title: Fine scale time-series RNA-Seq of shoot and root responses to Nitrogen supply

status: Public on May 11 2018

city: West Lafayette

first: Kranthi

last: Varala

state: IN

address: 625 Agriculture Mall Drive

department: Horticulture and Landscape Architecture

institute: Purdue University

summary: Arabidopsis plants grown in a hydroponic media with sufficient Nitrogen were given a 60mM supply of Nitrogen. Triplicate sets of plants were sampled at time points 0,5,10,15,20,30,45,60,90 and 120 minutes after supply from treated and control plants (20mM KCl). The samples were flash frozen in liquid N and used to construct RNA-Seq libraries to assay transcriptional changes in the shoots and roots, separately, in response to Nitrogen.

overall_design: Time series of shoot and root mRNA profiles from Root and shoot were generated at 10 time points after Nirogen supply using Illumina HiSeq platform.

first: Amy

last: Marshall-Colon

first: Gloria

last: Coruzzi


title: Targeted mutagenesis recapitulates brain tumor initiation in cerebral organoids (RNA-seq data set: 45d)

status: Public on May 30 2018

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

type: Expression profiling by high throughput sequencing

summary: Introduction of brain tumor-relevant genetic aberrations initiates different subtypes of brain tumor-like neoplasms in cerebral organoids

overall_design: Comparison of transcriptomes from different brain tumor organoid groups

first: Shan

last: Bian

middle: R

first: Zhenming

last: Guo

first: Juergen

middle: A

last: Knoblich


title: To investigate whether alcohol drinking modulates gene expression in mouse forestomach

status: Public on Dec 21 2017

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Ave

country: USA

institute: Coriell Institute for Medical Research

summary: Whole forestomach of mice treated with 20% ethanol for 4 weeks; Whole forestomach of mice treated with 15% ethanol for 40 weeks; negative control (0% alcohol treated mice)

overall_design: WT 0% alcohol; WT 20% alcohol and  WT 15% alcohol

first: David

last: Huang

middle: L


title: Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy

status: Public on Jul 06 2018

city: Helsinki

first: Outi

last: Monni

address: Haartmaninkatu 8

department: Research Programs Unit

country: Finland

institute: University of Helsinki

type: Genome variation profiling by genome tiling array

summary:
This SuperSeries is composed of the SubSeries listed below.
GSE107918
GSE108061

overall_design: Please see individual series GSE107918 and GSE108061


title: Targeted mutagenesis recapitulates brain tumor initiation in cerebral organoids (RNA-seq data set: 130d)

overall_design: Comparison of abundances (TPM) from different brain tumor organoid groups


title: Study target genes of STAT3

status: Public on Jan 03 2018

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

country: Denmark

institute: Aarhus University

summary:
This study is to identify downstream genes regulated by STAT3 in response cytosolic acidification.
Dysregulated intracellular pH is emerging as a hallmark of cancer. In spite of their acidic environment, cancer cells maintain alkaline intracellular pH (≥7.4) that promotes cancer progression by inhibiting apoptosis and increasing glycolysis, cell growth, migration and invasion. Here, we identify signal transducer and activator of transcription 3 (STAT3) as a key player in the maintenance of alkaline cytosolic pH. STAT3 associates with the vacuolar H+-ATPase on lysosomal membranes in a coiled coil domain-dependent manner and increases its activity in living cells and in vitro. Accordingly, STAT3 depletion disrupts intracellular proton equilibrium by decreasing and increasing cytosolic and lysosomal pH, respectively. This dysregulation can be reverted by reconstitution with wild type STAT3 as well as STAT3 mutants unable to activate target genes (Tyr-705-Phe and DNA binding mutant) or to regulate mitochondrial respiration (Ser-727-Ala). Upon cytosolic acidification, phospho-Tyr-705-STAT3 is rapidly dephosphorylated, transcriptionally inactivated and further recruited to lysosomal membranes to reestablish intracellular proton equilibrium and to enhance cell survival. These data reveal STAT3 as a regulator of intracellular pH, and vice versa intracellular pH as a regulator of STAT3 localization and activity.

overall_design: Twelve samples in total have been analysed. HeLa WT is the control for HeLa STAT3 KO. HeLa blank is the control for PA+EIPA. Each group has 3 replicates.

first: Bin

last: Liu

first: Johan

last: Palmfeldt

first: Lin

last: Lin

first: Alexandria

last: Colaço

first: Jinrong

first: Fengping

last: Xu

first: Xin

first: Kenji

last: Maeda

first: Marja

last: Jäättelä


title: Generic drug screen identifies paracetamol as 5-aza-2’-deoxycytidine sensitizer in head and neck squamous cell carcinoma cells

status: Public on Nov 02 2018

city: Birmingham

first: Malgorzata

last: Wiench

address: 5 Mill Pool Way

department: School of Dentistry

country: United Kingdom

institute: University of Birmingham

summary: Aberrant DNA methylation (5mC) is one of the key characteristics of many cancers including head and neck squamous cell carcinoma (HNSCC). The DNA demethylating agent 5-aza-2’-deoxycytidine (DAC) has anti-cancer therapeutic potential, but its clinical efficacy is currently hindered by dose-limiting side effects. Here we investigated the potential use of DAC in the treatment of HNSCC and show that its efficacy is primarily dependent on the ability of DAC to demethylate DNA. In order to establish whether HNSCC cells can be sensitized to DAC, a panel of 100 generic drugs were screened in combination with DAC. While the 100-drug panel did not sensitise DAC-resistant HNSCC cell lines to DAC treatment, the screen identified that paracetamol (acetaminophen), valproic acid and zinc acetate significantly enhanced DAC efficacy in the DAC-responsive cell lines. DAC and paracetamol were established to work in synergy, allowing DAC to be used at therapeutically relevant low doses (below 500nM). The mechanisms underlying the DAC-paracetamol synergy are multifactorial and encompass both effects of DAC on paracetamol action (alterations in the cyclooxygenase (COX) pathway and mimicry of paracetamol overdose) as well as decreased DNA methylation by paracetamol.   Therefore, we propose DAC to be a potential therapeutic in a subset of HNSCC patients with its efficacy significantly increased by use of the common analgesic paracetamol. The DAC-paracetamol synergy should also be considered in cancers with an approved DAC treatment regime.

overall_design: There are four RNA-seq samples. VU40T squamous cell cacrcinoma cells were treated for 96h with 500nM 5-aza-2'-deoxycytidine (DAC), 132.3μM Paracetamol (Para), or both and compared to the untreated cells (control). For each sample three biological replicates were pooled for each RNA-seq library.

first: Wiench

last: Malgorzata

first: Clokie

last: Samuel


title: MicroRNA expression data from human brain tissue with focal cortical dyplasia, type II

status: Public on Apr 03 2018

city: Campinas

first: Cristiane

middle: de Souza

last: Rocha

state: São Paulo

address: Av Tessália Vieira de Camargo, 126 Cidade Universitária "Zeferino Vaz"

department: Medical genetics

country: Brazil

institute: Unicamp

summary:
Focal cortical dysplasia (FCD) is a type of malformation of cortical development and its main clinical manifestation is medically intractable epilepsy
We aimed to investigate whether abnormal gene regulation, mediated by microRNA, could be involved in FCD type II, in view of to help clarify the molecular mechanism leading to this type of  cortical malformation.

overall_design: Microarray profiling of microRNA was performed on human brain tissue. We used formalin-fixed paraffin-embedded (FFPE) tissue and  GeneChip® 1.0 miRNA array (Affymetrix, Santa Clara, USA). We included nine samples from patients with FCD type II (type IIa, n = 4; type IIb, n = 5) and five controls.

first: S

middle: H

last: Avansini


title: Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy [gene expression]

summary: There is an unmet need for effective targeted therapies for patients with advanced head and neck squamous cell carcinoma (HNSCC). We correlated gene expression, gene copy numbers, and point mutations in 45 human papillomavirus-negative HNSCC cell lines with the sensitivity to 220 anticancer drugs to discover predictive associations to genetic alterations. The drug response profiles revealed diverse efficacy of the tested drugs across the cell lines. Several genomic abnormalities and gene expression differences were associated with response to mTOR, MEK, and EGFR inhibitors. NOTCH1 and FAT1 were the most commonly mutated genes after TP53 and also showed some association with response to MEK and/or EGFR inhibitors. MYC amplification and FAM83H overexpression associated with sensitivity to EGFR inhibitors, and PTPRD deletion with poor sensitivity to MEK inhibitors. The connection between high FAM83H expression and responsiveness to the EGFR inhibitor erlotinib was validated by gene silencing and from the data set at the Cancer Cell Line Encyclopedia. The data provide several novel genomic alterations that associated to the efficacy of targeted drugs in HNSCC. These findings require further validation in experimental models and clinical series.

overall_design:
Gene expression profiles of forty-five head and neck squamous cell carcinoma UT-SCC cell lines were analyzed using HT-12 human Illumina arrays.

Drug sensitivity scores (DSS) of the 220 compounds across 45 UT-SCC HNSCC cell lines are provided in the 'Drug_classes_DSS_drug screen.xlsx'

first: Tatiana

last: Lepikhova

first: Piia-Riitta

last: Karhemo

first: Riku

last: Louhimo

first: Bhagwan

last: Yadav

first: Astrid

last: Murumägi

first: Evgeny

last: Kulesskiy

first: Mikko

last: Kivento

first: Harri

last: Sihto

first: Reidar

last: Grénman

first: Stina

middle: M

last: Syrjänen

first: Olli

last: Kallioniemi

first: Tero

last: Aittokallio

first: Krister

last: Wennerberg

first: Heikki

last: Joensuu


title: Re-routing central metabolism in Aspergillus nidulans

status: Public on Feb 26 2018

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

summary: Plant biomass is the most abundant and renewable carbon source for many fungal species. The composition of biomass consists of about 40-45% cellulose, 20-30% hemicellulose, and 15-25% lignin and varies among plant species. In the bio-based industry, Aspergillus species and other fungi are used for the production of lignocellulolytic enzymes to pretreat agricultural waste biomass (e.g. wheat bran). In this study, we aimed to evaluate if it would be possible to create an Aspergillus strain that releases but does not metabolize hexoses from plant biomass. For this purpose, metabolic mutants were generated that were (partially) impaired in glycolysis, by deleting the hexokinase (hxkA) and glucokinase (glkA) genes. To prevent repression of enzyme production due to the accumulation of hexoses, strains were generated in which these mutations were combined with a mutation in creA, encoding the repressor involved in carbon catabolism. Phenotypic analysis revealed that growth of the ΔhxkAΔglkA mutant was reduced on wheat bran. However, hexoses did not accumulate during growth of the mutants on wheat bran, suggesting that glucose metabolism is re-routed towards alternative carbon catabolic pathways. Deletion of creA combined with blocking glycolysis resulted in an increased expression of pentose catabolic and phosphate pathway genes. This indicates that the reduced ability to use hexoses as carbon sources has resulted in a shift towards the pentose fraction of wheat bran as a major carbon source to support growth.

overall_design: This study compares the gene expression of several A. nidulans strains growing on MM + wheat bran. The different A. nidulans samples (wildtype, ΔhxkAΔglkA, ΔcreA, and ΔcreAΔhxkAΔglkA) were taken after 2 hours of incubation.

first: Claire

last: Khosravi

first: Evy

last: Battaglia

first: Maria Victoria

last: Aguilar-Pontes

first: Sacha

last: Dulhuijsen

first: Miaomiao

last: Zhou

first: Heino

last: Heyman

first: Young

last: Kim

first: Scott

last: Baker

middle: P


title: RNASeq of C. elegans exposed to silver (Ag) or silicon dioxide (SiO2) nanoparticles

status: Public on Nov 20 2018

city: Montreal

first: Orcun

last: Hacariz

state: Quebec

address: 1001 Boul Décarie, Site Glen Pavilion E / Block E. E02.2143

country: Canada

institute: Research Institute of the McGill University Health Centre

summary: RNAseq was carried out to compare the gene expression profiles underlying the Ag and SiO2 toxicities on C. elegans.

overall_design: C. elegans worms were exposed to silver (Ag) or silicon dioxide (SiO2) nanoparticles (at 10 µg/ml concentration) and RNAseq was performed to understand the biological effects of the nanoparticles on the worm at gene level.

first: Charles

last: Viau

first: Orçun

last: Haçariz

first: Jianguo

last: Xia


title: ROP: Dumpster Diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

status: Public on Jan 23 2018

city: San Francisco

first: Srilaxmi

last: Nerella

state: CA

address: HSE1355A, 513 Parnassus ave

department: Department of Medicine

institute: UCSF

summary: High-throughput RNA sequencing technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at http://smangul1.github.io/rop/.

overall_design: During bronchoscopy airway epithelial brushings, samples were obtained from 3rd-4th generation bronchi. RNA was extracted from the epithelial brushing samples using the Qiagen RNeasy mini-kit (Qiagen, Valencia, CA), according to manufacturer's protocol. We used 100ng of isolated RNA from a total of 61 samples to construct ribo-depleted RNA-seq libraries using the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat library preparation kit, per manufacturer's protocol. Barcoded bronchial epithelial RNA-seq libraries were multiplexed and sequenced as 2 x 100bp paired-end reads on an Illumina HiSeq 2500. On average, 37 million reads were generated per sample. We excluded 12 samples from further analyses due to high ribosomal RNA read counts (library preparation failure), leaving a total of 49 samples suitable for further analyses.

first: Serghei

last: Mangul

first: Harry

middle: T

last: Yang

first: Nicolas

last: Strauli

first: Franziska

last: Gruhl

first: Hagit

last: Porath

first: Kevin

last: Hsieh

first: Linus

last: Chen

first: Timothy

last: Daley

first: Stephanie

last: Christenson

first: Agata

last: Wesolowska-Andersen

first: Roberto

last: Spreafico

first: Cydney

last: Rios

first: Celeste

last: Eng

first: Andrew

middle: D

last: Smith

first: Ryan

last: Hernandez

first: Roel

last: Ophoff

first: Jose

last: Rodriguez Santana

first: Erez

middle: Y

last: Levanon

first: Prescott

middle: G

last: Woodruff

first: Esteban

last: Burchard

first: Max

last: Seibold

first: Sagiv

last: Shifman

first: Eleazar

last: Eskin

first: Noah

last: Zaitlen


title: Dissecting the genetic basis of an evolved acute heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei reveals a complex and unique genetic architecture

status: Public on Dec 19 2017

city: Eugene

first: Patrick

middle: C

last: Phillips

state: OR

address: 272 Onyx Bridge 5289 University of Oregon

department: Biology

institute: University of Oregon

summary: Analysis of constitutive changes in gene expression patterns in populations of the nematode Caenorhabditis remanei experimentally evolved to either acute heat stress, acute oxidative stress or the lab environment. Results of this study demonstrate that acute heat stress and acute oxidative stress are complex traits with a unique genetic basis. Overall design: Pooled population RNA sequencing libraries were obtained from the ancestor population and three evolved populations: one biological replicate of the control selected population, one heat stress selected population and one oxidative stress selected population per replicate. Tissue was collected from populations of L1 larval worms.

overall_design: mRNA profiles of ancestral and three experimentally evolved populations of C. remanei at 20°C, 6- 8  replicates/evolved line for each population

first: Christine

last: Oconnor

first: Kristin

last: Sikkink

first: Thomas

last: Nelson

first: Janna

last: Fierst


title: Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy [CGH]

first: Outi

last: Monni

overall_design: Two-color experiment. DNA from forty-five head and neck squamous cell carcinoma UT-SCC cell lines were hybridized each against Human Reference Female or Male DNA (Agilent).

first: Tatiana

last: Lepikhova

first: Piia-Riitta

last: Karhemo

first: Riku

last: Louhimo

first: Bhagwan

last: Yadav

first: Astrid

last: Murumägi

first: Evgeny

last: Kulesskiy

first: Mikko

last: Kivento

first: Harri

last: Sihto

first: Reidar

last: Grénman

first: Stina

last: Syrjänen

first: Olli

last: Kallioniemi

first: Tero

last: Aittokallio

first: Krister

last: Wennerberg

first: Heikki

last: Joensuu


title: Mesenchymal–Epithelial Transition in fibroblasts of human normal lungs and interstitial lung diseases

status: Public on Dec 05 2017

city: Mexico City

first: Marco

last: Checa

address: Calada de Tlalpan 4502, Colonia XVI Delegación Tlalpan

department: Pulmonary Fibrosis

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias

summary:
To evaluate the possible occurrence of MET, fibroblasts from normal lungs and from interstitial lung diseases were cultured under standard conditions.
When was observed an unusual epithelial-like phenotypic change gene expression was evaluated by complete transcriptome microarrays.

overall_design: Fibroblasts from normal lungs and from interstitial lung diseases were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Carina

last: Becerril

first: Martha

last: Montaño

first: Carlos

last: Ramos


title: Gene expression analysis of macrophage response to LPS stimulation and/or to treatment with melatonin

status: Public on Dec 01 2017

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

country: Japan

institute: AIST

summary: We compared the gene expression patterns of macrophages upon LPS stimulation with or without melatonin pretreatment

overall_design: RAW 264.7 macrophage were pretreated with 1mM of melatonin for 1 hour or left untreated. The cells were stimulated with 100 ng/ml LPS for 1, 3 or 5 hours after pretreatment.

first: Hirotaka

last: Kuwata


title: The three-component system EsrISR regulates a cell envelope stress response in Corynebacterium glutamicum

status: Public on Nov 21 2017

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

summary: When the cell envelope integrity is compromised, bacteria trigger signaling cascades that result in the production of proteins that counteract these extracytoplasmic stresses. Here, we show that the two-component system EsrSR regulates a cell envelope stress response in the Actinobacterium Corynebacterium glutamicum. The sensor kinase EsrS possesses an amino-terminal phage shock protein C (PspC) domain, a property that sets EsrSR apart from all other two-component systems characterized so far. An integral membrane protein, EsrI, whose gene is divergently transcribed to the esrSR gene locus and which interestingly also possesses a PspC domain, acts as an inhibitor of EsrSR under non-stress conditions. The EsrISR three-component system is activated among others by antibiotics inhibiting the lipid II cycle, such as bacitracin and vancomycin, and it orchestrates a broad regulon including the esrI-esrSR gene locus itself, genes encoding heat shock proteins, ABC transporters, and several putative membrane-associated or secreted proteins of unknown function. Among those, the ABC transporter encoded by cg3322-3320 was shown to be directly involved in bacitracin resistance of C. glutamicum. Since similar esrI-esrSR loci are present in a large number of actinobacterial genomes, EsrISR represents a novel type of stress-responsive systems whose components are highly conserved in the phylum Actinobacteria.

overall_design: For global transcriptome analyses, cells of the C. glutamicum delta esrI (cg0706) deletion mutant, of the esrSR deletion mutant expressing EsrR from plasmid, and cells of the wild type in the presence of bacitracin were compared with the corresponding control.

first: Britta

last: Kleine

first: Ava

last: Chattopadhyay

first: Thorsten

last: Mascher

first: Michael

last: Bott

first: Melanie

last: Brocker

first: Roland

last: Freudl


title: Gene expression profile correlates with overall survival in patients with resected pancreatic adenocarinoma

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

summary:
Purpose/Objective(s): To correlate gene expression and overall survival (OS) in patients with pancreatic adenocarcinoma who have undergone definitive surgery
Materials/Methods: Patients were identified that were treated with definitive surgery without neoadjuvant and adjuvant therapy for pancreatic adenocarcinoma. The Beaumont BioBank consented patients then collected and stored tissue samples. Patients were grouped into short term (<10 months, n=13) and long term (>20 months, n=11) survivors. RNA was extracted from fresh frozen tissues, and global gene expression patterns in the short and longer-term survivors were compared. Pathway analysis of the significant genes was also performed.
Results: The median age at the time of surgery was 64 years. The mean overall survival in each group was 7.5 months and 32.0 months. We identified 163 genes that were differentially expressed between patients who survived <10 months and >20 months from their definitive surgery. Many of the genes identified have known prognostic importance in oncology; however, less than half of these genes have been reported to be associated with survival in pancreatic adenocarcinoma. Pathway analysis identified expression targets of SP1, JUN, and EGF to be highly regulated based upon differences in overall survival.
Conclusions: In pancreatic adenocarcinoma patients who have undergone definitive resection, we have identified multiple genes associated with inferior survival. Many of the genes reported in this study have not previously been linked to overall survival in this patient population.

overall_design: Samples from pancreatic ductal adenocarcinoma patients that survived > 20 months (n=11) were compared to samples from pancreatic ductal adenocarcinoma patients that survived < 10 months (n=13).

middle: J

first: Robert

last: Jury

first: Brandon

last: Stone

first: Laura

middle: E

last: Fortier

first: Andrew

last: Baschnagel

first: Amro

last: Almradi

first: George

last: Wilson


title: To compare the transcriptome of ompR null strains with wild-type strain of S. Typhimurium during  osmotic stress

status: Public on Nov 08 2017

city: singapore

first: smarajit

last: chakraborty

address: T-Lab, 5A Engineering Drive 1, NUS

country: Singapore

institute: Mechanobiology Institute

summary: In bacteria, one paradigm for signal transduction is the two-component regulatory system, consisting of a sensor kinase (usually a membrane protein) and a response regulator (usually a membrane protein) and a response regulator (usually a DNA binding protein). The EnvZ/OmpR two-component system in S. Typhimurium responds to osmotic stress and regulates expression of outer membrane proteins. Furthermore, bacteria were believed to regulate pH by acidifying after external acid stress, then immediately recovering. Using a pH-sensor in single living cells, we show that S. Typhimurium maintain an acidic cytoplasm under sucrose-driven osmotic stress which requires OmpR. Thus, we set out to identify the OmpR targets of S. Typhimurium under osmotic stress.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: To identify OmpR targets under osmotic stress conditions, we performed a microarray and compared the transcriptome of ompR null strains with wild-type strains of  S. Typhimurium at high osmolality.  S. Typhimurium strain was grown in MgM media at  7.2 and 7.2 with 15% (w/v) sucrose to O.D ~0.6.  The total RNA was isolated using an RNeasy mini kit (Qiagen) and proceeded for Microarray

first: Smarajit

last: Chakraborty

first: Linda

last: Kenney


title: Arg1 functions in the physiological adaptation of undifferentiated plant cells to spaceflight

status: Public on Sep 01 2017

city: Gainesville

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary:
Scientific access to spaceflight and especially the International Space Station has revealed that physiological adaptation to spaceflight is accompanied or enabled by changes in gene expression that significantly alter the transcriptome of cells in spaceflight. A wide range of experiments have shown that plant physiological adaptation to spaceflight involves gene expression changes that alter cell wall and other metabolisms. However, while transcriptome profiling aptly illuminates changes in gene expression that accompany spaceflight adaptation, mutation analysis is required to illuminate key elements required for that adaptation.
In this study transcriptome profiling was used to gain insight into the spaceflight adaptation role of Altered response to gravity-1 (Arg1), a gene known to affect gravity responses in plants on Earth. The study compared expression profiles of cultured lines of Arabidopsis thaliana derived from wild type (WT) cultivar Col-0 to profiles from a knock-out line deficient in the gene encoding (ARG1 KO), both on the ground and in space. The cell lines were launched on SpaceX CRS-2 as part of the Cellular Expression Logic (CEL) experiment of the BRIC17 spaceflight mission. The cultured cell lines were grown within 60mm Petri plates in Petri Dish Fixation Units (PDFUs) that were housed within the Biological Research In Canisters (BRIC) hardware. Spaceflight samples were fixed on orbit. Differentially expressed genes were identified between the two environments (spaceflight and comparable ground controls) and the two genotypes (WT and ARG1 KO). Each genotype engaged unique genes during physiological adaptation to the spaceflight environment, with little overlap. Most of the genes altered in expression in spaceflight in WT cells were found to be Arg1-dependent, suggesting a major role for that gene in the physiological adaptation of undifferentiated cells to spaceflight.

overall_design: The CEL (Cellular Expression Logic) experiment setup and organization was a modification of a previous Arabidopsis cell culture experiment in BRIC16 (Paul, Zupanska et al. 2012). The CEL BRIC17 experiment was launched on board the Dragon capsule of SpaceX-3 CRS mission to the International Space Station (ISS) on the 1st of March 2013.  The cultured cell lines (both the ground control and the spaceflight samples) were grown within 60mm Petri plates in Petri Dish Fixation Units (PDFUs) that were housed within the Biological Research In Canister (BRIC) hardware. Two BRIC containers (A and B) were assigned to CEL within the BRIC17 payload. Each chamber housed 5 PDFUs, each PDFU holding one 60mm Petri plate. In each BRIC container there were 2 plates with wild type (WT) cells and 3 plates with knock-out cells of two genotypes. The exact same PDFU composition was recapitulated in BRICs on the ground in the ISS Environmental Simulator (ISSES) chamber at Kennedy Space Center (KSC) as Ground Controls. The Ground Controls were initiated with a 48 hrs delay so that the precise temperature environment of the ISS could be recreated for the ground controls in the ISSES chamber. Cells were fixed in-flight in RNAlater on the 10th day on orbit, and the ground controls were fixed 48 hours later. RNAlater fixation was initiated by the crew using an activation tool that moves RNAlater from a storage container in the PDFU into the Petri Plate. Twenty four hours after fixation, the entire BRIC was moved to the MELFI (Minus Eighty-degree Laboratory Freezer for ISS) where it resided until cold stowage transport back to Earth within the Dragon capsule.  After returning to Earth the samples were reclaimed at KSC, and then transported to the University of Florida (UF) laboratories. The total RNA was extracted from spaceflight samples and corresponding Ground Control samples and subjected to microarrays.

first: Agata

middle: K

last: Zupanska

first: Eric

last: Shultz

first: JiQiang

last: Yao

first: Natasha

last: Sng

first: Mingqi

last: Zhou

first: Jordan

last: Callaham

first: Anna-Lisa

last: Paul


title: Gene expression analysis of macrophage response to infection with Streptococcus oralis or to treatment with hydrogen peroxide

first: Yutaro

last: Kumagai

summary: We compared the gene expression patterns of macrophages infected with S. oralis wild type and SpxB KO, a strain that does not produce H2O2.

overall_design: RAW 264.7 macrophages that were infected with S. oralis wild type and SpxB KO strains at multiplicity of infection (MOI) of 5 for 16 hours. RAW 264.7 cells were also stimulated with 100 ng/ml LPS for 1, or 3 hours after pretreat with or without 1 mM H2O2 for 30 mins.

first: Hirotaka

last: Kuwata


title: Promyelocytic Leukemia (PML) protein is an essential regulator of stem cell pluripotency and somatic cell reprogramming

status: Public on Jun 13 2017

city: Heraklion, Crete

first: Christiana

last: Hadjimichael

address: Nikolaou Plastira 100

department: Institute of Molecular Biology and Biotechnology (IMBB)

country: Greece

institute: Foundation for Research and Technology - Hellas (FORTH)

summary: Promyelocytic Leukemia Protein (PML) was first identified as a fusion product with the retinoic acid receptor alpha in Acute Promyelocytic Leukemia (APL). Although PML has previously been studied in cancer progression and various physiological processes, little is known about its functions in Embryonic Stem Cells (ESC). Here, we report that PML contributes to the maintenance of the ESC self-renewal by controlling the cell-cycle and sustaining the expression levels of crucial pluripotency factors. Transcriptomic analysis showed that the ablation of PML renders ESC prone to exit from the naïve and acquire a primed-like pluripotent cell state. During differentiation PML influences cell fate decision by regulation of Tbx3. PML loss compromises the reprogramming ability of embryonic fibroblasts to induced Pluripotent Stem Cells (iPSC) by inhibiting the TGFβ pathway at the very early stages. Collectively, these results designate PML as a member of the regulatory network for ESC pluripotency and somatic cell reprogramming.

overall_design: gene expession profile of ESCs and differentiated EBs D4 in the presence or deletion of PML. Samples were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Christoforos

last: Nikolaou

first: Androniki

last: Kretsovali


title: To compare the transcriptome of ompR null strains with wild-type strain of E. coli and S. Typhimurium during stress

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

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

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Refer to individual Series


title: Neuroblastoma cells undergo transcriptomic alterations during dissemination into the bone marrow and subsequent tumor progression

status: Public on Aug 21 2017

city: Vienna

first: Fikret

last: Rifatbegovic

address: Zimmermannplatz 10

department: Tumor biology

institute: Children's Cancer Research Institute

summary: Background: Neuroblastoma is the most common extracranial solid tumor in childhood. The vast majority of stage M patients present with disseminated tumor cells (DTCs) in the bone marrow (BM). Although these cells represent a major obstacle in the treatment of neuroblastoma patients, their transcriptomic profile was not intensively analyzed so far. Results: RNA-Seq of stage M primary tumors, enriched BM-derived DTCs and the corresponding non-tumor mononuclear cells (MNCs) revealed that DTCs largely retained the gene expression signature of tumors. However, we identified 322 genes that were differentially expressed (q < 0.001, |log2FC|>2). Particularly genes encoded by mitochondrial DNA were highly up-regulated in DTCs, whereas e.g. genes involved in angiogenesis were down-regulated. Furthermore, 224 genes were highly expressed in DTCs and only slightly, if at all, in MNCs (q < 8x10-75 log2FC > 6). Interestingly, we found that the gene expression profiles of diagnostic DTCs largely resembled those of relapse DTCs with only 113 differentially expressed genes under relaxed cut-offs (q < 0.01, |log2FC| > 0.5). Notably, relapse DTCs showed a positional enrichment of 31 down-regulated genes encoded by chromosome 19, including five tumor suppressor genes (SIRT6, PUMA, STK11, CADM4 and GLTSCR2).  Conclusion: This first RNA-Seq analysis of DTCs from neuroblastoma patients revealed their unique expression profile in comparison to the corresponding MNCs and tumor samples, and, interestingly, also expression differences between diagnostic and relapse DTCs preferentially affecting chromosome 19. As these alterations might be associated with treatment failure and disease relapse, they should be considered for further functional studies.

overall_design: Tumor (n=16), bone marrow-derived disseminated tumor cells (n=42) and corresponding bone marrow-derived non-tumor cells (n=28) of stage M neuroblastoma patients were used for RNA-Seq

first: Christian

last: Frech

first: M

middle: R

last: Abbasi

first: Sabine

last: Taschner-Mandl

first: Tamara

last: Weiss

first: Wolfgang

last: Schmidt

first: Iris

first: Ruth

last: Ladenstein

first: Inge

last: Ambros

first: Peter

middle: F


title: Comparison of Corynebacterium glutamicum chassis C1 with MB001

status: Public on Aug 23 2017

first: Tino

last: Polen

summary: To identify genes which are differentially expressed in Corynebacterium glutamicum chassis C1 in comparison to the prophage free strain MB001, we performed DNA microarray analyses of C. glutamicum C1 against MB001. For this purpose RNA was isolated from cells cultivated in CGXII minimal medium with 2% glucose (w v-1) and harvested in the exponential growth phase at an OD600 of 5. Four biological replicates were performed.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

first: Meike

last: Baumgart


title: cAMP phosphodiesterase CpdA of Corynebacterium glutamicum: identification, characterization, influence on cAMP level, growth, and global expression, and transcriptional activation by GlxR

status: Public on Nov 15 2016

summary: DNA microarrays were applied to investigate the effect of cpdA deletion (del) or overexpression (over) on the global gene expression of C. glutamicum cells. For overexpression of cpdA the gene was cloned into plasmid pEKEx2 under control of the IPTG-inducible tac promoter, which was induced by addition of 250 µM IPTG.

overall_design: DNA microarray experiments were performed with three biological replicates. The transcriptome of C. glutamicum cells in which cpdA was either deleted (∆cpdA/pEKEx2) or overexpressed by plasmid-based expression (WT/pEKEx2-cpdA) was compared to the transcriptome of C. glutamicum wt cells containing empty plasmid pEKEx2 (WT/pEKEx2). For overexpression of CpdA, 250 µM IPTG was added to the medium (also for the control samples).

first: Julia

last: Schulte

first: Michael

last: Bott


title: Beta cell markers of aging have heterogeneous distribution in islets and are induced by insulin resistance

status: Public on Mar 22 2017

city: Boston

first: Jonathan

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: Our hypothesis was that at any given point in time, islets will contain differing populations of beta cells at different stages of their lifecycle, with further changes occurring with metabolic stress and aging. We examined subpopulations of beta cells isolated from MIP-GFP mice on the basis of their insulin transcriptional activity and in their expression of p16Ink4a. In addition, using aging C57Bl/6 mice as a model, markers of beta cell aging were identified and validated: Igf1r and Cd99 expression increased with age, whereas Kcnq5 was decreased with age. These markers were correlated with an age-related decline in function. The functional aging of beta cells was accelerated by S961, an antagonist to the insulin receptor, which induced insulin resistance. Particularly surprising was the finding of marked islet heterogeneity as demonstrated with the marked staining differences of the markers: Igf1r, Cd99 and Kcnq5. These novel findings about beta cell and islet heterogeneity, and how they change with age, open up an entirely new set of questions that must be addressed about the pathogenesis of type 2 diabetes. The present study has identified new markers of aging in beta cells and found that the expression of these and other markers can be increased by insulin resistance. This provides insight into how insulin resistance might accelerate the death of beta cells. In addition, striking heterogeneity among islets was found, which opens up new ways to think about islet biology and the pathogenesis of T2D.

overall_design: We performed Affymetrix microarrays (n=3 or 4  per group) on RNA from FACS-purified MIP:GFP beta cells from different aged mice: 1) 3.5-9 w Young; 2) 1 y-old; 3) 2 y-old.

first: Cristina

last: Aguayo-Mazzucato

first: Mark

last: van Haaren

first: Magdalena

last: Mruk

first: Caitlin

last: Crawford

first: Jennifer

last: Hollister-Lock

first: Brooke

middle: A

last: Morris

first: James

middle: W

last: Johnson

first: Gordon

last: Weir

first: Susan

last: Bonner-Weir


title: Next Generation Sequencing Facilitates Quantitative Analysis of HCC cells transfected with NCsiRNA or CDCA8siRNA

status: Public on Feb 14 2017

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

summary: We hypothesized if targeting of CDCA8 with small interfering (si) RNA could inhibit HCC progression. We also investigated molecular mechanism to mediate HCC cell death caused by CDCA8 silencing. To accomplish this, Huh1 and Huh7 human HCC cells were transfected with CDCA8 siRNA and tested for growth inhibition and apoptotic induction using MTS, FACS and microscopic analysis. To obtain insights into the molecular changes in response to CDCA8 knockdown, global changes in gene expression were examined using RNA sequencing. As results, siRNA silencing of CDCA8 inhibited HCC cell growth by blocking cell-cycle progression and inducing apoptosis. RNA sequencing showed that, representatively, the anti-proliferative effects were driven by a subset of molecular alterations including the upregulation of tumor suppressive ATF3 and GADD34 genes, whereas a key regulator of cell growth and invasiveness BGLAP was repressed. Subsequent Western blotting also revealed that CDCA8 silencing decreases the levels of pro-caspase 3 and PARP-1, accelerating apoptotic signaling in HCC cells. In addition, targeting CDCA8 effectively suppressed HCC tumor growth growth in a murine xenograft model. Taken together, these findings suggest that CDCA8 could be a promising molecular target for systemic therapy of HCC.

overall_design: Examination of 2 different siRNA transfected cells in 2 cell lines.

first: Tae-Won

last: Jeon

first: Yun-Han

last: Lee


title: The expression profiles of microRNAs in Kaposi’s sarcoma

status: Public on Mar 05 2017

city: Urumqi

first: Xiu-Juan

last: Wu

state: Xinjiang

address: 91 Tianchi Road

department: Department of Dermatology

country: China

institute: People’s Hospital of Xinjiang, Uygur Autonomous Region

summary:
MicroRNAs (miRNAs) are non-protein-coding small RNAs in the size range 19–25 nucleotides (nt) that are cleaved from 70-100 nt hairpin pre-miRNA precursors.MiRNAs bind to complementary sequences in the 3′-untranslated regions of their target mRNAs and induce mRNA degradation or translational repression. Recent intensive studies have revealed that miRNAs play important roles in a large number of biological processes, including cellular differentiation, proliferation and death. These wide-ranging biological roles suggest that miRNAs may be involved in cancer development. MiRNAs regulate a variety of biological processes, including developmental timing, signal transduction, cell growth, and cell death.Kaposi’s sarcoma (KS) is a multicentric angioproliferative tumor of mesenchymal origin.8, 9 In 1872, the disease was first described by Moritz Kaposi, and it mostly affects elderly men of Italian, Jewish, or Mediterranean origin. In China, more than 90% of KS cases occur in Xinjiang,12-14 which is a multiethnic gathering place where Uyghur (45.7%) and Han (39.7%) are the main ethnic groups; other groups include the Kazakh (7%) and Hui(4.5%). The specific geographical environment and ethnic specificity may characterize some of the specific features of KS in this area, which might also be reflected in the miRNA expression profile in KS tissues.
MicroRNAs (miRNAs) are non-protein-coding small RNAs in the size range 19–25 nucleotides (nt) that are cleaved from 70-100 nt hairpin pre-miRNA precursors.MiRNAs bind to complementary sequences in the 3′-untranslated regions of their target mRNAs and induce mRNA degradation or translational repression. Recent intensive studies have revealed that miRNAs play important roles in a large number of biological processes, including cellular differentiation, proliferation and death. These wide-ranging biological roles suggest that miRNAs may be involved in cancer development. MiRNAs regulate a variety of biological processes, including developmental timing, signal transduction, cell growth, and cell death.Kaposi’s sarcoma (KS) is a multicentric angioproliferative tumor of mesenchymal origin.8, 9 In 1872, the disease was first described by Moritz Kaposi, and it mostly affects elderly men of Italian, Jewish, or Mediterranean origin. In China, more than 90% of KS cases occur in Xinjiang,12-14 which is a multiethnic gathering place where Uyghur (45.7%) and Han (39.7%) are the main ethnic groups; other groups include the Kazakh (7%) and Hui(4.5%). The specific geographical environment and ethnic specificity may characterize some of the specific features of KS in this area, which might also be reflected in the miRNA expression profile in KS tissues.

overall_design: KS tissues and matched normal tissues were obtained from surgical specimens immediately after resection from Jan 2012 to Sep 2013 in the Department of Dermatology, People’s Hospital of the Xinjiang Uyghur Autonomous Region, China.The samples were flash frozen in liquid nitrogen and stored at -180℃until RNA extraction.  RNA labeling and hybridization were completed by KangChen Bio-tech Inc. (Shanghai, China) according to the manufacturer's instructions. Briefly,Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions. After having passed RNA quantity measurement using the NanoDrop 1000, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.18.0) which contains probes for 3100 mature miRNA.Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner.Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

first: Xiong-Ming

last: Pu


title: Col-0 leaves and root, control and iron-deficient

status: Public on Oct 08 2016

city: Taipei

first: Louis

last: Grillet

address: 128 Sec.2, Academia Rd., Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

summary: RNAseq transcriptome of leaves and roots of Arabidopsis thaliana Columbia-0 grown under control (ES media) and Fe-deficiency (-Fe +100 µM FRZ) conditions.

overall_design: Control Col-0 leaves and roots compared to Fe-deficient leaves and roots

first: Wolfgang

last: Schmidt


title: Microarray gene expression profiling of isolated class III Drosophila dendritic arborization sensory neurons

status: Public on Sep 21 2016

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

summary: Class III Drosophila dendritic arborization sensory neurons were isolated via magnetic bead sorting and total RNA isolated from the samples was used for gene expression profiling to explore molecular functions of this sensory neuron subtype.

overall_design: Gene expression profiling of class III da neurons, isolated via magnetic bead sorting (using protocols as described in Iyer et al., 2009), was performed at the third instar larval stage of development.  40-50 aged-matched third instar larvae of genotype ppk-Gal4,UAS-mCD8::GFP,ppk-Gal80 (labels class III dendritic arborization sensory neurons (Iyer et al., 2013)) were used to perform independent class III-specific cell isolations.  These datasets were also directly compared with GSE46154 containing microarray datasets for class I and class IV dendritic arborization sensory neurons and age matched whole larval homogenate RNA.

first: S

last: Iyer

last: Bhattacharya

first: D

middle: N

last: Cox


title: IMA1 OE #7-4 line compared to EYFP OE line (control)

summary: RNAseq transcriptome of IRON MAN1 OE line. IMA1 OE plants accumulate Fe in their tissue and exhibit a constitutive induction of their root Fe uptake system.

overall_design: Control and Fe-deficient IMA1 OE leaves and root compared to EYFP OE (control plants) grown under control conditions


title: Differential gene expressions in the heart of hypertrophic cardiomyopathy patients

status: Public on Nov 10 2016

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Differential gene expressions were constructed through expression profiling of a total of 20,127 genes in the heart tissue of hypertrophic cardiomyopathy patients, then 1799 significant differential genes were filtered based on the criteria (p<0.05 and fold change > 1.5), respectively.

overall_design: In the study presented here, human hypertrophic heart tissue samples were obtained from patients previously diagnosed with hypertrophic cardiomyopathy, undergoing septal myectomy surgery (n=5). Control samples were obtained from normal heart donor left ventricles (n=4). The heart tissues were collected and performed transcriptome analysis by RNA-sequencing. Compared to normal heart, 1799 significant differentially expressed genes (filtering criteria p<0.05, fold change>1.5) were identified 7-days or 28 days post-Ang II infusion.

first: Yulin

last: Li

first: Hongchang

last: Guo


title: Silencing of cryptic prophages in Corynebacterium glutamicum

status: Public on Sep 14 2016

first: Tino

last: Polen

summary: DNA microarrays were applied to investigate the transcriptome of C. glutamicum cells and to identify potential target genes under CgpS countersilencing conditions. The silencing activity of CgpS was reduced by overexpression of the N-terminal part, which was placed under the control of the inducible tac promoter in the pAN6 plasmid. The expression of the N terminal part was induced with 100 µM IPTG.

overall_design: DNA microarray analysis were performed with three biological replicates. The transcriptome of C. glutamicum cells in which CgpS activity was downregulated by countersilencing was compared to the transcriptome of C. glutamicum wt cells containing the empty plasmid. Countersilencing was achieved by overexpression of the N-terminal part of CgpS with 100 µM IPTG.

first: Eugen

last: Pfeifer

first: Max

last: Hünnefeld

first: Ovidiu

last: Popa

first: Meike

last: Baumgart

first: Dietrich

last: Kohlheyer

first: Julia

last: Frunzke


title: The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas

status: Public on Oct 06 2016

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Over 90% of chondroblastomas contain a heterozygous mutation replacing lysine 36 with methionine (K36M) in the histone H3 variant H3.3. The role of the H3.3K36M mutation in tumorigenesis of this typically benign bone tumor with high recurrence rates is unknown. Here, we show that H3K36 di- and tri-methylation (me2 and me3) levels are reduced globally in chondroblastomas, as well as in chondrocytes stably expressing the H3.3K36M mutation because the H3.3M36 mutation protein inhibits the activity of lysine methyl transferases, MMSET and SetD2. Remarkably, at gene bodies, H3K36me2 increases and H3K36me3 decreases, which correlates with elevated and reduced expression of the underlying genes, respectively. Genes with altered H3K36me2/me3 and gene expression are associated with cancer pathways and chondrocyte differentiation.  Chondrocytes harboring the H3.3K36M mutation exhibit cancer-associated cellular phenotypes and delayed chondrocyte differentiation associated with reduced Bmp2 and Runx2 expression.  Exogenous Bmp2 partially rescued the delays in chondrocyte differentiation.  Thus, H3.3K36M mutant proteins dominantly reprogram H3K36me2/me3 and chondrocyte gene expression, inhibiting terminal chondrocyte differentiation and contributing to tumorigenesis.

overall_design: To analyze how H3K36me2 and H3K36me3 are altered throughout the epigenome, we performed H3K36me2 and H3K36me3 ChIP-seq in chondrocyte cell lines and tissue samples. And RNA-seq in chondrocyte cell lines and tissue samples.

first: Jing

last: Han

first: Jeong-Heon

last: Lee

first: Andre

last: van Wijnen

first: Scott

last: Riester

last: Oliveira

first: Dong

last: Fang

first: Haiyun

last: Gan

first: Zhiguo

last: Zhang


title: Non-canonical Wnt signaling via FZD5 and ROR2 contributes to the maintenance of the stemness of human mesenchymal stem cells

status: Public on Sep 02 2016

city: Tokyo

first: Yo

last: Mabuchi

address: 35 Shinanomachi, Shinjuku-ku

department: Physiology

institute: Keio University School of Medicine

summary: We previously showed that the combination of markers LNGFR+ and THY-1+ can be used selectively to isolate human mesenchymal stem cells (hMSCs) in bone marrow and several tissues. However, the molecular mechanisms regulating stemness of hMSCs remain to be elucidated. In this study, we found that Frizzled 5 (FZD5) and Receptor tyrosine kinase-like orphan receptor 2 (ROR2) were highly enriched in LNGFR+THY-1+ derived clones that retain a high potential for proliferation (rapidly expanding clones; RECs). WNT5A, the ligand of FZD5, causes FZD5 and ROR2 to co-localize and activates non-canonical Wnt pathway in RECs. Moreover, FZD5 knockdown attenuated proliferation and caused senescence. In contrast, FZD5 overexpression delayed senescence. These results indicate that intrinsic activation of non-canonical Wnt signaling via FZD5 and ROR2 modulates stemness and senescence of RECs. Thus, control of non-canonical Wnt signaling would enable us to regulate hMSC quality and to enhance the efficacy of cell-replacement therapy using hMSCs.

overall_design: Several human MSC clones that did not have any copy-number abnormality (two REC clones, three MEC clones, and three SEC clones) were cultured, and total RNA was extracted.Next, 300 ng of total RNA was labeled with Cy3 and hybridized to an Agilent human whole-genome chip (4x44K, AMADID=14850, Agilent technologies), which was scanned in a microarray scanner system (Agilent Technologies).These candidate genes were split into four clusters according to K-means (n=63). We performed quantitative PCR to validate the expression levels of genes whose expression levels were over two-fold (Group 1) and one- to two-fold (Group 2) higher in RECs than in MECs/SECs.

first: Seiko

last: Harada

first: Jun

last: Kohyama

first: Sadafumi

last: Suzuki

first: Yoshimi

last: Kawamura

first: Daisuke

last: Araki

first: Masunori

last: Kajikawa

first: Hideyuki

last: Okano

first: Yumi

last: Matsuzaki


title: PolyA RNAseq from HCT116 cells in normoxia and hypoxia

status: Public on Jun 02 2016

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: To determine the effects of depleting TIP60, CDK8, or HIF1A on the transcriptional response to hypoxia, we performed RNAseq analysis of four HCT116 colorectal carcinoma cell lines (shNT, HIF1A-/-, shTIP60 and shCDK8) in normoxic and hypoxic (24hrs, 1% O2) conditions.

overall_design: PolyA RNA for two independent biological replicates was purified from HCT116 cells stably expressing an shRNA against a non-targeting control (shNT), TIP60 (shTIP60) or CDK8 (shCDK8), or genetically deleted HIF1A (HIF1A-/-) subjected to 24hrs 1% O2 (hypoxia) or maintained under ambient oxygen (21%; normoxia) was sequenced on the Ion Torrent platform. Reads were aligned to the human genome and gene-level counts were used for differential expression analysis.

first: Veronica

middle: L

last: Dengler

first: Ahwan

last: Pandey


title: Genome-wide RNA-sequencing of human islets 48 hour after transduction with adenoviruses expressing either GFP (control), or histone chaperone ASF1B.

status: Public on Sep 10 2016

city: Madison

first: Pradyut

last: Paul

state: Wisconsin

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

summary: Comparison of gene expression in pancreatic islets of BTBR-ob/ob mouse model of obesity-induced type 2 diabetes, and in non-diabetic control mice, B6-ob/ob identified Asf1b as an important gene candidate predictive of diabetic outcome. Asf1B expression was suppressed in response to age in both B6 and BTBR islets, induced by obesity only in B6 islets. This is consistent with other studies reporting a decline in -cell proliferation with age. Asf1b also strongly correlated (R ~ 0.98) with cellular proliferation marker Mki67. Overexpression of Asf1B induced β-cell proliferation in human islets. We show that many genes involved in regulation of cell cycle or programmed cell death are differentially regulated by Asf1B overexpression.

overall_design: Ten different human islet preparations were obtained from 9 individual donors (from IIDP program). Each preparation contained approximately 20,000 islet equivalent units. Each islet preparation was separated into two portions for adenoviral transduction to overexpress GFP (control) or ASF1B genes.


title: NOTCH1 mediates a reciprocal switch between two distinct secretomes during senescence [CSM]

status: Public on Jun 22 2016

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: ER:RAS-G12V expressing IMR90 cells were treated with either 100nM 4-OHT for 6 days or 100uM Etoposide for 2 days, followed by further culture for 5 days, leading to RAS-induced senescence (RIS) and DNA-damage induced senescence (DDIS) respectively.

overall_design: IMR90 cells expressing a 4-hydroxytamoxifen (4-OHT) inducible estrogen receptor (ER)-coupled RAS-G12V (ER:RAS-G12V) were treated with either 100nM 4-OHT for 6 days or 100uM Etoposide for 2 days, followed by further culture for 5 days, leading to RAS-induced senescence (RIS) and DNA-damage induced senescence (DDIS) respectively.  The total RNA was then analysed for transcriptional profiling using mRNA-sequencing. There were 8 (eight) biological replicatesfor each of the experimental conditions. Untreated ER:RAS IMR90 cells were the control condition

last: Hoare

first: Masashi

last: Narita

first: Suraj

last: Menon


title: RNA sequencing of  C57BL/6J mice, heterozygous for knockout of Hnrnph1 gene, as well as C57BL/6J mice controls

status: Public on Feb 01 2017

city: Medford

first: Eric

last: Reed

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

summary: Previous studies of congenic lines of C57BL/6J-DBA/2J mice compared to C57BL/6 mice revealed a 0.23 QTL for sensitivity to methamphetamine on chromosome 11, which contains two protein coding genes, Rufy1 and Hnrnph1.  Subsequent transcription activator-like effector nucleases (TALENs)-mediated introduction of frameshift deletions in the first coding exon of one copy of Hnrnph1 of C57BL/6J mice, revealed comparable association to phenotype.  Analysis of the transcriptome and splicesome between these Hnrnph1 heterozygous knockouts and C57BL/6J mice revealed genome-wide differentially expression and exon usage of more than 1000 genes in either.

overall_design: For this study, 3mm punches from both striatal hemispheres were collected and pooled from 16 mice (8 C57BL/6J controls (B6) and 8 C57BL/6J Hnrnph1 heterozygous knockouts (H), and RNA was extracted and prepared for cDNA library preparation using the Illumina TruSeq Stranded mRNA LT (100bp paired-end reads). Samples 1-16, consisting of alternating experiments were run in four lanes total (each sample run on each lane) across 3 different flow cells. Raw samples provided are labeled with the "H1-" prefix, followed by the the sample number and the lane that it was run (L001, L002, or L008) and paired-end read number (R1 or R2). The tail of the file name pertains to the flow cell number (0009, 0012, or 0014).

first: Neema

last: Yazdani

first: Camron

last: Bryant


title: NOTCH1 mediates a reciprocal switch between two distinct secretomes during senescence

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

overall_design: Refer to individual Series


title: ATAC-seq data

status: Public on Jun 01 2016

first: Jason

middle: Daniel

last: Buenrostro

address: 415 Main Street

institute: Broad Institute

summary: A single hematopoietic stem cell can give rise to all blood cells with remarkable fidelity. Here, we define the chromatin accessibility and transcriptional landscape controlling this process in thirteen primary cell types that traverse the hematopoietic hierarchy. Exploiting the finding that enhancer landscapes better reflect cell identity than mRNA levels, we enable "enhancer cytometry" for accurate enumeration of pure cell types from complex populations. We further reveal the lineage ontogeny of genetic elements linked to diverse human diseases. In acute myeloid leukemia, chromatin accessibility reveals distinctive regulatory evolution in pre-leukemic HSCs (pHSCs), leukemia stem cells, and leukemic blasts. These leukemic cells demonstrate unique lineage infidelity, confirmed by single cell regulomes. We further show that pHSCs have a competitive advantage that is conferred by reduced chromatin accessibility at HOXA9 targets and is associated with adverse patient outcomes. Thus, regulome dynamics can provide diverse insights into human hematopoietic development and disease.

overall_design: ATAC-seq profiles of hematopoietic and leukemic cell types, across 13 normal hematopoietic cell types and 3 acute myeloid leukemia cell types. The complete data set contains a total of 132 samples.


title: C.glutamicum Δpup mutant senses a stronger iron limitation than the wild type.

status: Public on Apr 04 2016

city: Juelich

first: Tino

last: Polen

address: Wilhelm-Johnen-Str 1

institute: Forschungszentrum Jülich GmbH

summary: Pupylation is a posttranslational protein modification in bacteria resembling ubiquitination in eukaryotes. The prokaryotic ubiquitin-like protein Pup is covalently attached to other proteins via an isopeptide bond between its carboxyterminal glutamate residue and a lysine residue in the target. In mycobacteria, pupylation was shown to mark proteins for unfolding by the ATPase Mpa and subsequent degradation by the proteasome. However, the occurrence of pupylation in species without a proteasome like Corynebacterium glutamicum suggests that degradation may not be the only fate of pupylated proteins.  The Δpup mutant senses a stronger iron limitation than the wild type. Among the 125 genes showing at least 2-fold changes in transcript levels in the Δpup mutant (p-value ≤ 0.05) were 54% of all genes known to be regulated by the master regulator of iron homeostasis DtxR (Brune et al., 2006; Wennerhold and Bott, 2006). Except for ftn, which is activated by DtxR and showed a 2-fold decreased mRNA level, the other DtxR target genes showed increased mRNA levels in the Δpup strain. These included ripA, encoding a transcriptional regulator of iron proteins, which represses a number of prominent iron-containing proteins under iron limitation, such as aconitase or succinate dehydrogenase (Wennerhold et al., 2005). 79% of the known RipA target genes showed decreased mRNA levels in the Δpup strain.

overall_design:
DNA microarray analyses were performed to compare the mRNA levels of the C. glutamicum Δpup mutant and its parent wild type under iron-limited conditions. The two strains precultivated in CGXII medium with 4% (w/v) glucose and 1 µM FeSO4 were inoculated into fresh medium to an OD600 of 1, cultured for 2 h, and harvested on ice by centrifugation (5 min at 4,000 g and 4°C).

Please note that the GPL16989 array design comprises oligos for 4 different bacterial genomes. In the GPR-files in this study, all IDs/Names (oligonucleotides) which are not from the host C. glutamicum were replaced by the text EMPTY since only C. glutamicum expression was analyzed.

first: Andreas

last: Küberl

first: Michael

last: Bott


title: Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution

relation:
SuperSeries of: GSE74246
SuperSeries of: GSE74310
SuperSeries of: GSE74912


title: Gene expression profiling of small intestinal eosinophils of BALB/c mice after stimulation with GM-CSF

status: Public on Apr 30 2016

city: Tsukuba

first: Yutaro

last: Kumagai

address: Central 5-41, Higashi 1-1-1

institute: AIST

summary: Next generation sequencing was performed to conprehensively investigate the changes of gene expression of small intestinal eosinophils of mice after stimulation with GM-CSF in vitro.

overall_design: Lamina propria eosinophils were collected from small intestine of wild-type BALB/c mice. Eosinophils were stimulated with 10 ng/ml GM-CSF for 4 hours. Cells were cultured in triplicate. Total RNA was extracted and subjected to next generation sequencing analysis.

first: Naoki

last: Takemura

first: Satoshi

last: Uematsu

first: Yutaka

last: Suzuki


title: FAIRE-seq 1,25(OH)2D3 time course in THP-1 cells

status: Public on Jan 02 2016

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

institute: University of Eastern Finland

summary: Assessment of regions of open chromatin by FAIRE-seq in THP-1 cells treated with 1,25(OH)2D3 for 0-48 h

overall_design: Three independent experiments of 1,25(OH)2D3 time course in THP-1 cells

first: Sabine

last: Seuter

first: Antonio

last: Neme


title: Long noncoding RNA expression during human B-cell development

status: Public on Feb 09 2016

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

institute: Aalborg University Hospital

summary: Long noncoding RNAs (lncRNAs) have emerged as important regulators of diverse cellular processes, but their roles in the developing immune system are poorly understood. In this study, we analysed lncRNA expression during human B-cell development by array-based expression profiling of eleven distinct flow-sorted B-cell subsets, comprising pre-B1, pre-B2, immature, naive, memory, and plasma cells from bone marrow biopsies (n=7), and naive, centroblast, centrocyte, memory, and plasmablast cells from tonsil tissue samples (n=6), respectively. A remapping strategy was used to assign the array probes to 37630 gene-level probe sets, reflecting the most recent updates in genomic and transcriptomic databases, which enabled expression profiling of 19579 long noncoding RNAs, comprising 3947 antisense RNAs, 5277 lincRNAs, 7625 pseudogenes, and 2730 additional lncRNAs. As a first step towards inferring the functions of the identified lncRNAs in developing B-cells, we analysed their co-expression with well-characterized protein-coding genes, a method known as “guilt by association”. By using weighted gene co-expression network analysis, we identified 272 lincRNAs, 471 antisense RNAs, 376 pseudogene RNAs, and 64 lncRNAs within seven sub-networks associated with distinct stages of B-cell development, such as early B-cell development, B-cell proliferation, affinity maturation of antibody, and terminal differentiation. These data provide an important resource for future studies on the functions of lncRNAs in development of the adaptive immune response, and the pathogenesis of B-cell malignancies that originate from distinct B-cell subpopulations.

overall_design: Tonsils were collected from six patients (homo sapiens) during routine tonsillectomy. Mononuclear cells were isolated from tonsils and prepared for multiparametric flow cytometry using an optimized and validated protocol. B-cell subsets of naive, centroblasts, centrocytes, menory and plasmablast cells were isolated and a total of 30 gene expression profiles were generated using the HuEx-1_0-st-v2-micro array chip from Affymetrix.

last: Petri

first: Karen

last: Dybkær

first: Martin

last: Bøgsted

first: Charlotte

last: Thrue

first: Peter

middle: H

last: Hagedorn

first: Alexander

last: Schmitz

middle: S

first: Hans

last: Johnsen

first: Sakari

last: Kauppinen


title: Identification of a gene cluster involved in the utilization of phenylpropanoids in Corynebacterium glutamicum [set1]

status: Public on Nov 30 2015

first: Tino

last: Polen

department: IBG-1: Biotechnology

summary: DNA microarray experiments with phenylpropanoid pulses were performed in order to get hints on expression of relevant genes or gene clusters activated in presence of phenylpropanoid compounds. We determined the relative mRNA-levels of wild-type cells confronted with phenylpropanoids and unpulsed cells. A pulsing time of 30 minutes was sufficient to find regulation of gene expression in response to the phenylpropanoid amount of 5 mM (final concentration) added. A relatively short pulsing time was preferred over the cultivation of the strain with phenylpropanoids in comparison to growth on glucose because a completely different growth behavior was expected when using two completely unrelated carbon sources.

overall_design: DNA microarray experiments were performed in two biological replicates. The transcriptome of C. glutamicum cells pulsed for 30 minutes before harvest with 5 mM of phenylpropanoids (p-coumaric acid) was compared to the transcriptome of C. glutamicum wt cells.

first: Nicolai

last: Kallscheuer

last: Vogt

last: Bott

first: Jan

last: Marienhagen


title: Identification of a gene cluster involved in the utilization of phenylpropanoids in Corynebacterium glutamicum [set2]

overall_design: DNA microarray experiments were performed in two or three biological replicates. The transcriptome of C. glutamicum cells pulsed for 30 minutes before harvest with 5 mM of phenylpropanoids (cinnamic acid or p-coumaric acid or caffeic acid or ferulic acid or 3-(4-hydroxyphenyl-)propionic acid) was compared to the transcriptome of C. glutamicum wt cells. Additional pulse experiments were done with a 5 mM 4-hydroxybenzoic acid pulse under identical conditions. Furthermore, relative mRNA-levels for deletion strain C.g. Δcg0343 / C.g. wt was analyzed.

first: Michael


title: 1,25(OH)2D3 time course in THP-1 cells

status: Public on Jan 01 2016

last: Carlberg


title: Identification of a gene cluster involved in the utilization of phenylpropanoids in Corynebacterium glutamicum


title: RNAseq Analysis of Transcriptome expression profiles in E13.5 Foxf2-/-Osr2RFP/+ and control palatal mesenchymal cells

status: Public on Dec 28 2015

city: Cincinnati

first: Jingyue

last: Xu

state: Ohio

address: 3333 burnet avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose:  The purpose of this study is to compare the transcriptome expression profiles of E13.5 Foxf2-/-;Osr2RFP/+ and control palatal mesenchyme by using RNA-seq analysis.
Methods: Foxf2+/- female mice were crossed with Foxf2+/-;Osr2RFP/+ male mice.The embryos were harvested at E13.5. The pair of palatal shelves were dissected from each Osr2-RFP+ embryo. The RFP+ palatal mesenchyme cells were isolated by using fluorescence-activated cell sorting (FACS). RNA-seq analysis was carried out using the FACS-isolated palatal mesenchyme from Foxf2-/-;Osr2RFP/+, Foxf2+/-;Osr2RFP/+ and Osr2RFP/+embryos, respectively.

overall_design: The transcriptome expression profiles of E13.5 control and Foxf2-/-Osr2RFP/+ palatal mesenchyme by using RNA-seq analysis,  in duplicates, using Illumina HisEq 2000.

first: Rulang

last: Jiang


title: A cross species and multi-omics (including metabolomics) analysis in pancreatic neuroendocrine tumours

status: Public on Oct 30 2015

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

institute: Institute of Cancer Research (ICR), London

summary: Pancreatic neuroendocrine tumor (PanNET) is relatively infrequent but is nevertheless metastatic. Seeking to extend a new paradigm of personalized medicine, we performed an integrative analysis of transcriptomic (mRNA and microRNA) and mutational profiles and defined three clinically relevant human PanNET subtypes. Importantly, cross-species analysis revealed two of these three subtypes in a well-characterized, genetically engineered mouse model (RIP1-Tag2) of PanNET and its cell lines. Each subtype share similarities to distinct cell types in pancreatic neuroendocrine development, features are reflected in their metabolic profiles. Subtype-specific molecular signatures metabolites are proposed to identify these subtypes.

overall_design: RNA was extracted from fresh frozen archival patient PanNET samples and hybridized on Affymetrix GeneChip human Gene 1.0 ST arrays. The CEL files were processed using R based bioconductor and normalized values were obtained using RMA.

first: A

first: C

last: Grotzinger

first: B

last: Wiedenmann

first: D

last: Hanahan


title: RNA-seq 1,25(OH)2D3 time course in THP-1 cells

first: Carsten

summary: gene expression profiling by RNA-seq in THP-1 cells treated with 1,25(OH)2D3 for 2.5-24 h

overall_design: three independent experiments of 1,25(OH)2D3 time course in THP-1 cells

first: Sabine

last: Seuter

first: Antonio

last: Neme


title: Gene expression changes in Corynebacterium glutamicum at increased growth temperature in the absence of PPIase FkpA

status: Public on Sep 08 2015

summary: Comparative transcriptome analyses revealed 69 genes exhibiting ≥2-fold mRNA level changes in C. glutamicum DfkpA.Overall, 34 genes exhibited ≥2-fold increased and 35 genes at least 0.5-fold decreased mRNA levels in JVO1 DfkpA. About half of these genes (32) encode for hypothetical/putative proteins. LdhA encoding L-lactate dehydrogenase exhibited by far the strongest increased mRNA level (8.5-fold) in the absence of FkpA. Determination of the respective specific LdhA activities revealed about 2-fold increased activity in JVO1 DfkpA (0.73 ± 0.05 U/mg) compared to the reference JVO1 (0.41 ± 0.02 U/mg). Notably, the two short gene lists include four genes encoding transcriptional regulators exhibiting increased mRNA levels (farR, lexA, divS, znr) and two exhibiting decreased mRNA levels (ramB, mmpLR) in the absence of FkpA under the conditions tested. The mRNA level of cysK was increased (2.05-fold) which is repressed by RamB whose mRNA level was decreased (0.27-fold). In contrast, the mRNA level of RamB-repressed ald was decreased (0.31-fold) and not increased.

overall_design: To identify the influence of PPIase FkpA on global gene expression, DNA microarray analyses were performed with a ΔfkpA mutant compared to the reference C. glutamicum JVO1. For this purpose RNA was isolated from exponentially growing cells cultivated in CgXII minimal medium with 4% glucose at increased temperature (35°C) above growth optimum of C. glutamicum. Two biological replicates were performed with each representing an intra-array duplicate.

first: M

first: J

last: van Ooyen

first: T


title: An integrated genetic-epigenetic analysis of schizophrenia: Evidence for co-localization of genetic associations and differential DNA methylation

status: Public on Aug 01 2016

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

institute: University of Exeter

type: Methylation profiling by genome tiling array

summary:
Background: Schizophrenia is a severe, highly heritable, neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. Despite success in identifying genetic variants associated with schizophrenia, there remains uncertainty about the causal genes involved in disease pathogenesis and how their function is regulated. Insights into the functional complexity of the genome have focussed attention on the role of non-sequence-based genomic variation in health and disease. Although a better understanding of the molecular mechanisms underlying disease phenotypes is best achieved using an integrated functional genomics strategy, few studies have attempted to systematically integrate genetic and epigenetic epidemiological approaches.
Results: We performed a multi-stage epigenome-wide association study (EWAS), quantifying genome-wide patterns of DNA methylation in a total of 1,801 individuals from three independent sample cohorts. We identified multiple differentially methylated positions (DMPs) and region (DMRs) associated with schizophrenia, independently of important confounders such as smoking, with consistent effects across the three independent cohorts. We also show that polygenic burden for schizophrenia is associated with epigenetic variation at multiple loci across the genome, independently of loci implicated in the analysis of diagnosed schizophrenia. Finally, we show how DNA methylation quantitative trait loci (mQTL) analyses can be used to annotate the extended genomic regions nominated by genetic studies of schizophrenia, with Bayesian co-localization analyses highlighting potential regulatory variation causally involved in disease.
Conclusion: This study represents the first systematic integrated analysis of genetic and epigenetic variation in schizophrenia, introducing a methodological pipeline that can be used to inform EWAS analyses of other complex traits and diseases. We demonstrate the utility of using polygenic risk score (PRS) for identifying molecular variation associated with etiological variation, and mQTLs for refining the functional/regulatory variation associated with schizophrenia risk variants. Finally, we present strong evidence for the co-localization of genetic associations for schizophrenia and differential DNA methylation.

overall_design: 675 whole blood derived DNA samples (353 schizophrenia cases and 322 controls)  representing phase 1 of our meta-analysis. Bisulfite converted DNA from these samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip v1.0.

first: Eilis

last: Hannon

first: Emma

last: Dempster

first: Joana

last: Viana

first: Joe

last: Burrage

first: Adam

last: Smith

first: Ruby

last: Macdonald

first: David

last: St. Clair

first: Colette

last: Mustard

first: Gerome

last: Breen

first: Sebastian

last: Therman

first: Jaakko

last: Kaprio

first: Timothea

last: Toulopoulou

first: Hilleke

last: Hulshoff Pol

first: Marc

middle: M

last: Bohlken

first: Rene

last: Kahn

first: Igor

last: Nenadic

first: Christina

last: Hultman

first: Robin

last: Murray

last: Collier

first: Nick

last: Bass

first: Hugh

last: Gurling

first: Andrew

last: McQuillin

first: Leonard

last: Schalkwyk


title: Gene expression analyses of primary tumors and metastases, using p53 mouse models

status: Public on Mar 12 2015

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Osteosarcoma (OS) is the most frequent malignant bone tumor with a high propensity for metastases.  Through the tissue-specific alteration of p53 status, we have developed a genetically engineered mouse model of localized and metastatic OS.   Gene expression analysis revealed naked cuticle homolog 2 (NKD2), a negative regulator of the Wnt signaling pathway, to be significantly downregulated in metastatic OS.  An assessment of human OS tumors revealed downregulation of NKD2 in metastatic and recurrent OS.  We determined that downregulation was secondary to methylation of the NKD2 promoter region for both mouse and human tumors.  Furthermore, in vivo investigations indicate that NKD2 overexpression significantly diminishes OS tumor growth and metastasis and small molecule Wnt inhibitors can decrease OS growth and metastatic potential.

overall_design:
Development of novel osteoblast-specific alteration of a p53 mouse model that forms de novo localized and gross, macroscopic osteosarcoma that mimics the human disease allowing determination of novel genetic alterations involved in OS progression. Gene expression profiling of primary osteosarcomas (OS) and OS metastases to lung and liver. In order to identify genes and pathways that regulate OS metastasis, we performed an initial screen comparing the gene expression profiles of six localized, non-metastatic OS with those of 12 primary OS that produced metastatic lesions.  In addition, seven lung metastatic lesion gene expression profiles were compared to those of the primary tumor from which they originated.
multiple group comparison

first: Jason

last: Yustein

first: Larry

last: Donehower


title: A prophage encoded actin-like protein mediates viral DNA segregation/replication in bacteria [Set1]

status: Public on May 01 2015

first: Tino

last: Polen

summary: Active segregation of DNA in bacteria is catalyzed by cytomotive structures. Mediators of subcellular plasmid positioning are Walker-type ATPases (ParA), actin-like proteins, or tubulin homologs. These motor proteins are coupled to the DNA via adaptor proteins that recognize specific DNA motifs. Here, we describe that a temperate phage, CGP3, integrated into the genome of Corynebacterium glutamicum ATCC 13032 encodes an actin-like protein, AlpC. Biochemical characterization confirms that AlpC is a bona fide actin-like protein and cell biological analysis shows that AlpC forms dynamic filamentous structures upon phage induction. The co-transcribed AlpA protein binds to a specific region of the phage DNA, possibly functioning as an adaptor protein that connects circular phage DNA to the tips of the AlpC filaments. The AlpC filaments transport phage DNA to the cell membrane of the host cell. Furthermore, both AlpA and AlpC are required for efficient phage replication. This is remarkably similar to actin-assisted membrane localization of eukaryotic viruses that use the actin cytoskeleton to concentrate virus particles at the egress sites.

overall_design: To identify the stress response induced by the antibiotic agent mitomycin C, DNA microarray analyses were performed of ATCC 13032 wild type cells treated with 0.6 µM mitomycin C in comparison to untreated cells at one, three, and six hours after addition of mitomycin C.  For this purpose RNA was isolated from cells cultivated in CGXII minimal medium with 4% glucose, either treated with 0.6 µM Mitomycin C or untreated. Mitomycin C was added at an OD of 3 and cells were harvested after one, three, and six hours after addition of mitomycinC. Three biological replicates were performed for each time point.

first: Catriona

last: Donovan

first: Antonia

last: Heyer

first: Anja

last: Wittmann

first: Reinhard

last: Krämer

first: Julia

last: Frunzke

last: Bramkamp


title: A prophage encoded actin-like protein mediates viral DNA segregation/replication in bacteria [Set2]

overall_design: To identify the stress response induced by the antibiotic agent mitomycin C, DNA microarray analyses were performed of ATCC 13032 wild type cells treated with 0.6 mM mitomycin C in comparison to untreated cells at one, three, and six hours after addition of mitomycin C.  For this purpose RNA was isolated from cells cultivated in CGXII minimal medium with 4% glucose, either treated with 0.6 µM Mitomycin C or untreated. Mitomycin C was added at an OD of 3 and cells were harvested after one, three, and six hours after addition of mitomycinC. Three biological replicates were performed for each time point.

first: Marc


title: Expression data from zebrafish embryos

status: Public on Sep 26 2015

first: Junchao

last: Duan

address: Xi Tou Tiao 10, You An Men street, FengTai, Beijing,100069, China

department: School of Public Health

institute: Capital Medical University

summary:
Zebrafish embryos are sensitive to chemical substance and often used as a in vivo model for enviromental toxicology research.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes after treated with chemical substance

overall_design: Zebrafish embryos were selected at early development stages for RNA extraction and hybridization on Affymetrix microarrays. We tested the expression data of zebrfish embryos treated with  silica nanoparticles (SiNPs), benzo[a]pyrene (B[a]P), and SiNPs+B[a]P, respectively.

first: Zhiwei

last: Sun


title: dDsk2 stabilizes dHP1c binding at TSS [ChIP-Seq]

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: The Drosophila ubiquitin receptor dDsk2 associates to chromatin and stabilizes binding of the euchromatic dHP1c/WOC/ROW-complex (dHP1EU) to the transcription-start site (TSS) of active genes

overall_design: ChIP-Seq peak calling of WOC, ROW, Z4, HP1c and Dsk2 against Input sample in Drosophila melanogaster S2 cells

first: Roman

last: Kessler

first: Fernando

last: Azorín


title: A prophage-encoded actin-like protein required for efficient viral DNA replication in bacteria

overall_design: Refer to individual Series

first: Eugen

last: Pfeifer


title: Differential microarray expression profile analysis of long non-coding RNAs in umbilical cord vein plasma from normal and gestational diabetes-induced macrosomia

status: Public on Feb 25 2015

city: Nanjing

first: Shi

last: Zhonghua

address: Tianfei Lane, Mochou Road

institute: Nanjing Maternity and child health care hospital

summary: To investigate the umbilical cord lncRNA profiles in gestational diabetes-induced  macrosomia, the umbilical cord vein blood from normal and gestational diabetes-induced macrosomia was hybridized to a microarray containing probes representing 33,000 lncRNA genes. Quantitative real-time polymerase chain reaction (qPCR) was used to validate selected differentially expressed lncRNAs. The gene ontology (GO), pathway and network analysis were performed. The microarray identified 8814 lncRNAs that were expressed in the umbilical cord blood, of which 349 were significantly upregulated and 892 were significantly downregulated (fold-change ≥ 2.0) in GDM group. The highest enriched GOs targeted by downregulated transcripts were biological regulation. Pathway analysis indicated that nine pathways corresponded to downregulated transcripts.

overall_design: Thirty pairs of GDM macrosomia and normal controls were divided into three subgroups randomly, and the umbilical cord vein blood from each subgroup was mixed, and hybridized to a microarray.

first: Zhonghua

last: Shi

first: Chun

last: Zhao

first: Wei

last: Long

first: Hongjuan

last: Ding

first: Rong

last: Shen


title: dDsk2 stabilizes dHP1c binding at TSS

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


title: RNA sequencing of pancreatic islets and islet-derived macrophages and endothelial cells modulated by vascular endothelial growth factor-A signaling

status: Public on Sep 01 2015

city: Nashville

first: Alvin

last: Powers

state: Tennessee

address: 2213 Garland Avenue

department: Medicine

institute: Vanderbilt University Medical Center

summary: Pancreatic islet endocrine cell and endothelial cell (EC) interactions mediated by vascular endothelial growth factor-A (VEGF-A) signaling are important for islet endocrine cell differentiation and the formation of highly vascularized islets. To dissect how VEGF-A signaling modulates intra-islet vasculature and innervation, islet microenvironment, and β cell mass, we transiently increased VEGF-A production by β cells. VEGF-A induction dramatically increased the number of intra-islet ECs but led to β cell loss. After withdrawal of the VEGF-A stimulus, β cell mass, function, and islet structure normalized as a result of a robust, but transient, burst in proliferation of pre-existing β cells. Bone marrow-derived macrophages (MΦs) recruited to the site of β cell injury were crucial for the β cell proliferation, which was independent of pancreatic location and circulating factors such as glucose. Identification of the signals responsible for the proliferation of adult, terminally differentiated β cells will improve strategies aimed at β cell regeneration and expansion.

overall_design: Examination of RNA profiles from isolated whole islets from RIP-rtTA; TetO-VEGF-A mice with no doxycycline (Dox) treatment (3 samples) and after 1 week of Dox (3 sample); and islet-derived macrophages (3 samples) and endothelial cells (3 samples) isolated from dispersed purified islets from RIP-rtTA; TetO-VEGF-A mice after 1 week Dox treatment by fluorescence-activated cell sorting using antibodies against CD11b and CD31, respectively.

first: Marcela

last: Brissova


title: Expression data from skin biopsies in pateints with systemic sclerosis treated with anti-TGF-beta, fresolimumab

status: Public on Jun 05 2015

city: Boston

first: Robert

last: Lafyatis

address: 72 E Concord St

department: Rheumatology

institute: Boston University School of Medicine

summary:
Systemic sclerosis is associated with skin fibrosis thought mediated by TGFb. This open label clinical trial examines the effect of TGFb inhibition on skin gene expression.
Patients 1-9 received two doses 1 mg/kg dose of fresolimumab at baseline and 3 weeks; patients 10-19 received a single 5 mg/kg dose

overall_design: Patients with diffuse cutaneous systemic sclerosis within 2 years of first raynauds had skin biopsies before treatment and the 3-4 weeks, 7 weeks and 24 weeks after treatment with fresolimumab


title: Gene expression in primary human bone marrow plasma cells sorted according to CD19 expression

status: Public on Dec 31 2014

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: To characterize human bone marrow plasma cells that express or lack CD19 on a molecular level, we compared the global gene expression of primary CD38high/CD138+ plasma cells with or without CD19 expression.

overall_design: Primary human bone marrow plasma cells (PC) from immunologically healthy donors were enriched according to CD138 expression by magnetic cell separation. From the enriched fraction, CD19-positive and CD19-negative PC were isolated by flow cytometric cell sorting, according to the phenotype CD38high/CD138+/CD20-/CD3-/CD14-/DAPI-/CD19+ and CD38high/CD138+/CD20-/CD3-/CD14-/DAPI-/CD19-, respectively, using a BD Aria or DIVA cell sorter (Becton Dickinson). Dead cells were excluded using DAPI. Total RNA was extracted using the RNeasy Mini kit (Qiagen). The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Double-stranded complementary RNA was synthesized from 100 ng total RNA using Message AmpII Biotin (Ambion, USA). To obtain sufficient cRNA, the Affymetrix two-cycle amplification protocol was used. Fifteen micrograms of fragmented cRNA of each sample were hybridized to a total of 8 HG-U133 Plus 2.0 GeneChips (Affymetrix). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, version 1.4, both Affymetrix. All relevant GCOS data of quality-checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously.

first: Henrik

last: Mei

first: Ina

last: Wirries

first: Daniela

last: Frölich

first: Mikael

last: Brisslert

first: Claudia

last: Giesecke

first: Joachim

last: Grün

first: Tobias

last: Alexander

first: Stefanie

last: Schmidt

first: Katarzyna

last: Luda

first: Anja

last: Kühl

first: Robby

last: Engelmann

first: Michael

last: Dürr

last: Scheel

first: Maria

last: Bokarewa

first: Carsten

last: Perka

first: Andreas

last: Radbruch

first: Thomas

last: Dörner


title: Human RORγt+ CD34+ cells are lineage-specified progenitors of group 3 RORγt+ innate lymphoid cells

status: Public on Nov 25 2014

first: Chiara

last: Romagnani

address: Chariteplatz 1

institute: Deutsches Rheuma Forschungszentrum -      Leibniz-Gemeinschaft

summary: Group 3 innate lymphoid cells (ILC3) are defined by the expression of RORγt, which is selectively required for their development. The lineage-specified progenitor cells of human ILC3 and their developmental site after birth remain undefined. Here we identified a novel population of human CD34+ hematopoietic progenitor cells (HPC) expressing RORγt and sharing with ILC3 a distinct transcriptional signature. RORγt+ CD34+ HPC were located in tonsils and intestinal lamina propria (LP) and selectively differentiated towards ILC3. Conversely, RORγt- CD34+ HPC displayed commitment potential for both ILC3 and NK cells and the differentiation fate towards these two cell lineages was determined by cytokine and aryl hydrocarbon receptor (AhR) signaling. Thus, we propose that RORγt+ CD34+ cells represent human lineage-specified progenitors of IL-22+ ILC3 and that tonsils as well as intestinal LP might be preferential sites of their differentiation.

overall_design: ILC3, NK cells and the CD34+ HPC subsets were sorted from tonsils of 6 distinct donors to purity above 95%. cRNA of the sorted cell populations was hybridized to an Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494)

first: Elisa

last: Montaldo

first: Luiz

middle: G

last: Teixeira-Alves

first: Timor

last: Glatzer

first: Pawel

last: Durek

first: Ulrik

last: Stervbo

first: Wiebke

last: Hamann

first: Marina

last: Babic

last: Paclik

first: Katharina

last: Stölzel

first: Jörn

last: Gröne

first: Laura

last: Lozza

first: Kerstin

last: Juelke

first: Nadine

last: Matzmohr

first: Fabrizio

last: Loiacono

first: Francesca

last: Petronelli

first: Nicholas

middle: D

last: Huntington

first: Lorenzo

last: Moretta

last: Mingari


title: Pupylated proteins in Corynebacterium glutamicum revealed by MudPIT analysis

status: Public on Jun 24 2014

first: Tino

last: Polen

summary: In a manner similar to ubiquitin, the prokaryotic ubiquitin-like protein (Pup) has been shown to target proteins for degradation via the proteasome in mycobacteria. However, not all actinobacteria possessing the Pup protein also harbor a proteasome, suggesting fates for pupylated proteins other than degradation via a proteasome or degradation at all. In the present study we set out to study pupylation in the proteasome-lacking non-pathogenic model microorganism and biotechnological workhorse Corynebacterium glutamicum. A defined pup deletion mutant of C. glutamicum ATCC 13032 grew as the control indicating that pupylation seems to be dispensable under the conditions tested. By expression of homologous Pup carrying a poly-histidine tag in C. glutamicum ATCC 13032 we purified the first pupylome of a microorganism lacking a proteasome. Multidimensional Protein Identification Technology (MudPIT) unraveled 54 proteins being pupylated in this organism. Similar to mycobacteria, the majority of pupylated proteins in C. glutamicum can be classified as enzymes of the metabolism or as involved in translation. These results help to elucidate the common target pathways of pupylation in bacteria.

overall_design:
Sample 1: For growth in CGXII minimal media, a preculture 1 was grown in 5 ml BHI medium inoculated with a single colony from a fresh BHI agar plate and incubated at 170 rpm for 8 hours. Then 500 µl of preculture 1 were used to inoculate preculture 2 in 100 ml shake flasks with 20 ml CGXII minimal medium containing 4 % (w/v) glucose and incubated over night (140 rpm , 30 °C ). Subsequent main cultures (50 ml CGXII medium with 4 % glucose) were inoculated with cells from preculture 2 to an OD600 of about 0.4. For DNA microarray  analysis, cells were harvested in the exponential growth phase at an OD600 of 4 to 5. After extraction of total RNA 25µg of total RNA from C. glutamicum Delta-pup and C. glutamicum WT were compared in two-color microarray analysis. Overall three biological replicates were done.
Sample 2-4: For growth in CGXII minimal media, a preculture 1 was grown in 5 ml BHI medium inoculated with a single colony from a fresh BHI agar plate and incubated at 170 rpm for 8 hours. Then 500 µl of preculture 1 were used to inoculate preculture 2 in 100 ml shake flasks with 20 ml CGXII minimal medium containing 4 % (w/v) glucose and incubated over night (140 rpm , 30 °C ). Subsequent main cultures (50 ml CGXII medium with 4 % glucose) were inoculated with cells from preculture 2 to an OD600 of about 0.4. For growth experiments in complex BHI medium, 20 ml brain heart infusion (BHI) medium (Difco Laboratories, Detroit, USA) were inoculated with a single colony from a fresh BHI agar plate and incubated at 140 rpm as overnight cultures. Subsequent main cultures (50 ml BHI medium) were inoculated with cells from overnight cultures to an optical density at 600 nm (OD600) of about 1. For DNA microarray  analysis, cells were harvested in the exponential growth phase at an OD600 of 4 to 5. After extraction of total RNA 25µg of total RNA from C. glutamicum Delta-pup and C. glutamicum WT were compared in two-color microarray analysis.  Overall three biological replicates were done for each growth medium.
Sample 5-6: For growth experiments in complex BHI medium, 20 ml brain heart infusion (BHI) medium (Difco Laboratories, Detroit, USA) were inoculated with a single colony from a fresh BHI agar plate and incubated at 140 rpm as overnight cultures. Subsequent main cultures (50 ml BHI medium) were inoculated with cells from overnight cultures to an optical density at 600 nm (OD600) of about 1. For DNA microarray  analysis, cells were harvested in the exponential growth phase at an OD600 of 4 to 5. After extraction of total RNA 25µg of total RNA from C. glutamicum Delta-pup and C. glutamicum WT were compared in two-color microarray analysis. Overall three biological replicates were done.

first: Andreas

last: Küberl

first: Benjamin

last: Fränzel

first: Dirk

last: Wolters

first: Lothar

last: Eggeling

first: Michael

last: Bott