cell Carcinoma

status: Public on May 26 2015

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Oral squamous cell carcinoma (OSCC) is a prevalent form of cancer that develops from the epithelium of the oral cavity. OSCC is on the rise worldwide, and death rates associated with the disease are particularly high. Despite progress in understanding of the mutational and expression landscape associated with OSCC, advances in deciphering these alterations for the development of therapeutic strategies have been limited. Further insight into the molecular cues that contribute to OSCC is therefore required. Here we show that the transcriptional regulators YAP (YAP1) and TAZ (WWTR1), which are key effectors of the Hippo pathway, drive pro-tumorigenic signals in OSCC. Regions of pre-malignant oral tissues exhibit aberrant nuclear YAP accumulation, suggesting that dysregulated YAP activity contributes to the onset of OSCC. Supporting this premise, we determined that nuclear YAP and TAZ activity drives OSCC cell proliferation, survival, and migration in vitro, and is required for OSCC tumor growth and metastasis in vivo. Global gene expression profiles associated with YAP and TAZ knockdown revealed changes in the control of gene expression implicated in pro-tumorigenic signaling, including those required for cell cycle progression and survival. Notably, the transcriptional signature regulated by YAP and TAZ significantly correlates with gene expression changes occurring in human OSCCs identified by The Cancer Genome Atlas (TCGA), emphasizing a central role for YAP and TAZ in OSCC biology.
Expression profiling was conducted following the repression of the transcriptional regulators TAZ and YAP (YAP/TAZ) in human SCC2 oral cancer cells.

overall_design: Human SCC2 oral cancer cells were transfected with control siRNA, or siRNAs targeting TAZ, YAP, or YAP/TAZ for 48 hours. Total RNA from three independent experiments carried out on separate days was isolated and purified and the samples were then profiled on Affymetrix Human Gene 2.0 Chips at the Boston University Microarray Core. The expression profiles were processed and normalized using the Robust Multi-array Average (RMA) procedure (23) based on a custom Brainarray CDF (24). For each of the siRNA experiments, signatures of genes differentially expressed between treatment and corresponding siRNA control with an FDR q-value ≤0.05 and a fold change ≥2 were identified as either activated (up-regulated in control) or repressed (up-regulated in treatment). The overlap between the differentially expressed gene signatures was evaluated by Fisher test. Hierarchical gene and sample clustering was performed on the top 3000 genes with highest median absolute deviation (MAD; a robust version of the variance) across 12 samples, using “ward” as the agglomeration rule, and 1 minus Pearson correlation and Euclidean as the distance measures for genes and samples, respectively.

first: Samantha

last: Hiemer

first: Liye

last: Zhang

first: Vinay

middle: K

last: Kartha

first: Trevor

middle: S

last: Packer

first: Munirah

last: Almershed

first: Vikki

last: Noonan

first: Maria

last: Kukuruzinska

first: Manish

middle: V

last: Bais

first: Stefano

last: Monti

first: Xaralabos

last: Varelas


title: Toll-like receptor 10 in Helicobacter pylori infection

city: Houston

first: Hiroyuki

last: Nagashima

state: Texas

address: 2002 Holcombe Blvd. (3B-172)

department: Department of Medicine Gastroenterology and Hepatology

institute: Baylor College of Medicine

summary: Helicobacter pylori is a highly successful and important human pathogen that causes chronic gastritis, peptic ulcer diseases and gastric cancer. Innate immunity plays an important role of the primary defense against pathogens and epidemiological studies have suggested a role of toll-like receptor 1 (TLR1) in the risk of H. pylori acquisition. We performed microarray analysis of gastric mucosal biopsy specimens from H. pylori-positive and uninfected subjects; infection was associated with an ~15-fold up-regulation of TLR10 (p <0.001). Quantitative RT-PCR confirmed  TLR10 mRNA levels were increased 3-fold in H. pylori-infection (p <0.001) and immunohistochemistory using anti-TLR10 polyclonal antibodies showed increased TLR10 expression in gastric epithelial cells of infected individuals. In vitro experiments where H. pylori was co-cultured with NCI-N87 gastric cells showed significant H. pylori-specific up-regulation of TLR10 mRNA levels and a correlation with TLR2 mRNA levels (R = 0.87, P <0.001).  We compared combinations of TLRs for their ability to mediate NF-_B activation. NF-_B activation was increased following exposure to heat killed H. pylori or H. pylori-LPS only with the TLR2/TLR10 heterodimer. These findings suggest TLR10 is a functional receptor involved in the innate immune response to H. pylori infection and that TLR2/TLR10 heterodimer possibly functions in the recognition of H. pylori-LPS.

overall_design: We have employed whole genome microarray expression profiling of gastric epithelium in H.pylori infection. We compare 1) Hp positive and negative group. 2) by gastritis grade 3) by countries.

first: Yoshio

last: Yamaoka


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

status: Public on Sep 18 2015

city: Pittsburgh

first: SungHwan

last: Kim

address: 200 Lothrop, BST W1200

institute: University of Pittsburgh

summary: These subjects were diagnosed as being controls or having interstitial lung disease (ILD) or chronic obstructive pulmonary disease (COPD) as determined by clinical history, CT scan, and surgical pathology. There was no intervention, these are cross-sectional data. All samples are from the Lung Tissue Research Consortium (LTRC) and are indexed by their LTRC tissue label.

overall_design: These are 319 total subjects, 183 have ILD and 136 have COPD, who went for surgery for the investigation of a nodule and have no chronic lung disease by CT or pathology. Each sample is total RNA extracted from flash frozen human whole lung homogenate. Between the two platforms were analyzed. Samples are titled by source (LT=LTRC), 6-digit tissue label, lobe of extraction, and major disease state.

first: N

last: Kaminski

first: J

last: Tedrow

first: B

last: Guardela

first: D

last: Schwartz


title: RNA-seq profiling of gene expression in Ezh2-deficient and control murine lung epithelial and stromal cell populations at day E16.5

status: Public on May 11 2015

city: Parkville

first: Marie-Liesse

last: Asselin-Labat

state: VIC

address: 1G Royal Parade

department: Stem Cells and Cancer

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Epithelial (CD31-CD45-EpCAM+) and stromal (CD31-CD45-EpCAM-) lung cells were derived by FACS from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ mouse embryos at day E16.5 (3 biological replicates per genotype-tissue combination). Total RNA extracted from the samples was subjected to NGS library preparation using TruSeq Stranded Total RNA with Ribo-Zero (Illumina). Completed libraries from different samples were sequenced on HiSeq 2000 TruSeq with SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility.

overall_design: RNA-seq gene expression profiles from Ezh2 deficient and control lung epithelial and stromal cell populations at day E16.5 (3 replicates per genotype-tissue combination).

first: Aliaksei

middle: Z

last: Holik


title: Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Gene expression (RNA-seq) and H3K27me3 binding (ChIP-seq) profiling of wild type and Ezh2-deficient mouse lung epithelium.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Lungs from wild type and Ezh2-deficient mice (Ezh2 deletion is specific to lung epithelium) were collected at day e16.5. Lung cells were separated into epithelial and stromal populations based on EpCAM expression. Epithelial cells were profiled for both gene expression (Total RNA-seq) and H3K27me3 binding (ChIP-seq). Additionally, stromal cells were also profiled for gene expression.

Refer to individual Series


title: ChIP-seq profiling of H3K27 tri-methylation in Ezh2-deficient and control murine lung epithelium at day E16.5

summary: Epithelial (CD31-CD45-EpCAM+) lung cells were derived by FACS from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ mouse embryos at day E16.5 (2 biological replicates per genotype). Chromatin from each of the replicates was immunoprecipitated with H3K27me3 antibody (Millipore #07-449) and subjected to NGS library preparation using TruSeq Nano DNA Sample Preparation Kit (Illumina). Completed libraries from different samples were sequenced on HiSeq 2500 TruSeq with SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility.

overall_design: ChIP-seq profiles of H3K27 tri-methylation from Ezh2 deficient and control lung epithelium (2 replicates per genotype).


title: Root transcriptome of the facultative parasitic plant Phtheirospermum japonicum

status: Public on May 31 2015

city: Yokohama

first: Juliane

middle: Karine

last: Ishida

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

institute: RIKEN

summary:
47,984 unigenes with putative coding regions with at least 50 amino acids were selected  from whole transcriptome (SAMN03271814) of Phtheirospermum japonicum
Microarray slides were hybridized with labeled cRNA from roots of 2-week-old Phtheirospermum japonicum plants growing axenically and treated with haustoria-inducer DMBQ (10 µM) for 0, 0.5, 1, 3, 6, 12, 24 and 48 h

overall_design: In this study the expression data from three biological replicates of each time-point are presented. In addition, one single biological replication of a mock-treated sample for each time-point. As a control of the background and uneven hybridization, ten probes for randomly selected fifty unrelated sequences were designed and fixed in different locations of the array

first: Y

last: Satoko


title: Gene expression responses to chronic low dose arsenite exposure

status: Public on May 05 2015

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Arsenic (As) exposure is a significant worldwide environmental health concern. Low dose, chronic arsenic exposure has been associated with higher risk of skin, lung, and bladder cancer, as well as cardiovascular disease and diabetes.  While arsenic-induced biological changes play a role in disease pathology, little is known about the dynamic cellular changes due to arsenic exposure and withdrawal.  In these studies, we seek to understand the molecular mechanisms behind the biological changes induced by chronic low doses of arsenic exposure.  We used a comprehensive approach involving chromatin structural studies and mRNA microarray analyses to determine how chromatin structure and gene expression patterns change in response to chronic low dose arsenic exposure and its subsequent withdrawal.  Our results show that cells exposed to low doses of sodium arsenite have distinct temporal and coordinated chromatin, gene expression and miRNA changes that are consistent with differentiation and activation of multiple biochemical pathways.  Most of these temporal patterns in gene expression are reversed when arsenic was withdrawn.  However, some of the gene expression patterns remained altered, plausibly as a result of an adaptive response by these cells.  Additionally, these gene expression patterns correlated with changes in chromatin structure, further solidifying the role of chromatin structure in gene regulatory changes due to arsenite exposure.  Lastly, we show that arsenite exposure influences gene regulation both at the transcription initiation as well as at the splicing level.  Thus our results suggest that general patterns of alternative splicing, as well as expression of particular gene regulators, can be indicative of arsenite-induced cell transformation.

overall_design: A total of eight (8) samples with two biological replicates under four separate conditions: wild-type treated with deionized H2O for 36 days (NT); chronic low-dose arsenic exposure of 1 uM of sodium arsenite (iAs-T) for 36 days; chronic arsenic exposure of 1 uM of sodium arsenite for 26 days followed by removal of sodium arsenite for 10 days, measured at day 36 (iAs-Rev); and chronic arsenic exposure of 1 uM of sodium arsenite for 26 days, followed by removal of sodium arsenite exposure for 10 days, followed by 1 uM of chronic sodium arsenite exposure for 10 days (measured at day 46) (iAs-Rev-T).

first: Caitlyn

last: Riedmann

first: Millie

last: Ma

first: Manana

last: Melikishvili

first: S

middle: G

last: Godfrey

first: Zhou

last: Zhang

first: Kuey

last: Chen

first: Yvonne

middle: N

last: Fondufe-Mittendorf


title: Transcriptomic and proteomic analyses of Clostridium termitidis CT1112 during growth on α-cellulose, xylan, cellobiose and xylose.

status: Public on May 01 2015

city: winnipeg

first: Riffat

last: Munir

state: MB

address: dafoe road

department: biosystems

institute: University of manitoba

summary:
High throughput “omics technologies” such as transcriptomics and proteomics provide insights into the metabolic potential of an organism and have been used to understand the genetic and the central carbon metabolism mechanisms for the production of desired end products in various cellulolytic clostridia cultured on different substrates
In this study, C. termitidis was cultured on lignocellulose derived simple and complex sugars: cellobiose, xylose, xylan and α–cellulose as sole carbon sources. 2D HPLC-MS/MS quantitative Proteomic profiles and RNA seq transcriptome profiles (next generation sequencing to identify and quantify RNA in biological samples) were analyzed to identify the genes involved in substrate degradation, cellodextrin transport and end product synthesis related genes
Identification of these genes is important in understanding the metabolic networks of C. termitidis and could be valuable engineering targets for improving biomass to biofuel production.

sample_organism: Ruminiclostridium cellobioparum subsp. termitidis CT1112

overall_design: Closridium termitidis was cultured on 2g/L each of α-cellulose, xylan, cellobiose and xylose. Samples were collected from the exponential phase. 2 replicate experiments were conducted under each substrate condition

first: Oleg

last: Krokhin

first: Dmitry

last: Shamshurrin

first: John

middle: A

last: Wilkins

first: Vic

last: Spicer

first: Xiangli

first: Nazim

last: Cicek

first: Richard

last: Sparling

first: David

middle: B

last: Levin


title: TMEM203 is a Novel Regulator of Intracellular Calcium Homeostasis and is required for Spermatogenesis

status: Public on Apr 15 2015

city: Cambridge

first: Joseph

middle: Jorge

last: Loureiro

address: 250 Massachusetts Ave 6A-144

institute: Novartis

summary: Intracellular calcium signaling is critical for initiating and sustaining diverse cellular functions including transcription, synaptic signaling, muscle contraction, apoptosis and fertilization.    Trans-membrane 203 (TMEM203) was identified here in cDNA overexpression screens for proteins capable of modulating intracellular calcium levels using activation of  a calcium/calcineurin regulated transcription factor as an indicator. Overexpression of TMEM203 resulted in a reduction of Endoplasmic Reticulum (ER) calcium stores and elevation in basal cytoplasmic calcium levels. TMEM203 protein was localized to the ER and found associated with a number of ER proteins which regulate ER calcium entry and efflux. Mouse Embryonic Fibroblasts (MEFs) derived from Tmem203 deficient mice had reduced ER calcium stores and altered calcium homeostasis.  Tmem203 deficient mice were viable though male knockout mice were infertile and exhibited a severe block in spermiogenesis and spermiation.  Expression profiling studies showed significant alternations in expression of calcium channels and pumps in testes and concurrently Tmem203 deficient spermatocytes demonstrated significantly altered calcium handling. Thus Tmem203 is an evolutionarily conserved regulator of cellular calcium homeostasis, is required for spermatogenesis and provides a causal link between intracellular calcium regulation and spermiogenesis.

overall_design: Testes were  harvested from control and Tmem203 null mice at 24 weeks of age.  4 wild type testes and 5 null mice testes were probed  using Affymetrix Mouse Genome 430 2.0 platform.

first: Mark

last: Labow

first: Prashant

last: Shambharkar

first: Somnath

last: Bandyopadhyay


title: Expression data from fatty acid and bile acid receptor agonist treated liver sinusoidal endothelial cells

status: Public on May 07 2015

city: Aurora

first: Michael

last: Edwards

state: CO

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

summary:
Liver sinusoidal endothelial cells (LSEC) are unique endothelial cell typelining the sinusoids of the liver and we have shown that these cells respond in a unique matter when exposed to saturated and unsaturated free fatty acids (FFA) and bile acids.
We used microarray to analyze the transcriptional differences between the LSEC exposed to free fatty acids and bile acid receptor agonists to further shed light on their role in non-alcoholic fatty liver disease.

overall_design: The Murine Liver Sinusoidal Endothelial Cell Line (TSEC) was treated with palmitic and oleic acid or the bile acid receptor agonist INT-767 for 8 hours. Total RNA was then harvested to determine transcriptional differences.

first: Rachel

middle: H

last: McMahan

first: Cara

last: Porsche

first: Hugo

last: Rosen


title: Expression data from root tissues of 35S:AtHMA4 and wild-type tomato plants grown in the presence of Zn

status: Public on May 08 2015

city: Warsaw

first: Maria

last: Kendziorek

address: Miecznikowa 1

department: Biology

country: Poland

institute: Uniwersity of  Warsaw

summary:
Ectopic expression of AtHMA4 in tomato modified Zn accumulation in a Zn-supply dependent manner. It suggests that HMA4-expression under a range of Zn-supply differentially modifies the expression of endogens, which contributes to different Zn-related phenotypes.
To identify genes differentially regulated in 35S:AtHMA4-expressing and wild-type tomato, the transcription profiles were compared between roots of transgenic and WT-plants grown in the presence of 5 µM Zn. An effort was undertaken to recognize tissue specific alterations underlying the difference in Zn root:shoot distribution between tested plant lines and LCM technique was used to isolate epidermis+cortex and stele from roots.Understanding the interplay between the transgene and the endogens is crucial for planning genetic modification for Zn-biofortification purpose.

overall_design: 10-day old tomato plant (35S:AtHMA4 expressing and WT) were subjected to 5 µM Zn (added as ZnSo4) for 15 days. Three independent experiments were performed. At the end of each experiment 2.0 cm long root fragments from six plants (excluding 1.5 cm long apical fragments) were pooled, embedded in NEG-50 Frozen Section Medium (Thermo Scientific), and frozen in liquid nitrogen. Total RNA isolated from three batches of roots was amplified and used for three independent microarray analysis.

last: Klimecka

first: Soren

last: Borg

first: Danuta

last: Antosiewicz


title: 35S:AtHMA4 and wild-type tomato plants grown in the presence of Zn

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

overall_design: Refer to individual Series


title: Expression data from leaf tissues of 35S:AtHMA4 and wild-type tomato plants grown in the presence of Zn

summary:
Arabidopsis HMA4 transformation facilitates Zn root-to-shoot translocation, but in Zn-supply dependent manner. It implies that distinct effects of HMA4 expression on Zn root:shoot distribution in transgenics grown under different Zn supply regimes results from the interaction between the transgene activity and the molecular background of the host plant.
Microarray analysis was performed to compare expression profiles in leaves of transgenic and WT-plants grown in the presence of 5 µM Zn to identify the molecular mechanism underlying the difference in Zn root:shoot distribution between 35S:AtHMA4-expressing and wild-type tomato. To recognize tissue specific alterations in gene transcription in tomato leaves invoked by AtHMA4 expression, spongy paerenchyma + lower epidermis and palisade paerenchyma + upper epidermis were isolated using LCM technique. Understanding the interplay between the transgene and the endogens is crucial for planning genetic modification for Zn-biofortification purpose.

overall_design: 10-day old tomato plant (35S:AtHMA4 expressing and WT) were subjected to 5 µM Zn (added as ZnSo4) for 15 days. Three independent experiments were performed. At the end of each experiment the 3rd and 4th leaf (counting upwards) were collected, 1-2 mm long and 2-3 mm wide fragments were cut out from between the vascular bundles in the middle part of each leaf, embedded in NEG-50 Frozen Section Medium (Thermo Scientific), and frozen in liquid nitrogen. Total RNA isolated from three batches of leaves was amplified and used for three independent microarray analysis.


title: Affymetrix CytoscanHD data for genomic plasticity of osteosarcoma cell lines

city: Zurich

last: Baudis

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

summary: To identify chromosomal aberrations during passaging of parental SAOS-2 osteosarcoma cells with low metastatic potential and of SAOS-2-derived LM5 cells with increased metastatic potential

overall_design: DNA of early and late passage SAOS-2 and LM5 cells was analyzed by Affymetrix Cytoscan HD genotyping arrays

first: Roman

last: Muff


title: Identification of N6-adenine methylation in C. elegans DNA

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

country: Germany

institute: Max Planck Institute for heart and lung research

summary: In mammalian cells, DNA methylation on the 5th position of cytosine (5mC) plays an important role as an epigenetic mark. However, DNA methylation was considered to be absent in C. elegans because of the lack of detectable 5mC as well as homologs of the cytosine DNA methyltransferases. Here, using multiple approaches, we demonstrate the presence of adenine N6-methylation (6mA) in C. elegans DNA. We further demonstrate that this modification increases trans-generationally in a paradigm of epigenetic inheritance. Importantly, we identify a DNA demethylase, NMAD-1, and a potential DNA methyltransferase, DAMT-1, which regulate 6mA levels and crosstalk between methylation of histone H3K4me2 and 6mA, and control the epigenetic inheritance of phenotypes associated with the loss of the H3K4me2 demethylase spr-5. Together, these data identify a novel DNA modification in C. elegans and raise the exciting possibility that 6mA may be a carrier of heritable epigenetic information in eukaryotes.

overall_design:
SMRT-sequencing for a mixed cell population of wildtype worms
6mA ChIP-Seq for a mixed cell population of wildtype worms

first: Eric

middle: L

last: Greer

first: Mario

last: Blanco

first: Erdem

last: Sendinc

first: Jianzhao

last: Liu

last: Aristizabal-Corrales

first: Chih-Hung

last: Hsu

first: L

last: Aravind

first: Chuan

last: He

first: Yang

last: Shi


title: Malaria-associated atypical memory B cells exhibit markedly reduced B cell receptor signaling and effector function

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Plasmodium falciparum malaria is a deadly infectious disease for which we have no licensed vaccine. Antibodies confer protection against malaria and individuals exposed to P. falciparum acquire protective antibodies, but only after years of repeated infections. We recently showed that malaria exposure is associated with a large expansion of a population of atypical memory B cells (MBCs) that phenotypically resemble B cell populations expanded in chronic viral infections, including HIV. At present the relationship of atypical MBCs to classical MBCs and their function are not known. We provide evidence that the expressed VH gene repertoires and somatic hypermutation rates of atypical and classical MBCs are indistinguishable, indicating the two populations are closely related developmentally. Atypical MBCs can be distinguished by their expression of multiple inhibitory receptors, including Fc receptor-like-5. B cell receptor (BCR) signaling is stunted in atypical MBCs, resulting in impaired Ca2+ mobilization, proliferation and cytokine production. Atypical MBCs do not spontaneously secrete antibodies and cannot be stimulated to differentiate into antibody-secreting cells in vitro. These results suggest that in individuals chronically exposed to malaria, atypical MBCs differentiate from classical MBCs and assume a phenotype refractory to BCR-mediated activation, potentially contributing to the inefficient acquisition of immunity to malaria.

overall_design: Comparison of human atypical B cell versus classical B cell versus naïve B cell.

first: Silvia

last: Portugal

first: Christopher

last: Tipton

first: Hae

middle: W

last: Sohn

first: Younoussou

last: Kone

first: Jing

last: Wang

first: Shanping

last: Li

first: Jeff

last: Skinner

first: Kimmo

last: Virtaneva

first: Daniel

first: Steve

last: Porcella

first: Ogobara

last: Doumbo

first: Safiatou

first: Kassoum

last: Kayentao

first: Aissata

last: Ongoiba

first: Boubacar

last: Traore

first: Ignacio

last: Sanz

first: Susan

last: Pierce

first: Peter

middle: D

last: Crompton


title: Antagonizing miR-128 abrogates chemoresistance-associated metastasis and is therapeutic in non-small cell lung cancer [miRNA]

status: Public on Apr 10 2015

city: Guangzhou

first: junchao

last: Cai

address: zhongshan er road

country: China

institute: Sun-yat sen university

summary: This experiment is designed to screen miRNAs that are deregulated during chemoresistance-associated metastasis of lung cancer cells. Chemoresistant metastatic in vivo tumor model of A549-luc-Vector cells was established after four rounds of cisplatin (CDDP) treatments compared to corresponding control solvent treatments. Upon examining profiles of miRNA expression differential between tumor-derived cultured cells from the Ctrl-4th and CDDP-4th treatments, most markedly upregulated and downregulated miRNAs in chemoresistant, metastatic A549-luc-CDDP-4th cells were identified.

overall_design: In order to establish a chemoresistant in vivo tumor model, after inoculation of A549-luc-Vector cells, cisplatin (CDDP) or control solvent was intraperitoneally (i.p.) injected six rounds in a two-week period and cells were isolated from corresponding resultant tumors, cultured and re-transplanted into syngeneic mice to receive the next round of treatment. In our experimental model, human lung cancer xenografts developed chemoresistance in the third round of CDDP treatment (CDDP-3rd) and chemoresistance-associated metastases following the fourth round of treatment. Tumor-derived cultured cells from Ctrl-4th and CDDP (cisplatin)-4th treatment were subjected to miRNA array (Agilent-031181 human miRNA (8*60k) V16.0) analysis, with two biological replications for each treatment.

first: Junchao

first: Mengfeng


title: Antagonizing miR-128 abrogates chemoresistance-associated metastasis and is therapeutic in non-small cell lung cancer

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


title: Emerging genomic assays for identification of chikungunya virus infection in asymptomatic blood donors from Puerto Rico, 2014

status: Public on Mar 25 2015

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

summary: The Virochip microarray (version 5.0, Viro5AGL-60K platform) was used to verify the presence or absence of Chikungunya virus in RNA extracts from asymptomatic blood donors located in Puerto Rico.

overall_design: We used the Virochip microarray as secondary verification of Chikungunya positive and negative samples.

first: Guixia

last: Yu

first: Samia

last: Naccache

first: Deanna

last: Lee

first: Jacob

last: Pfeil


title: Antagonizing miR-128 abrogates chemoresistance-associated metastasis and is therapeutic in non-small cell lung cancer [mRNA]

summary: This experiment is designed to evaluate gene expression alteration and significant pathway(s) following miR-128 transduction in A549 lung cancer cells. We find several significant pathways, including the Wnt/β-catenin signaling and TGF-β signaling activated by miR-128 overexpression.

overall_design: Total RNA were extracted from A549 lung cancer cells stably transduced with miR-128 precursor or vector control and subjected to mRNA microarray (Agilent-014850 Whole Human Genome Microarray 4x44K) analysis, with two biological replications for each treatment.

last: Li


title: Broad spectrum antibodies to self-antigens and cytokines in RAG deficiency

status: Public on Jul 08 2015

city: Stanford

last: Rosenberg

address: 269 Campus Drive, CCSR 2240

institute: Stanford

summary: Overall, this work describes the largest cohort of patients with RAG mutations and an associated phenotype consisting of combined immunodeficiency and granulomatous lesions and/or autoimmunity (CID-G/AI). By using multiple methods (microarray, ELISA and multiplex bead technology), we have consistently identified a distinctive signature of anti-cytokine antibodies in patients with RAG-dependent immunodeficiencies, especially in those with CID-G/AI and a history of severe viral infections. These autoantibodies were not detected in a large panel of patients with other forms of primary immunodeficiency, and may therefore represent a novel biomarker panel of this condition.

sample_organism:
Homo sapiens
synthetic construct

overall_design: Known autoantigens, cytokines, chemokines, growth factors and receptors were printed onto microarrays. All targets were printed in triplicate. Arrays were probed with diluted plasma and autoantibodies were detected with a AF647 conjugated anti-human IgG secondary.

first: Jolan

last: Walter


title: Prenatal Exposure to DEHP Affects Spermatogenesis and Sperm DNA Methylation in a Strain-Dependent Manner

status: Public on Mar 24 2015

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

institute: University of Geneva

summary: We investigated the impact of prenatal exposure to DEHP on spermatogenesis and DNA sperm methylation in F1 mice strains FVB/N and C57BL/6J. Prenatal exposition was performed orally on mothers with 300 mg/kg/day of DEHP from gestation day 9 to 19. 20 sperm-extracted DNA samples of males born from DEHP-treated and control mothers were analysed by MBD-seq at NXT-DX company.

overall_design: We test 22480 probes of 2.2kb size ranging from 2kb upstream to 200bp downstream of the start of genes in quintuplicates comparing controls to DEHP conditions in both strains.

first: Ludwig

last: Stenz

first: Emmanuel

last: Somm

first: Christelle

last: Stouder

first: Alexandre

last: Dayer

first: Ariane

last: Giacobino


title: Expression data of human neuroblastoma SK-N-AS treated with the PLK1 inhibitor GSK461364

status: Public on Mar 21 2015

city: Essen

first: Sven

last: Lindner

address: Hufelandstraße 55

institute: University Hospital Essen

summary: Polo-Like Kinase 1 (PLK1), a serine/threonine kinase involved in cell cycle regulation at the G2/M transition, is associated with high-risk neuroblastoma (NB) and unfavorable patient outcome. Recently, we and others demonstrated that PLK1 is a potential drug target in neuroblastoma and reported antitumoral actvity of the PLK1 inhibitor BI2536 in preclinical models of NB. We here analyzed the effects of the ATP-competitive PLK1 inhibitor GSK461364 on typical tumorigenic properties of preclinical in vitro and in vivo models of NB. Treatment of NB cells with GSK461364 resulted in decreased cell viability and reduction of proliferative capacity, and led to cell cycle arrest and massive induction of apoptosis. These phenotypic consequences were observed at low-dose nanomolar levels and were independent of the MYCN copy number status of the cell lines. In vivo treatment with GSK461364 led to a strong delay in tumor development and to a highly significant increase in survival in the treatment group. These preclinical findings highlight the promise of PLK1 inhibitors as novel agents for NB and serve as rationale to move forward with early phase clinical trials in children.

overall_design: Three biological samples of the human neuroblastoma cell line SK-N-AS were treated with DMSO or GSK461364 [1 nM]

first: Johannes

last: Schulte


title: miRNA profiles of tubular cells (Rodent A and Rodent B)

status: Public on Mar 17 2015

city: Osaka

first: Kosuke

last: Endo

address: 5-7-1 Fujishirodai, Suita

department: Dept. of Genomic Medicine

institute: National Cerebral and Cardiovascular Center

summary: MicroRNAs (miRNAs) are endogenous small RNAs of 18–23 nucleotides that regulate gene expression. Recently, plasma miRNAs have been investigated as biomarkers for various diseases. In the present study, we assessed whether the miRNA expression profiles of tubular tissues could discriminate proximal tubule injury and diagnose acute kidney injury (AKI) and the renal tubular dysfunction without morphological changes.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: rat RNA from various tissues (kidney, pancreas, salivary gland, prostate, lacrimal gland, lung, bile duct, liver, heart, skeletal muscle, spleen, small intestine, bronchial gland, mammary gland, intestinal villus, proximal tubule and glomerulus) were used. The bronchial gland, mammary gland, intestinal villus, proximal tubule and glomerulus were isolated from tissue sections using laser microdissetion (LMD). Expression profiling of rodent miRNAs was performed using the ABI TaqMan Rodent MicroRNA Array kit (Card A & B; Applied Biosystems, CA, USA) according to the manufacturer’s instructions. LMD samples were pre-amplified 12 cycles. The ABI Prism 7900 HT Sequence Detection System (Applied Biosystems) was used for amplification and detection. Ct values were obtained from the amplification plot using the SDS software (Applied Biosystems).

first: Naoko

last: Kito

first: Masahiro

last: Ikesue

first: Huachun

last: Weng

first: Naoharu

last: Iwai


title: miRNA profiles of tubular cells

overall_design: Human RNA from various tissues (brain, pancreas, kidney, lung, salivary gland, trachea, colon, prostate, liver, heart, skeletal muscle, spleen, proximal tubule and mesangial cell) were used. Expression profiling of 377 human miRNAs was performed using the ABI TaqMan Human MicroRNA Array kit (Card A; Applied Biosystems, CA, USA) according to the manufacturer’s instructions. The ABI Prism 7900 HT Sequence Detection System (Applied Biosystems) was used for amplification and detection. Ct values were obtained from the amplification plot using the SDS software (Applied Biosystems).


title: Transcriptomic profiling of a heme-deficient mutant (hemA) of Escherichia coli after addition of CORM-3 and inactive CORM-3 (iCORM-3).

status: Public on Apr 01 2015

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

summary:
Wild type and hemA strains of Escherichia coli MG1655 were grown under anaerobiosis in batch culture in custom-made, stirred (200 rpm) 250 ml mini-fermenter vessels at 37 °C during continuous sparging with 100 % nitrogen gas. Cells were grown in defined medium (pH 7.0) containing  0.5 % glucose as the sole and limiting source of energy and carbon. The medium was supplemented with 0.1 % casamino acids and 5 % LB to support the growth of the hemA mutant. For maintenance of the hemA mutation, 50 mg/ml kanamycin were added to cultures of the heme-deficient mutant only. CORM-3 (final concentration of 100 uM) was added to wild type and mutant cultures at an OD600 of 0.2. iCORM-3 (final concentration of 100 uM) was added to only mutant cultures at an OD600 of 0.2.
Samples were taken immediately prior to the addition of CORM-3 or iCORM-3 and at consecutive time-points thereafter (10, 20, 40, 60 and 120 min) for microarray analysis. Cells were harvested directly into phenol:ethanol to stabilise RNA and total RNA was purified using Qiagen’s RNeasy Mini Kit, according to the manufacturer's instructions.

overall_design: Time-course experiments with samples taken immediately prior to or 10, 20, 40, 60 and 120 min after addition of 100 uM CORM-3, or 100 uM iCORM-3 for the hemA mutant only, under 100 % anaerobiosis; 2 independent biological experiments were performed for each condition with 2 technical (dye swap) repeats per biological experiment.

first: Jayne

last: Wilson


title: Identification of genes regulated during passaging of mouse osteosarcoma cell lines

status: Public on Mar 10 2015

first: Ram Mohan

last: Ram Kumar

address: Forchstrasse 340

department: Orthopaedics

institute: University Hospital Balgrist, University of Zurich, Zurich, Switzerland

summary: To identify the genes that are regulated during passaging of the parental mouse Dunn osteosarcoma cells with low metastatic potential and Dunn-derived LM8 cells with increased metastatic potential, we performed global gene expression profiling in early and late passage cells.

overall_design: Total RNA was extracted from early and late passage cells cultured in three independent replicates for each condition. Cy3-labeled cRNA was synthesized and hybridized to Agilent mouse 4 x 44K microarrays. Raw data, obtained after array image analysis were normalized and used to retrieve differentially expressed genes in early and late passage cells.

first: Roman

last: Muff

first: Prisni

last: Rath

first: Ram

first: Maria

middle: R

last: Lecca

first: Knut

last: Husmann

first: Walter

last: Born

first: Michael

last: Baudis

first: Bruno

last: Fuchs


title: Identification of genes regulated during passaging of human osteosarcoma cell lines

summary: To identify the genes that are regulated during passaging of the parental osteosarcoma cells SAOS-2 and HOS with low metastatic potential, and SAOS-2-derived LM5 cells and Ki-ras transformed HOS cells (143B) with increased metastatic potential, we performed global gene expression profiling in early and late passage cells.

overall_design: Total RNA was extracted from early and late passage cells cultured in three independent replicates for each condition. Cy3-labeled cRNA was synthesized and hybridized to Agilent human 8 x 60K microarrays. Raw data, obtained after array image analysis were normalized and used to retrieve differentially expressed genes in early and late passage cells.

middle: M


title: Identification of genes regulated during passaging of human and mouse osteosarcoma cell lines

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Achilles Heels of Senescent Cells: From Transcriptome to Senolytic Drugs

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

institute: Boston University

summary:
The healthspan of mice is enhanced by selectively killing senescent cells using a transgenic suicide gene. Achieving the same using small molecules would have a tremendous impact on quality of life and burden of age-related chronic diseases.
As senescent cells resist apoptosis, we used microarrays to identify transcripts and pathways that differ between senescent and non-senescent preadipocytes, and might be involved in resistance to apoptosis.

overall_design: Primary human abdominal subcutaneous preadipocytes were isolated from  8 healthy lean kidney donors. All subjects were matched by age,gender and BMI. The protocol was approved by the Mayo Clinic Foundation Institutional Review Board for Human Research. Preadipocytes were radiated at 10 Gy to induce senescence or were sham-radiated. From senescent cells RNA was isolated 20 days after irradiation.

first: James

last: Kirkland

first: Tamar

last: Tchkonia


title: Mapping of genome-wide DSBs in HEK293T cells using the RAFT procedure.

status: Public on Mar 05 2015

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: Large DNA fragments (mainly of 50-250 kb, denoted as forum domains) were isolated inside agarose plugs as described below in the extract protocol section. After ligation of 5'-bio-oligos to the blunt DNA termini the digestion with Sau3A enzyme was performed followed by selection of genome-wide preparation of forum domains termini on streptavidin-paramegnetic particles. After ligation of Sau3A adapter the termini were PCR amplified and used for deep sequencing.

overall_design: Mapping of Double-Strand DNA Breaks/Forum Termini

first: Yuri

last: Kravatsky


title: Expression analysis of effect of Intestine-specific knockdown of KLF5 on radiation induced intestinal injury

city: Suzhou

first: Ming

last: Li

address: No. 199 Ren'ai Road

institute: Soochow University

summary: The objective was to determine the role of Krüppel-like factor 5 (KLF5) in radiation-induced intestinal injury. Mice with intestinal-specific knockdown of KLF5 (Cre+ mice) were generated and their response to radiation was compared with controls (Cre- mice). Mice were given 15 Gy total body irradiation (TBI). The mice intestines were harvested at 6h post TBI and screened for differentially expressed genes by microarray analysis. We identified 11,004 and 2,466 differentially expressed genes in non-irradiated and irradiated mice at 6h post TBI, respectively. KLF5 knockdown down-regulated genes related to DNA damage repair pathways such as nucleotide excision repair, mismatch repair, non-homologous end joining and the Fanconi anemia pathway, which may suggest a novel function of KLF5.

overall_design: A four chip study using total RNA recovered from four pooled intestine tissues of four experimental groups. The four experimental groups respectively were the 6h-cre+ group, 6h-cre- group, con-cre+ group and con-cre- group. Equal mass amounts of total RNA were pooled from each small intestine to yield a sample representing RNA from 3 separate mice in each group. One pooled sample in every group were tested with one chip. Each chip measures the expression level of 44,170 genes from C57BL/6 mouse (background) with three 60-mer probe pairs per gene.

first: Xueguang

last: Zhang


title: Mouse mammary epithelial and stromal cells: Hormone Treated vs. Vehicle Control

status: Public on Feb 19 2015

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

institute: Ontario Institute for Cancer Research

summary: Transcriptional profiling of different mouse mammary cellular compartments (basal, luminal and stromal) under define hormone treatments: estrogen, progesterone, estrogen plus progesterone and the vehicle control. Goal was to determine the effect of ovarian hormones on mammary cellular compartment gene expression.

overall_design: Four-condition experiment within each cellular compartment. vehicle vs. estrogen, progesterone and estrogen plus progesterone. Biological replicates: 3 vehicle control, 4 estrogen treatment, 3 progesterone treatment, 4 estrogen plus progesterone treatment in each epithelial  compartment (luminal, basal). 3 vehicle control, 3 estrogen, 3 progesterone, 3 estrogen plus progesterone in the stromal compartment.

first: Rama

last: Khokha

first: Purna

last: Joshi

first: Alexander

last: Beristain


title: Gene expression analysis of PANC-1 cells inducibly expressing the bHLH protein E47

status: Public on Apr 20 2015

city: La Jolla

first: Pamela

last: Itkin-Ansari

address: 9500 Gilman Drive, MC0816

department: Pediatrics

institute: University of California, San Diego

summary: Analysis of induced E47 expression on PDA cells at the gene expression level.The hypothesis tested in the present study was that PDA cells can be reprogrammed to revert to their original quiescent acinar cell phenotype by stimulating a tamoxifen inducible form of E47 fused to a modified estrogen (E47-ER) receptor . Results provide important information on the remarkable ability of E47ER to trigger reactivation of the acinar cell differentiation program and cell cycle arrest in PDA cells.

overall_design: PANC-1 cells stably expressing a tamoxifen inducible form of the bHLH protein E47 were treated with tamoxifen at 2 doses to induce E47 activity


title: Micro-RNAs expressed in oligometastases inhibit genes involved with adhesion, invasion and motility

status: Public on Mar 01 2015

city: Chicago

first: Ralph

last: Weichselbaum

state: IL

address: 5841 S. Maryland Avenue, MC 9006

department: Radiation & Cellular Oncology

institute: University of Chicago

summary: Analysis of MDA-MB-231 cells 48 hours after transfection with non-targeting control, micro-RNA mimics or corresponding micro-RNA inhibitor. The hypothesis tested was that micro-RNAs previously identified as expressed in oligometastatic patients' metastases at a higher level than polymetastatic patients' metastases suppress genes regulating adhesion, motility, invasion and growth. Results showed that multiple micro-RNAs can suppress multiple genes involved in these pathways.

overall_design: Total RNA was obtained from MDA-MB-231 cells after transfection with micro-RNA mimic,  micro-RNA inhibitor, or non-targeting control MB231, performed in duplicate

first: Abhineet

last: Uppal

first: Sean

middle: C

last: Wightman

first: Stephen

last: Mallon

first: Go

last: Oshima

middle: P

last: Pitroda

first: Xiaona

last: Huang

first: Thomas

middle: E

last: Darga

first: Lei

first: Jorge

last: Andrade

first: Huiping

last: Liu

first: Mark

middle: K

last: Ferguson

first: Mitchell

last: Posner

first: Samuel

last: Hellman

first: Geoffrey

last: Greene

first: Nikolai

last: Khodarev


title: BolA is a transcriptional switch that turns off motility and turns on biofilm development

city: Oeiras

first: Cecilia

middle: M.

last: Arraiano

address: Av. Republica, Apt 127

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica (ITQB) / Univ. Nova de Lisboa

summary: Bacteria are extremely versatile organisms which rapidly adapt to changing environments. When Escherichia coli cells switch from planktonic growth to biofilm, flagellum formation is turned off, and the production of fimbriae and extracellular polysaccharides is switched on. Here we show that BolA protein is a new bacterial transcription factor which modulates the switch from planktonic to sessile lifestyle. BolA negatively modulates flagella biosynthesis and thus swimming capacity. Furthermore, BolA overexpression favors biofilm formation and involvesinvolving fimbriae-like adhesins and curli production. Our results unraveled for the first time that BolA is a protein with high affinity to DNA, involved in the regulation of several genes of E. coli at a genome-wide scale level. Moreover, this observation further demonstrated that the most significant targets of this protein involved a complex network of genes encoding proteins extremely necessary in biofilm development processes. Herein we propose that BolA is a motile/adhesive transcriptional switch, specifically involved in the transition between the planktonic and the attachment stage of biofilm formation process.

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

overall_design: In the study presented here mRNA levels were analyzed in 2 different strains with different levels of BolA protein. Samples were measured at two differet growth phases and include 3 replicates of each.

first: Clémentine

last: Dressaire

first: Ricardo

last: Moreira

first: Susana

last: Barahona

first: António

last: Alves de Matos

first: Cecília


title: Gene expression profiling of sequential metastatic biopsies for biomarker discovery in breast cancer

status: Public on Apr 14 2015

city: Stockholm

first: John

last: Lövrot

address: Cancer Center Karolinska

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

summary:
The feasibility of longitudinal metastatic biopsies for gene expression profiling in breast cancer is unexplored. Dynamic changes in gene expression can potentially predict efficacy of targeted cancer drugs.
Patients enrolled in a phase III trial of metastatic breast cancer with sunitinib combined with docetaxel (SU+DOC) versus docetaxel alone (DOC) were offered to participate in a translational substudy comprising longitudinal fine needle aspiration biopsies (FNAB) and positron emission imaging before (T1) and two weeks after start of treatment (T2). Aspirated tumor material was used for microarray analysis, and treatment-induced changes (T2 versus T1) in gene expression and standardized uptake values were investigated.
Twenty-one patients were included in the docetaxel ± sunitinib trial at Karolinska and 18 of them agreed to participate in the substudy. Of the 18 women enrolled, 8 were randomly assigned to SU+DOC and 10 to DOC. Metastatic FNAB were carried out in 17 of the 18 patients at both time points with no complications reported. Representative tumor material, sufficient for RNA extraction was obtained in 15 patients at T1 and 14 patients at T2. Matched samples both at T1 and T2 were obtained for 14 subjects, 7 in each arm.
The main objective was to determine whether gene expression profiling is feasible using sequential, intra-patient FNAB. Secondary objectives were to identify potential biomarkers of early response by gene expression and/or functional imaging and to explore drug action in vivo by changes in gene expression.

overall_design:
A Karolinska substudy of the docetaxel ± sunitinib phase III clinical trial utilising sequential metastatic fine needle aspiration biopsies (FNAB) and 18-F-2-fluoro-2-deoxyglucose positron emission tomography/computed tomography (FDG PET/CT).
In brief, the randomized docetaxel ± sunitinib trial compared sunitinib combined with docetaxel (SU+DOC) versus docetaxel alone (DOC), as first line therapy in patients with HER2 negative metastatic breast cancer. Patients in the exploratory substudy were subjected to baseline FDG PET/CT assessment, followed by FNAB of one tumor lesion prior to start of treatment (Time point T1). FDG PET/CT and FNAB were repeated at Day 14 ± 1 (Time point T2) when sunitinib has achieved steady state.

first: Theodoros

last: Foukakis

first: Patricia

last: Sandqvist

first: Hanjing

last: Xie

first: Linda

middle: S

last: Lindström

first: Carla

last: Giorgetti

first: Hans

last: Jacobsson

first: Elham

last: Hedayati

first: Jonas

last: Bergh


title: Complete genome sequence of Vibrio parahaemolyticus CHN25 and transcriptomic analysis of cold shock proteins of VpaCspA and VpaCspD in the adaptation of low temperature growth

status: Public on Feb 18 2015

city: Shanghai

first: Lanming

last: Chen

address: 999 Hu Cheng Huan Road

department: College of Food Science and Technology

institute: Shanghai Ocean University

summary: To investigate low-temperature tolerance of the bacterium, three in-frame gene deletion mutants of VpacspA and VpacspD were constructed using homologous recombination method. When compared to the wild type strain, the growth of ΔVpacspA mutant was strongly repressed at 10 0C, whereas the deletion of VpacspD gene greatly activated the bacterium growth at the low temperature. Transcriptome data revealed that 12.4% of the expressed genes in V. parahaemolyticus CHN25 was significantly changed in ΔVpacspA mutant grown at 10 0C, including those involved in amino acid degradation, ATP-binding cassette (ABC) transporters, secretion systems, sulfur and glycerophospholipid metabolisms, whereas the low temperature elicited 10.0% of the genes from ΔVpacspD mutant, such as phosphotransferase system, nitrogen and amino acid metabolisms. Moreover, the major changed metabolic pathways in dual-gene deletion mutant (ΔVpacspAD) differed radically from those in single-gene mutants. Comparison of transcriptome profiles further revealed a number of differentially expressed genes shared among the three mutants, as well as regulators specifically, coordinately and or antagonistically regulating in the adaptation of V. parahaemolyticus CHN25 to the low-temperature growth.

overall_design: mRNA profiles of mid-log phase WT(G), ΔVpacspA, ΔVpacspD and ΔVpacspAD at 10 °C were generated by deep sequencing using Illumina HiSeq 2500

first: Chunhua

last: Zhu

first: Boyi

last: Sun


title: Myeloid cell derived inducible nitric oxide synthase suppresses M1 macrophage polarization

status: Public on Feb 02 2015

city: manhattan

first: Geming

last: Lu

state: New York

address: 1425 madison ave

institute: mount sinai school of medicine

summary: Analysis of gene expression between WT and iNOS defecient M1 macrophage

overall_design: RNA microarray was performed using RNA isolated from M1 polarized macrophages from WT and iNOS deficient mice stimulated with LPS/IFNγ for 6 hours. Total RNA was extracted using a RNeasy plus kit (QIAGEN, Valencia, CA), and the array was performed on an Illumina MouseRef-8 v2.0 expression beadchip (Illumina, USA) by the Genomics Core Facility at the Mount Sinai School of Medicine.


title: LDLR-/- mice aorte: Control vs DHA

status: Public on Jan 10 2015

city: Saint-Genès-Champanelle

first: Cécile

last: Gladine

address: Centra INRA de Clermont-Ferrand/Theix

department: Human Nutrition

institute: INRA

summary: The omega-3 fatty acid docosahexaenoic acid (DHA) has potent anti-atherogenic properties but its mechanisms of action at the vascular level remain poorly explored. Knowing the broad range of molecular targets of omega-3 fatty acids, microarray analysis was used to open-mindedly evaluate the effects of DHA on aorta gene expression in LDLR-/- mice and better understand its local anti-atherogenic action . Mice were fed an atherogenic diet and received daily oral gavages with oils rich in oleic acid or DHA. Bioinformatics analysis of microarray data first identified inflammation and innate immunity as processes the most affected by DHA supplementation within aorta. More precisely, several down-regulated genes were associated with the inflammatory functions of macrophages (e.g. CCL5, CCR7), cell movement (e.g. ICAM-2, SELP, PECAM-1), and the major histocompatibility complex (e.g. HLA-DQA1, HLA-DRB1). Interestingly, the expression of several genes were identified as specifc biomarkers of macrophage polarization and their changes suggested a preferential orientation towards a M2 reparative phenotype. This observation was supported by the upstream regulator analysis highlighting the involvment of three main regulators of macrophage polarization, namely PPARγ (z-score=2.367, p=1.50x10-13), INFγ (z-score=-2.797, p=2.81x10-14) and NFκB (z-score=2.360, p=6.32x10-9). Moreover, immunohistological analysis of aortic root revealed an increased abundance of Arg1 (+111%, p=0.01), a specific biomarker of M2 macrophage.The present study showed for the first time that DHA supplementation during atherogenesis is associated with protective modulation of inflammation and innate immunity pathways within aorta putatively through the orientation of plaque macrophages towards a M2 reparative phenotype.

overall_design: Mice (LDLR-/-) Aorta samples. 2 groups: Control (K), DHA (C). Biological replicates=8. Dye switch.

first: Monika

last: Zmojdzian

first: Laurie

last: Joumard-Cubizolles

first: Marie-Anne

last: Verny

first: Blandine

last: Comte

first: Andrzej

last: Mazur


title: Analysis of gene expression profiles from the liver of rats treated with the mitochondrial electron transport chain complex III inhibitor GSK932121A (50mg/kg) or vehicle control

status: Public on Jan 29 2015

city: London

first: Ashley

last: Broom

address: Du Cane Road

institute: Imperial College London

summary: BACKGROUND: Correlating in vitro mitochondrial data to outcomes in vivo remains a challenge and improving methods to assess mitochondrial function in vivo would both guide safer candidate selection and support the growing number of discovery programmes targeting mitochondria for pharmacological intervention. OBJECTIVES: The aim was to assess the toxicity profile of a compound with complex III electron transport chain inhibitory activity (GSK932121A) in order to identify markers and mechanisms of mitochondrial perturbation in vivo. METHODS:Crl:CD(SD) rats were dosed IP with GSK932121A for up to 5 hours depending upon the severity of observed clinical signs. Respirometry, microscopy, lactate/pyruvate and transcriptomics profiling were used to aid identification of a mode of action and this data was compared with functional data in isolated mitochondria. RESULTS AND DISCUSSION: GSK932121A administered in vivo caused hypothermia and a metabolic shift in energy production provoking an increased lactate/pyruvate ratio, microvesicular steatosis and glycogen depletion; alongside gene expression changes indicative of a fasted state. Our data improves current understanding of the toxicological consequences of drug induced respiratory chain inhibition and guides endpoint selection for future investigative safety studies with mitochondrially active molecules.

overall_design: 50mg/kg GSK932121A treated rat livers (n=10) were used to assess differential gene expression when compared with 0mg.kg GSK932121A Vehicle Control (n=12). Two samples were excluded from the 50mg/kg group due to low plasma exposure to GSK932121A

middle: J

first: Jon

last: Lyon


title: Distinct gene signatures define pathogen- versus diet-induced atherosclerosis development

status: Public on Jan 06 2015

first: Boston University

last: Microarray and Sequencing Resource

department: Microarray and Sequencing Resource

summary: The goal of this study was to define gene expression profiles in aortic tissue in response to three pro-atherogenic stimuli at two time points. We identified gene expression profiles induced by oral P.gingivalis (Pg), intranasal C. pneumoniae (Cp), and Western diet (WD) at acute (1 day after last infection, Pg, Cp, and control groups) and chronic (9 weeks after last infection, Pg, Cp, and control groups; WD for 9 weeks) time points in aortas of Apolipoprotein E (Apoe-/-) mice. 3 replicates per group were analyzed. RNA was analyzed using Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA).

overall_design: Total RNA  from aortic tissue of  Apoe-/- mice  treated with P. gingivalis, C. pneumoniae,  or fed a Western diet  were compared to controls at acute and chronic time points.

first: Carolyn

last: Kramer

first: Ellen

last: Weinberg


title: Genome-wide identification of microRNAs and their targets involved in the phyB-mediated light signaling pathway in rice

status: Public on Jan 01 2015

city: Jinan

first: Xiao Hui

last: Xu

address: No. 202, Gongyebei Road

institute: Shandong Academy of Agricultural Sciences

summary: Phytochrome B (phyB), one member of phytochrome family in rice, plays important roles in regulating a range of developmental processes, and stress responses. However, little information about the mechanism involved in phyB-mediated light signaling pathway has been reported in rice. Another, it has been well-known that microRNAs (miRNAs) perform important roles in plant development and stress responses. Thus it is intriguing to explore the role of miRNAs in phyB-mediated light signaling pathway in rice. In this study, comparative high-throughput sequencing and degradome analysis were adopted to identify candidate miRNAs and their targets that participate in phyB-mediated light signaling pathway. A total of 838 known miRNAs, 663 novel miRNAs and 1,957 target genes were identified from wild-type (WT) and phyB mutant. Among them, 135 miRNAs showed differential expression, suggesting that the expressions of these miRNAs are under the control of phyB. In addition, 32 out of the 135 differentially expressed miRNAs were detected to slice 70 genes in rice genome. Analysis of these target genes showed that members of various transcription factor families constitute the largest proportion, indicating miRNAs are probably involved in phyB-mediated light signaling pathway mainly via regulating the expression of transcription factors. This study presented a comprehensive expression analysis of miRNAs and their targets that might be involved in phyB-mediated light signaling pathway for the first time. The results provide new clues for functional characterization of miRNAs in phyB-mediated light signaling pathway, which would be helpful in comprehensively uncovering molecular mechanism of phytochrome-mediated photomorphogenesis and stress responses in plant.

overall_design: Examination of miRNA profiles in wild type (WT) and phyB mutant at four-leaf stage by deep sequencing using Illumina Hiseq2500.

first: Xian-zhi

last: Xie

first: Xiao


title: SRC family kinases are involved in the regulation of CD20

status: Public on Dec 31 2014

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

institute: Warsaw University of Life Sciences

summary: CD20 is an integrate membrane protein expressed on the surface of normal and malignant B-cells. It is an excellent molecular target for monoclonal antibodies (mAbs) that are widely used in the treatment of non-Hodgkin’s lymphomas (NHL) and chronic lymphocytic leukemia (CLL). Anti-CD20-directed therapies are the most effective, successful and widely used therapeutic monoclonal antibodies, routinely incorporated into all phases of conventional treatment, including first-line, maintenance and salvage treatment. Nonetheless, the overall response rates to treatment have been reported to be 46-67% for rituximab, and in patients relapsing after initial rituximab treatment the response rate is ~40%. A number of mechanisms have been proposed to account for this inefficiency, including modulation of surface CD20 levels, occurring due to both transcriptional and posttranscriptional regulations. Our observations strongly imply that the observed CD20 down-regulation relies on transcriptional mechanism and delineate new perspectives in the field of CD20 regulation.   Since many of the new therapeutic agents selectively inhibit specific signaling pathways, combining the compounds that target different mechanisms of cell growth and survival is a particularly attractive approach. However, optimal combinations of novel treatment modalities with already existing ones should take into account potential ”off-target” activity yet to be identified that could unexpectedly result in high toxicity  and/or impaired outcomes of treatment

overall_design: Dye-swap experiment, Raji cells were treated with 100 nM dasatinib or 10 µM PP2 and then hybridized on microarray.

last: Winiarska

first: Kamil

last: Bojarczuk

first: Beata

last: Pyrzynska

first: Jacek

last: Bil

first: Marta

last: Siernicka

first: Nina

last: Miazek

first: Piotr

last: Zapala

first: Michal

last: Dwojak

first: Malgorzata

last: Bobrowicz

first: Agnieszka

last: Zagozdzon

last: Krol

first: Aleksandra

last: Syta

first: Paulina

last: Podszywalow-Bartnicka

first: Anna

last: Dabrowska-Iwanicka

first: Przemyslaw

last: Juszczynski

first: Dimitar

last: Efremov

first: Jakub

last: Golab


title: High throughput analysis of three human adipose cell lines PAZ6, SGBS and SW872

city: Doha

first: Andrea

last: Guennoun

address: PO Box 24144

department: Genetic Medicine

country: Qatar

institute: Weill Cornell Medical College in Qatar

summary: We report molecular characterization of human brown and white adipocytes. We showed that PAZ6 and SW872 cells exhibit classical molecular and phenotypic markers of brown and white adipocytes, respectively. However, SGBS cells presented a versatile phenotype of adipocyte

overall_design: Sequencing of three human adipocytes cell lines (SGBS, SW872 and PAZ6) in undifferentiated and differentiated stages.

last: Worschech

first: Melissa

last: Kazantzis

first: Remy

last: Thomas

first: Martin

last: Wabitsch

first: Daniel

last: Tews

first: Mouaadh

last: Abdelkarim

first: Vladimir

last: Zilberfarb

first: A

last: Strosberg

first: Lotfi

last: Chouchane


title: Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation

status: Public on Dec 18 2014

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

department: Bioinformatics

institute: BGI-SHENZHEN

summary: Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.

overall_design:
Two Pacific oysters were used for methylome profiling in this study. One is an inbred oyster (05x7-T-G4-1.051#20) that was produced by four generations of sister-brother mating (coefficient of inbreeding, F = 0.59) and has been used for whole genome-sequencing. The other was a wild oyster collected from Weihai, Shandong Province, China. Both oysters were about two years of age. The inbred oyster was produced as single oysters and cultured intertidally at southern Puget Sound, Washington, USA, where the water temperature ranges from 7 to 16 °C. The wild oyster was an attached oyster from an oyster farm in its native range at Weihai, China, where the water temperature ranges from 4 to 27 °C.

For DNA from each of the two individuals, we constructed two independent libraries. For each library, 5 µg genomic DNA mixed with 25 ng cl857 Sam7 Lambda DNA was fragmented by sonication with a Covaris S2 system (Covaris, MA) to a mean size of approximately 250 bp. End-repair, 3’-end dA addition and adapter ligation were subsequently performed. Methylated adapters were used according to the manufacturer’s instructions (Illumina). The bisulfite conversion of DNA was performed according to a modified NH4HSO3-based protocol and amplified with nine cycles of PCR. All libraries were subjected to 90-bp paired-end sequencing on an Illumina HiSeq 2000 platform.

first: Xiaotong

last: Wang

first: Qiye

last: Li

first: Jinmin

last: Lian

first: Li

first: Lijun

last: Jin

first: Huimin

last: Cai

first: Fei

last: Xu

first: Haigang

last: Qi

first: Linlin

last: Zhang

first: Fucun

last: Wu

first: Jie

last: Meng

first: Huayong

last: Que

first: Xiaodong

last: Fang

first: Ximing

last: Guo

first: Guofan


title: Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature

status: Public on Dec 17 2014

first: Samantha

last: Thomas

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

summary: Renewable in vitro cell cultures, such as lymphoblastoid cell lines (LCLs), have facilitated studies that contributed to our understanding of genetic influence on human traits. However, the degree to which cell lines faithfully maintain differences in donor-specific phenotypes is still debated. We have previously reported that standard cell line maintenance practice results in a loss of donor-specific gene expression signatures in LCLs. An alternative to the LCL model is the induced pluripotent stem cell (iPSC) system, which carries the potential to model tissue-specific physiology through the use of differentiation protocols. Still, existing LCL banks represent an important source of starting material for iPSC generation, and it is possible that the disruptions in gene regulation associated with long-term LCL maintenance could persist through the reprogramming process. To address this concern, we studied the effect of reprogramming mature LCLs to iPSCs on the ensuing gene expression patterns within and between six unrelated donor individuals. We show that the reprogramming process results in a recovery of donor-specific gene regulatory signatures. Since environmental contributions are unlikely to be a source of individual variation in our system of highly passaged cultured cell lines, our observations suggest that the effect of genotype on gene regulation is more pronounced in the iPSCs than in the LCL precursors. Our observations indicate that iPSCs can be a powerful model system for studies of phenotypic variation across individuals in general, and the genetic association with variation in gene regulation in particular. We further conclude that LCLs are an appropriate starting material for iPSC generation.

overall_design: Whole genome gene expression data was collected for 34 samples including 17 iPSC lines and 17 LCL lines on the Illumina HT-12 v4 Expression BeadChip array platform. Three biological replicates of each individual were included in the study, except for one individual for which only two replicates were obtained.


title: RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

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

overall_design: Refer to individual Series


title: Human Schwann cells generated from human epidermal neural crest stem cells (hEPI-NCSC)

status: Public on Dec 15 2014

city: Newcastle upon Tyne

first: Maya

last: Sieber-Blum

address: Centre for Life

department: Institute of Genetic Medicine

institute: Newcastle University

summary: The goal was to determine differentially expressed genes between hEPI-NCSC and Schwann cells generated thereof. RNA was isolated from (a) ex vivo expanded hEPI-NCSC (XP; Clewes O et al, 2011) and from (b) human Schwann cells that were differentiated from hEPI-NCSC (unpublished data)

overall_design: Three samples of each, XP and Schwann


title: Checkpoint blockade immunotherapy relies on T-bet but not Eomes to induce effector function in tumor infiltrating CD8+ T cells

city: St. Louis

first: Maureen

last: Donlin

state: MO

address: 1100 South Grand

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

summary:
Coinhibitory receptor blockade is a promising strategy to boost immunity against a variety of human cancers. However, many patients still do not benefit from this treatment, and responders often experience immune-related toxicities. These issues highlight the need for improved understanding of checkpoint blockade, but the T cell-intrinsic signaling pathways and gene expression profiles engaged during treatment are not well defined, particularly for combination approaches. We utilized a murine model of CD8+ T cell tolerance to address these issues.
We used microarrays to examine the global transcriptional response of T cells rendered tolerant in vivo by encounter with tumor/self-antigen versus T cells activated in response to an immunogenic tumor.

overall_design: RNA isolated from naive Gag-specific T cells was compared to RNA isolated from T-cells transferred into B6 mice with established FBL tumor (immune) and from Alb:Gag mice (tolerant). Two days after T cell transfer, recipient spleen and lymph nodes were harvested and pooled. Transferred cells were then sorted based on CD8+ CD90.1+ CD69hi to a >96% purity using a FACSAria III (BD Biosciences).  There were 3 biological replicates per condition.

first: Ryan

last: Teague

first: Melissa

last: Berrien-Elliot


title: RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure [RNA-seq]

summary: We have utilized the RNA-Seq technology to identify genes with distinct expression patterns between failing and non-failing hearts. In an era of next-generation sequencing studies, our study demonstrates how knowledge gained from a small set of samples with accurately measured gene expressions using RNA-Seq can be leveraged as a complementary strategy to discern the genetics of complex disorders.

overall_design: Identify the signature genes based on RNA-seq come from six Heart Failure and healthy individuals. Validation is based on Affymetrix microarray of a total of 313 individuals with/without Heart Failure.

first: Yichuan

last: Liu

first: Jeffrey

last: Brandimarto

first: Sridhar

last: Hannenhalli

first: Yu

last: Hu

first: Euan

middle: A

last: Ashley

first: W

last: Tang

first: Christine

last: Moravec

first: Kenneth

middle: B

last: Margulies

first: Thomas

last: Cappola

first: Mingyao

last: Li


title: Gene expression profile of wild-type and isoniazid resistant strains of Mycobacterium smegmatis

status: Public on Dec 13 2014

city: Bangalore

first: Nagasuma

last: Chandra

state: Karnataka

address: New Biological Science Building, IISc

department: Department of Biochemistry

country: India

institute: Indian Institute of Science

summary: Understanding emergence of drug resistance in pathogens systematically is a major challenge. To address this issue, lab-evolved strain resistant to first-line tuberculosis drug, isoniazid (INH), was analysed. Transcriptome analysis of different conditions revealed genes that are differentially regulated in wild-type (WT) and isoniazid resistant (2XR and 4XR) strains. Microarray analysis was performed for WT, sub-MIC, 2XR and 4XR strains of Mycobacterium smegmatis. Overall, the numbers of DEGs observed are 1529 in sub-MIC (596 - up, 933 - down), 1381 (899 – up, 482 – down) in 2XR and 716 in 4XR (267 – up, 449 – down) conditions. 52 of them are seen to be up-regulated across all drug concentrations as compared to WT while 185 are seen to be down-regulated in all. Transcriptome analysis revealed that there are variations in gene expression pattern in the resistant strains as compared to WT strain. This indicates that differential regulation of genes is, in some way, responsible for conferring the phenotype to the organism.

overall_design: Organism : Mycobacterium smegmatis, Agilent Custom Mycobacterium smegmatis Gene Expression 8x15k Array (AMADID:020791) designed by Genotypic Technology Private Limited.

first: Jyothi

last: Padiadpu

first: Priyanka

last: Baloni


title: Gene expression data of human dermal pilla cells, human induced pluripotent stem cell-derived CD271+CD90+ mesenchymal stem cells before and after the induction toward dermal papilla cells

city: Tokyo

first: Manabu

last: Ohyama

address: 6-20-2 Shinkawa Mitaka-shi

department: Department of Dermatology

institute: Kyorin University School of Medicine

summary: To assess if human induced pluripotent stem cell-derived mesenchymal stem cells (hiPSC-MSCs) could be induce to acquire dermal papilla (DP) properties (especially hair inductive capacity), hiPSCs were initially programmed in serum-free MSC medium with  FGF, TGFbeta and PDGF. Subsequently, hiMSCs were exposed to retinoic acid and activators of WNT, BMP and FGF signaling pathways. Global gene expression profiles were compared among primarily cultured human DP cells, hiPSC-MSCs before and after induction.

overall_design: Human dermal papillae were microdissected and cultured from different donors. Induction from hiPSCs to MSCs and subsequent sorting of CD271+CD90+ subpopulation and thier induction to DP was performed using WD39 hiPSC lines in two independent experimentations to generate hiPSC-MSC-1,hiPSC-MSC-2 ipDPSC-1 and ipDPSC-2. Funding: The Human Stem Cells Informatization Project of the Ministry of Health, Labour and Welfare, Japan

first: Takashi

last: Sasaki

first: Ophelia

last: Veraitch

first: Yo

last: Mabuchi

first: Aki

last: Tsukashima

first: Yumi

last: Matsuzaki

first: Hideyuki

last: Okano

first: Masayuki

last: Amagai


title: Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1

status: Public on Dec 04 2014

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: We report on the function of the D. dictyostelium argonaute proteins AgnA and AgnB in the silencing mechanism of the retrotransposon DIRS-1. By deep sequencing analysis we found that AgnA is involved in the accumulation of DIRS-1 siRNAs since in respective knockout strains siRNAs are strongly reduced. This was verified by northern blots. Reduction of siRNAs was accompanied by increased transcript accumulation and the appearance of an extrachromosomal single stranded DIRS-1 cDNA. In contrast, disruption of the closely related agnB gene had no effect on DIRS-1 siRNAs. agnA-/agnB- double knockouts suggested positively regulator effects by the AgnB protein on DIRS-1.

overall_design: Small RNA profiles of the Ax2 wildtype and different mutant strains were generated by deep sequencing on an Illumina platform.

first: Benjamin

last: Boesler

first: Doreen

last: Meier

first: Michael

last: Friedrich

first: Christian

last: Hammann

first: Cynthia

last: Sharma

first: Wolfgang

last: Nellen


title: Expression data from individual MEF2A isoform knockdown in C2C12 myotubes

status: Public on Dec 03 2014

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

institute: Boston University

summary:
Differentiation of muscle tissue is regulated by a complex network of transcription factors. The MEF2 family of transcription factors are important players in muscle development and differentiation.
We knocked down expression of MEF2 isoforms in a cell culture model of skeletal muscle differentiation and assessed global expression pattern changes between MEF2 knockdowns, and with a negative control.

overall_design: C2C12 myoblasts were transduced with shRNA viral vectors to knockdown expression of individual MEF2 proteins. Cells were then induced to differentiate and were harvested 3 days post-differentiation for Affymetrix global gene expression analysis. Each array was pooled RNA from two separate transductions, and each treatment group was analyzed in triplicate.

first: Francisco

last: Naya

first: Nelsa

middle: L

last: Estrella

first: Cody

last: Desjardins

first: Sarah

last: Nocco

first: Amanda

last: Clark

first: Yevgeniy

last: Maksimenko


title: Genetic background modulates lincRNA-coordinated tissue response to low dose ionizing radiation

status: Public on Dec 01 2014

city: Berkeley

first: Antoine

last: Snijders

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

summary: Long noncoding RNAs (lncRNAs) are emerging as key regulators of diverse cell functions and processes. However, the relevance of lncRNAs in the cell and tissue response to ionizing radiation has not yet been characterized.  Here we used microarray profiling to determine lncRNA and mRNA expression in mammary glands of BALB/c and SPRET/EiJ mice after low-dose ionizing radiation (LDIR) exposure. We found that unirradiated mammary tissues of these strains differed significantly in baseline expressions of 290 lncRNAs. LDIR exposure (10 cGy) induced a significant change in the expression of many lncRNAs. For BALB/c mice, a total of 357, 480, and 335 lncRNAs and 550, 911, and 389 coding RNAs were identified at 2, 4, and 8 weeks post-irradiation, respectively, while for SPRET/EiJ, a total of 327 lncRNAs and 424 mRNAs were identified at 4 weeks post-irradiation.

overall_design: Low dose radiation induced changes in mRNA and lncRNA expression were measured in mouse mammary gland tissues at 2,4 and 8 weeks after radiation exposure in BALB/c and 4 weeks after exposure in SPRET/EiJ mice.  BALB/c: 3 timepoints (2wk, 4 wk, 8 wk); 3 replicates per timepoint; 2 treatments per timepoint (10 cGy x-ray and sham).  SPRET/EiJ: 1 timepoint (4 wk); 3 replicates per timepoint; 2 treatments per timepoint (10 cGy x-ray and sham).

first: Jian-Hua

last: Mao


title: Studies on mature endothelial cells; exploring  mechanisms for improvement of cardiovascular diseases

city: Jeddah

first: Sherin

last: Bakhashab

address: Abdullah Sulyman

department: Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

summary: Transcriptomic analysis of primary human umbilical vein endothelial cells (HUVEC). HUVEC were treated in vitro with CoCl2 to induce hypoxia, high glucose and high glucose plus hypoxia in different intervals (1, 3, 12 hours). Subsequently, the effect of metformin (anti-diabetic drug) on all conditions was studied to take advantage of transcriptomics to prospectively explore the mechanism of this drug to reduce the risk of cardiovascular diseases in type II diabetic patients.

overall_design: Total RNA isolated from 66 HUVEC samples; 22 different conditions each has 3 biological repeats; labeled, and hybridized to Affymetrix Human Gene 1.0 ST Array.

first: Jolanta

last: Weaver

first: Iokim

last: Spyridopoulos

first: Hans-Juergen

last: Schulten

first: Jayapal

last: Manikandan

first: Sahira

last: Lary

first: Farid

last: Ahmed

first: Mohammed

middle: H

last: Alqahtani


title: Long-term maintenance time-course of cardiomyocytes differentiated from human pluripotent stem cells and comparison to human heart

status: Public on Dec 16 2014

city: Münster

first: Boris

last: Greber

address: Von-Esmarch-Str. 54

institute: Max Planck Institute for Molecular Biomedicine

summary: Analysis of culture-induced changes in cardiomyocytes (CMs) differentiated from human pluripotent stem cells (hPSCs) over a time-period of 8 weeks, and comparison of these samples to human atrial and ventricular tissue

overall_design: Total RNA isolated from differentiated in-vitro samples at the indicated time-points and of human heart in-vivo tissue