title: Pak1-ATF2 signaling axis induces miR-132 to inhibit hematogenous metastasis

status: Public on Jul 16 2016

city: Shenyang

first: Funan

last: Liu

address: 155 Nanjing North Street

department: Department of Surgical Oncology

institute: the First Affiliated Hospital of China Medical University

summary: Pak1 as a serine/threonine kinase, has been implicated in cytoskeletal remodelling, cell motility, apoptosis and transformation. Pak1 plays important roles in multiple signal pathways. Pak1 protects cells from apoptosis through at least three different pathways including forkhead box O1 (FOXO1), B-cell CLL/lymphoma 2 (Bcl-2) and DLC1. Pak1 also regulates activity of Raf and Aurora kinases to affect cellular proliferation. Overexpression of Pak1 is involved in the regulation of actin assembly and disassembly through phosphorylations of LIM Kinase and cytoskeletal associated proteins such as Filamin A, Paxillin, Caldesmon, Cortactin and Arp2/3. Pak1 also regulates microtubule dynamics via activation of tubulin cofactor B (TCoB) and DLC1, and inhibition of stathmin. In spite of a large body of work about the mechanism of Pak1 action in cancer, it remains unknown whether Pak1 signaling could potentially regulate the biology of regulatory miRNAs. This is particularly relevant for gastric cancer because Pak1 can activate many regulators of miRNAs expression in gastric cancer cells including NF-kappaB and ERK, and Pak1 signaling has profound phenotypic effects on the biology of gastric cancer cells. We constructed Pak1 knockdown stable cell lines. The stable Pak1 knockdown gastric cancer BGC823 cells and control cells were performed miRNA chip analysis by CapitalBio company.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Gastric cancer BGC823 cells with stable Pak1 knockdown and BGC-823 gastric cancer cells  transfected with U6 were used in this experiment. Total RNA was extracted  by trizol,Here we use a Capitalbio mammal microRNA V3.0(CapitalBio, Beijing, China) containing 509 well-characterized human, mouse and rat miRNAs and various controls to profile the expression levels of miRNA in 16 and conU6 group.three chip were test in each group, and the procedure was repeated twice.

first: Zhenguo

last: Cheng

first: Feng

last: Li


title: mRNA sequencing of wildtype and jhd2-delete strains

status: Public on Aug 09 2016

city: Toronto

first: Maria

last: Soloveychik

state: Ontario

address: 1 king's college circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

type: Expression profiling by high throughput sequencing

summary: RNA expression in WT and jhd2Δ cells in various nutritional sources

overall_design: Strand-specific total RNA was sequenced (Illumina stranded TruSeq, with dUTP second strand-incorporation) from wildtype and mutants cells, in biological replicates, normalized by RNA spike-in controls

first: Mengshu

last: Xu

first: Marc

last: Meneghini


title: ACTG A5258 Clinical administration of chloroquine to patients with untreated chronic HIV infection to reduce immune activation

status: Public on Jul 15 2016

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

summary: ACTG A5258, we asked whether chloroquine could reduce the immune activation in HIV infection posited to be driven by microbial TLR agonists, such as  bacterial elements translocated from the gut and HIV-1 RNAs . We anticipate that blocking this activation pathway might interfere with events in pathogenesis leading to AIDS- and non-AIDS-related clinical manifestations of HIV disease.

overall_design: Blood samples were taken from 20 individuals at week 0 (before treatement) and week 12. 10 individuals received chloroquine 250mg orally and 10 individuals received placebo.

first: Jeffrey

last: Jacobson

first: Michael

last: Lederman

first: Steven

middle: E

last: Bosinger

first: Roy

last: Matining


title: ACTG A5258 Clinical administration of chloroquine to HIV-infected patients receiving antiretroviral therapy to reduce immune activation


title: Clinical administration of chloroquine to HIV-infected patients that are untreated or receiving antiretroviral therapy

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

overall_design: Refer to individual Series


title: Embryonic stem cells culture conditions support distinct ES cell states associated with specific developmental stages and cell types

status: Public on Jul 14 2016

city: New York

first: Sophie

middle: M

last: Morgani

state: NY

address: Rockefeller Research Labs, 430 E 67th St

department: Development Program

institute: Sloan Kettering Institute, MSKCC

summary:
Identification of transcripts in murine embryonic stem (ES) cell lines growing under 3 different self-renewing conditions; GMEM + 10% FCS, N2B27 + 2i (1 μM PD032 and 3 μM CHIR99021) and knockout serum replacement (KOSR) medium (80% Knockout DMEM, 20% Knockout Serum Replacement). Under all conditions, ES cells were grown on gelatin-coated dishes and passaged by trypsinisation. ES cells were cultured in each condition for at least 3 passages prior to sample collection.
The aim of this array experiment is to identify significant differences in transcript levels of ES cells grown under different conditions. Differences of transcript levels from the different conditions should be consistent among the biological and technical replicates for each.

overall_design: Unsorted ES cells were maintained in serum/LIF, 2i/LIF or KOSR/LIF. Samples were collected from 3 independent ES cell clones from the 129/Ola background; E14, HVJu5.1 and HVJu9.3 For 2i/LIF (Morgani et al., 2013). For the 2i/LIF condition, 5 samples were collected with 2 samples each for HVJu5.1 and HVJu9.3 cell lines, for serum/LIF and KOSR/LIF conditions, 1 sample was collected for each cell line. RNA was extracted from all replicate clones. Therefore each condition is represented at least as biological triplicates. RNA isolation was performed using Qiagen RNeasy kits according to the manufacturer's instructions. RNA pellets were resuspended in Nuclease Free Water (ambion) and RNA concentration was measured using the Nanodrop system. 260/280 values for all samples were in the range of 1.8-2.0 RNA quality was additionally assessed using the Agilent 2100 BioAnalyzer with all samples having a RIN of ≥9.7.

first: Javier

last: Gonzalez

first: Kasper

last: Bonderup

first: Sahar

last: Abelchian

first: Cord

last: Brakebusch

first: Joshua

last: Brickman


title: Genome wide analysis of SMAD1 binding in mouse mesodermal cells treated or not with the WNT inhibitor IWR1

status: Public on Sep 01 2016

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Using chromatin-immunoprecipitation followed by next-generation sequencing, we studied the effect of WNT pathway inhibition of the binding of SMAD1 in mouse mesodermal cells from Embryoid Bodies (EB) cultures. The WNT inhibitor IWR1 (or the vehicle control DMSO) were added in day 3 EB cultures and cells were collected 24h later for ChIP assay.

overall_design: Analysis of SMAD1 genomic binding in IWR1- or DMSO-treated mouse day 4 reaggregated Embryoid Bodies.

first: Rita

last: Perlingeiro

first: June

last: Baik


title: Expression of protein-coding genes and lncRNAs in brain and other human tissues

status: Public on Jun 30 2016

city: Ghent

first: Sarah

last: Vergult

state: Not Applicable

address: De Pintelaan 185, MRB, second floor

country: Belgium

institute: Ghent University

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

summary: We used microarray expression profiling to assess protein-coding and non-coding gene expression across 8 brain samples and 7 other human tissues.

overall_design: We measured commercial human cDNA samples from 15 tissues: cerebellum, brain stem, frontal cortex, occipital cortex, parietal cortex, fetal brain, whole adult brain, colon, heart, kidney, liver, lung, breast and adrenal gland


title: Genome-scale analysis of DNA methylation in rheumatic heart disease

status: Public on Jul 06 2016

city: Ningbo

first: Shiwei

last: Duan

state: Zhejiang

address: 818 Fenghua Road

department: Medical Genetics Centre

country: China

institute: Ningbo University

type: Methylation profiling by genome tiling array

summary: The aim of the current study is to identify DNA methylation markers associated with rheumatic heart disease with secondary pulmonary arterial hypertension (RHD-PAH).

overall_design: Genome-wide DNA methylation study is performed among 6 RHD-PAH patients and 6 healthy controls using Illumina HumanMethylation 450K array.

first: Dawei

last: Zheng

first: Xiaoying

last: Chen

first: Ni

last: Li

first: Lebo

last: Sun

first: Qingyun

last: Zhou

first: Huoshun

last: Shi

first: Guodong

last: Xu

first: Jing

last: Liu

first: Limin

first: Guofeng

last: Shao


title: Transcriptional profiling of senescent cell-associated genes in adult mouse lung.

status: Public on Jun 27 2016

city: Obu

first: Masataka

last: Sugimoto

state: Aichi

address: 7-430 Morioka-cho

department: Cellular Pathology

country: Japan

institute: National Center for Geriatrics and Gerontology

summary: To evaluate the senescent cell-dependent gene expression in aged lung tissue, young (2mo) ARF-DTR mice and adult (12mo) ARF-DTR mice treated with PBS or DT every two weeks up to 1 month were analyzed using the Agilent Technologies SurePrint G3 Mouse Gene Expression Microarray.

overall_design: Gene expression in lungs of ARF-DTR mice (2mo, 12mo, 12mo+DT) was analyzed. WT mice was used to evaluate the transgene-independent effect of DT on gene expression.


title: Auxin signaling in the epidermis regulates stem growth via interactions with the brassinosteroid pathway

city: La Jolla

first: Carl

last: Procko

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: Growth of a complex multicellular organism requires coordinated changes in diverse cell types.  These cellular changes generate organs of the correct size, shape and functionality.  During plant development, the growth hormone auxin induces stem elongation; however, which cell types of the stem perceive the auxin signal and contribute to organ growth is poorly understood.  Here, we show that auxin signalling is required in many cell types for correct hypocotyl stem growth, with a key role for the epidermis.  Combining genetic manipulations in Arabidopsis thaliana with transcriptional profiling of the hypocotyl epidermis from Brassica rapa, we show that auxin functions in the epidermis in part by inducing activity of the locally-acting, growth-promoting brassinosteroid pathway.  Our findings clarify cell-specific auxin function in the hypocotyl, and highlight the complexity of cell-type interactions within a growing organ.

sample_organism:
Arabidopsis thaliana
Brassica rapa

platform_organism:
Arabidopsis thaliana
Brassica rapa

overall_design: We performed whole-genome transcriptome (mRNA-Seq) on 5 d-old W light-grown Arabidopsis thaliana plants (CER6pro>>axr3-1::mCit experimental plants and UAS::axr3-1::mCit hemizygous control plants; whole-seedling tissue) treated for 4 h W light or low R:FR shade. In addition, we performed mRNA-Seq on 4 d-old Brassica rapa plants (FPsc strain) treated for 9 h W light or shade. Brassica tissues collected were hypocotyl epidermal peels or whole hypocotyls.

first: Joanne

last: Chory


title: Dorsal root ganglia (DRG) and Sciatic nerve (SCN) in female BTBR ob/ob mice - diabetic peripheral neuropathy

status: Public on Jul 12 2016

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

summary: Female mouse models of diabetic peripheral neuropathy (DPN) have not yet been identified. Our aim is firstly to demonstrate that female BTBR ob/ob mice display robust DPN and secondly, to perform relevant comparisons with non-diabetic and gender-matched controls. Lastly, microarray technology was employed to identify dysregulated genes and pathways in the SCN and DRG of female BTBR mice. Dorsal root ganglia (DRG) and sciatic nerve (SCN) were removed from female mice, RNA isolated and processed for gene expression profiling to identify differentially expressed genes using Affymetrix GeneChip Mouse Genome 430 2.0 Arrays.

overall_design: Total RNA were extracted from DRG and SCN of 26 week old ob/+ and ob/ob mice (n=5 in each group) and hybridized on Affymetrix microarray.

first: Eva

middle: L

last: Feldman


title: Redifferentiation of expanded human islet β cells by inhibition of ARX

status: Public on Jun 20 2016

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: We applied RNA-seq analysis to human islet cells, received from 3 independent donors, treated with either redifferentiation cocktail + ARX shRNA, or redifferentiation cocktail + control shRNA or left untreated.

overall_design: Examination of the effect of ARX inhibition on redifferentiation of β-cell-derived (BCD) cells

first: Orr

last: Friedman-Mazursky

first: Shimon

last: Efrat


title: BevR-IgG array in glioblastoma xenografts

status: Public on Jun 21 2016

city: San Francisco

first: Garima

last: Yagnik

department: Neurosurgery

institute: UCSF

summary: Analysis of anti-angiogenic therapy resistance in xenografts of patient glioma samples serially passaged across generations of athymic nude mice

overall_design: 3 independent biological replicates with control (IgG) treatment; 9 samples with drug treatment (bevacizumab), comprised of three independent biological replicates from three separate generations of xenografts

first: Aghi

last: Manish

first: Yagnik

last: Garima

first: Jahangiri

last: Arman


title: RNA sequencing analysis of NGFR ablation in both p53-positive and negative non-small-cell lung cancer cell lines

status: Public on Jun 10 2016

city: New Orleans

first: HUA

last: LU

state: LA

address: 1430 Tulane Ave

department: Biochemistry and Molecular Biology

institute: TULANE UNIVERSITY

summary: We report the gene expression profiles by NGFR knockdown in H460 and H1299 cell lines and reveal that NGFR ablation activates p53 target gene expression.

overall_design: We examined gene expression in two different non-small-cell lung cancer cell lines, one with wild-type p53 and the other without p53.

first: Xiang

last: Zhou

first: Hua

last: Lu


title: Three different in vivo models of synovial sarcoma (xenograft: Fuji; PDX: CTG-0331 and CTG-0771) treated with or without the indicated dose of the EZH2 inhibitor, tazemetostat

status: Public on Jun 18 2016

city: Cambridge

first: Igor

address: 400 Technology Square

institute: Epizyme

summary: The catalytic activities of covalent and ATP-dependent chromatin remodeling are central to regulating the conformational state of chromatin and the resultant transcriptional output.  The enzymes that catalyze these activities are often contained within multiprotein complexes in nature.  Two such multiprotein complexes, the polycomb repressive complex 2 (PRC2) methyltransferase and the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler have been reported to act in opposition to each other during development and homeostasis.  An imbalance in their activities induced by mutations/deletions in complex members (e.g. SMARCB1) has been suggested to be a pathogenic mechanism in certain human cancers.  Here we show that preclinical models of synovial sarcoma - a cancer characterized by functional SMARCB1 loss via its displacement from the SWI/SNF complex through the pathognomonic SS18-SSX fusion protein - display sensitivity to pharmacologic inhibition of EZH2, the catalytic subunit of PRC2.  Treatment with tazemetostat, a clinical-stage, selective and orally bioavailable small-molecule inhibitor of EZH2 enzymatic activity reverses a subset of synovial sarcoma gene expression and results in concentration-dependent cell growth inhibition and cell death specifically in SS18-SSX fusion-positive cells in vitro.  Treatment of mice bearing either a cell line or two patient-derived xenograft models of synovial sarcoma leads to dose-dependent tumor growth inhibition with correlative inhibition of trimethylation levels of the EZH2-specific substrate, lysine 27 on histone H3.  These data demonstrate a dependency of SS18-SSX-positive, SMARCB1-deficient synovial sarcomas on EZH2 enzymatic activity and suggests the potential utility of EZH2-targeted drugs in these genetically defined cancers.

first: Alexandra

middle: R

last: Grassian

first: Scott

last: Ribich


title: Expression data from human monocytes stimulated with wild-type N. Meningitidis (Nm) and recombinant IL-10 [I]

status: Public on Jun 08 2016

city: Oslo

first: Unni

last: Gopinathan

address: Kirkeveien 166

department: Department of Medical Biochemistry

country: Norway

institute: Oslo University Hospital

summary: Background: Biological interpretation of gene expression data may differ depending on underlying assumptions and statistical tests used by the chosen bioinformatic tool. We used Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA) to analyze previously generated gene expression profiles induced in human monocytes by N. meningitidis and IL-10 (“the model system”), and by meningococcal sepsis plasma before and after immunodepletion of IL-10 (“the patient plasma system”). The objectives were to compare whether these two methods resulted in similar biological interpretation of the datasets; and identify whether GSEA provided additional insight about the human monocyte host response to meningococcal activation.    Results: In both experimental models, GSEA and IPA associated genes induced in monocytes by N. meningitidis with pro-inflammatory innate immune activation, including TNF-signaling, Toll-like receptor signaling, JAK-STAT-signaling, type I and type II interferon. GSEA associated genes regulated by the presence of IL-10 with similar gene sets in both the model system and the patient plasma system. In the model system, GSEA and IPA identified 170 genes associated with oxidative phosphorylation/mitochondrial function to be down-regulated in monocytes stimulated with meningococci. In the patient plasma system, GSEA and IPA combined identified 122 genes associated with oxidative phosphorylation/mitochondrial dysfunction to be down-regulated by meningococcal sepsis plasma depleted for IL-10.  Combining analyses from GSEA and IPA identified that some genes associated with oxidative phosphorylation/mitochondrial function that were inhibited by N. meningitidis were partially up-regulated by IL-10.  Conclusions: Biological processes associated with the gene expression changes in the model system of meningococcal sepsis was comparable to the results found in the patient plasma system. By combining GSEA with IPA, we have discovered an inhibitory effect exerted by N. meningitidis on genes associated with oxidative phosphorylation, and that IL-10 possibly partially dampen this strong inhibitory effect, thereby identifying, to our knowledge, yet another area where IL-10 regulates the effect of LPS. We suggest that relying on a single bioinformatic tool together with arbitrarily chosen filtering criteria for data analysis may result in overlooking relevant biological processes and signaling pathways associated with genes differentially expressed between compared experimental conditions.

overall_design: In the model system, human monocytes (from five different consenting, healthy donors) were stimulated for three hours with N. meningitidis, IL-10, N. meningitidis and IL-10, and vehicle. In the patient plasma system, human monocytes (from one consenting, healthy donor) were stimulated for three hours with plasma samples (n=3) from patients with meningococcal sepsis, before and after immunodepletion of IL-10 which is present in large quanitities in meningococcal sepsis plasma. The gene expression induced in these samples were compared with gene expression induced in human monocytes stimulated for three hours with plasma samples (n=3) from patients with mild meningococcal disease or meningitis, which contain low levels of LPS and IL-10. In both experimental models, total RNA was isolated and DNA micro-array analyses performed with Affymetrix GeneChip human gene 1.0 ST arrays.

first: Reidun

last: Øvstebø

first: Berit

last: Sletbakk Brusletto

first: Ole

last: Olstad

first: Peter

last: Kierulf

first: Petter

last: Brandtzaeg

first: Jens

middle: P

last: Berg


title: Expression data from human monocytes stimulated with wild-type N. meningitidis and recombinant IL-10 [II]

overall_design: In the model system, human monocytes (from five different consenting, healthy donors) were stimulated for three hours with N. meningitidis, IL-10, N. meningitidis and IL-10, and vehicle. In the patient plasma system, human monocytes (from one consenting, healthy donor) were stimulated for three hours with plasma samples (n=3) from patients with meningococcal sepsis, before and after immunodepletion of IL-10 which is present in large quanitities in meningococcal sepsis plasma. The gene expression induced in these samples were compared with gene expression induced in human monocytes stimulated for three hours with plasma samples (n=3) from patients with mild meningococcal disease or meningitis, which contain low levels of LPS and IL-10. In both experimental models, total RNA was isolated and DNA micro-array analyses performed with Affymetrix GeneChip human gene 1.0 ST  arrays.


title: Expression data from human monocytes stimulated with wild-type N. meningitidis and recombinant IL-10


title: Differentially expressed genes after miRNA or siRNA transfection in human cancer cell lines (III)

status: Public on Jun 03 2016

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (microRNAs or siRNAs) in human cancer, several cell lines (pancreatic cancer,  esophageal cancer, tongue squamous cell carcinoma, hypopharyngeal squamous cell carcinoma and lung squamous cell carcinoma) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (Panc-1, SW1990, TE8, TE9, SAS, FaDu and EBC-1) were treated with miRNAs (miR-216b-3p, miR-145-5p, miR-145-3p, miR-150-5p and miR-150-3p), siRNAs (si-ZFP36L2, si-MMP13, si-TPD52, and si-MTDH).

first: Yusuke

last: Goto


title: Gene expression analysis provides insight into the physiology of the important staple food crop cassava

status: Public on Jun 07 2016

city: St Louis

first: Rebecca

last: Bart

state: MO

address: 975 N Warson Rd

institute: Donald Danforth Plant Science Center

summary: Cassava (Manihot esculenta) is the food security crop that feeds approximately 800 million people worldwide. Although this crop displays high productivity under drought and poor soil conditions, it is susceptible to disease, postharvest deterioration and the roots contain low nutritional content. Cassava improvement programs are focused on addressing these constraints but are hindered by the crop’s high heterozygosity, difficulty in synchronizing flowering, low seed production and a poor understanding of the physiology of this plant. Among the major food crops, cassava is unique in its ability to develop massive, underground storage roots. Despite the importance of these structures, their basic physiology remains largely unknown, especially the molecular genetic basis of storage root development. Similarly, in cassava, the favored target tissue for transgene integration and genome editing is a friable embryogenic callus (FEC). Little is known concerning gene expression in this tissue, or its relatedness to the somatic organized embryogenic structures (OES) from which it originates. Here, we provide molecular identities for eleven cassava tissue types through RNA sequencing and develop an open access, web-based interface for further interrogation of the data. Through this dataset, we report novel insight into the physiology of cassava and identify promoters able to drive specified tissue expression profiles. The information gained from this study is of value for both conventional and biotechnological improvement programs.

overall_design: mRNA quantification in 11 tissue types of cassava and biological replicates for each tissue

first: Mark

middle: C

last: Wilson

first: Andrew

last: Mutka

first: Aaron

middle: W

last: Hummel

first: Jeffrey

last: Berry

first: Raj

middle: D

last: Chauhan

first: Anupama

last: Vijayaraghavan

first: Nigel

last: Taylor

first: Danial

middle: F

last: Voytas

first: Dan

last: Chitwood


title: High-concentrate feeding upregulates the expression of inflammation-related genes in the ruminal epithelium of dairy cattle

status: Public on Jun 06 2016

city: Nanjing

first: ruiyang

last: zhang

state: jiangsu

address: tongwei road weigang no. 1

department: College of Animal Science and Technology

institute: nanjing agricultural university

summary: The objective of this study was to characterize the mRNA expression profile in rumen epithelium from Holstein dairy cows fed high or low concentrate dits.

overall_design: Four ruminally cannulated Holstein cattle (average body weight, 460 ± 16.4 kg; 84 ± 25 d in milk at the beginning of the trial) were used in a 2 × 2 crossover design trial with 2 cows in each square and 2 periods. The dietary treatments were a low-concentrate diet (LC; 40% concentrate feed, DM basis) and a high-concentrate diet (HC; 70% concentrate feed, DM basis). Each experimental period was 21 d, with the first 11 d used for diet adaptation and 10 d of measurements. Rumen papillae samples were collected at 4 h after the morning feeding on d 21 of each experimental period.

first: R

last: Zhang

first: W

last: Zhu

first: S

last: Mao


title: Global ovary gene interaction network structure informs biological effects of Chemical stressors

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: Background: Complex biological networks control fundamental processes such as reproduction. The relationship of network structure to biological function was investigated in a global gene interaction network developed from ovary tissues of the model fish, fathead minnow (Pimephales promelas). Results: A global ovary gene interaction network was inferred from gene expression in ovaries of fathead minnow representing 288 different exposure conditions and 1,472 microarrays. More than 74 percent of the interactions in two subnetworks and 37% of the connections in a third subnetwork were also present as known connections found in curated databases and the literature. Subnetworks within the network were enriched in specific pathways and key ovarian functions. The network location of differentially expressed genes from different ovary stages was consistent with known functional changes at those stages. The global network provide additional insight into gene function when gene directly linked to differentially expressed genes are considered in enrichment analysis. Analysis of the impact of bisphenol A on ovarian gene expression demonstrated that the network provides an informative frame work in which to investigate mechanisms by which chemical effects occur. Conclusions: Our results suggest that the ovary transcriptional network is composed of several connected subnetworks where each is enriched in specific functions. Construction of a global gene regulatory network from multiple experiments provides valuable insight into the function of genes and the impact of chemicals on biological systems.

overall_design: total RNA from the ovary tissue of treated or control fish labeled in single color was hybridized to Agilent fathead minnow microarray (design 019597)

first: Edward

middle: J

last: Perkins

first: Tanwir

last: Habib

first: Lynn

last: Escalon

first: Xin

last: Guan

first: Lyle

last: Burgoon

first: Natàlia

last: Garcia-Reyero


title: Transcriptome analysis of dendritic cells activated by VLPs or ncRNAVLPs

status: Public on Jun 02 2016

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

summary: Analysis of the effect on dendritic cells of the injection in C57BL/6 mice of VLPs or ncRNAVLPs  at gene expression level.

overall_design: Total RNA obtained from murine splenic dendritic cells sorted 6 hours after injection of VLP, ncRNAVLP or PBS for control.

first: Fabien

last: PITOISET

first: Thomas

last: VAZQUEZ

first: Béatrice

last: LEVACHER

last: NEHAR-BELAID

first: Lea

last: TORRIERI-DRAMARD

first: James

last: VIGNERON

first: David

last: KLATZMANN

first: Bertrand

last: BELLIER


title: Transcriptome comparison between Bacillus cereus ATCC 10987 cells with and without iron starvation

status: Public on May 31 2016

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

summary: In this study we compared the transcriptomic profiles of cells grown in BHI, BHI supplemented with FeCl3, BHI supplemented with iron scavenger Bipyridine and both iron and the scavenger.

overall_design: Liquid cultures grown in above mentioned four conditions with different iron availability were sampled at 5 h (Exponential growth) and 12 h (stationary phase start) of growth

first: Hasmik

last: Hayrapetyan

first: Marcel

last: Tempelaars

first: Masja

last: Nierop Groot

first: Tjakko

last: Abee


title: The protein and transcript profiles of human semen

status: Public on Jun 01 2016

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

summary: Transcriptome of testes was examined for comparison of transcript abundance with that of sperm/seminal fluid (as sequenced in separate study)

overall_design: Commercially available (Ambion) human testes RNA was prepared and sequenced in two replicates

middle: A

first: Meritxell

last: Jodar

first: Edward

last: Sendler


title: The hemogenic competence of endothelial progenitors is restricted by Runx1 silencing during embryonic development

city: Manchester

first: Alexia

last: Eliades

address: Wilmslow Road

country: United Kingdom

institute: CRUK-Manchester Institute, The University of Manchester

summary: It has now been well established that hematopoietic stem and progenitor cells originate from a specialised subset of endothelium termed hemogenic endothelium (HE) via an endothelial-to-hematopoietic transition. However, the molecular mechanisms determining which endothelial progenitors possess or not this hemogenic potential is currently unknown. In this study, we investigated the changes in hemogenic potential in endothelial progenitors at the early stages of embryonic development. We use a microarray approach to profile the genes regulated between E7.5 and E8.5 embryonic day in the ETV2+FLK1+CD41- compartment.

overall_design: Cells were sorted based on ETV2::GFP+/FLK1+/CD41- immunophenotype from ETV2::GFP embryos at E7.5 and E8.5 developmental stage in triplicates

first: Valerie

last: Kouskoff


title: Altered gene expression in primitive murine hematopoietic progenitors expressing INV16

status: Public on Aug 16 2016

city: Birmingham

first: Chris

middle: Alan

last: Klug

state: AL

address: 1825 University Blvd

department: Microbiology

institute: University of Alabama at Birmingham

summary:
The role of the INV16 genetic translocation in acute myeloid leukemia may be to alter expression in primitive hematopoietic progenitors of genes important for regulating hematopoiesis.
To identify transcriptional targets of INV16 in primitive hematopoietic progenitors, FACS-purified progenitors from murine bone marrow were transduced with retrovirus encoding INV16 and analyzed for alterations in gene expression using whole transcriptome expression arrays.

overall_design: Normal murine bone marrow cells of the Lineage-negative, c-Kit+, Sca-1+, Flt3-negative phenotype (KSLF) were FACS-purified, transduced with retrovirus encoding INV16 (INV), the non-leukemogenic INV16 mutant deleted of the assembly competent domain (ACD) or empty retroviral vector control (MIB). Productively transduced, GFP-positive cells were FACS-sorted 24 hours later, and RNA isolated and analyzed using Affymetrix whole transcriptome expression arrays. Replicate numbers of sorts/transductions/analyses of 4, 3, and 5 were performed for INV, ACD, and MIB, respectively.


title: Cordyceps promotes MKK7-JNK signaling pathway by reducing NF-κB/GADD45b signaling activation to induce apoptosis in TK-10 renal cell carcinoma

status: Public on May 24 2016

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

summary: Cordyceps participates in various pharmacological activities including anti-tumor, and is involved in the regulation of NF-κB signaling pathway. However, the detailed role of cordycepin in suppression of NF-κB signaling pathway is less clear. In this study, we first analyzed the effect of cordyceps on NF-κB activity in TK-10 cells, and found that cordyceps resulted in a dose-dependent reduction in TNF-α-induced NF-κB activation. Here, we show that cordyceps mediated NF-kB inhibition induces apoptosis in TK-10 cells involved the serial activation of caspases. Moreover, we demonstrate that in addition to activating caspases, the cordyceps negatively modulates TNF-α-mediated NF-κB signaling to promote JNK activation, which results in apoptosis, and that NF-kB regulates antiapoptotic factor GADD45b and the JNK kinase MKK7. When the TNFα cytokine binds to the TNF receptor, IκB dissociates from NF-κB. As a result, the active NF-κB translocates to the nucleus. Cordyceps clearly prevented NF-κB from mobilizing to the nucleus, resulting in downregulation of GADD45b, whereas upregulation of MKK7 and phosphorylation of JNK (p-JNK). This increased Bax activation, leading to marked cordyceps-induced apoptosis. Bax subfamily proteins induced apoptosis through caspase-3. Furthermore, siRNA mediated inhibition of MKK7 downregulated p-JNK and The JNK inhibitor SP600125 strongly inhibited Bax. Thus, these results indicate that cordyceps inhibits NF-κB/GADD45b signaling activation to upregulate MKK7-JNK signaling pathway to induce apoptosis in TK-10 cells and support the potential of cordyceps as a therapeutic agent for renal cancer.

overall_design: TK-10 renal cells were treated with 0.1% DMSO, cordyceps 750 ug/mL, and sunitinib 10uM for 48hrs.

first: Jung

first: Ik-Soon

last: Jang


title: Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters

status: Public on May 13 2016

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: Mammalian transcriptomes are complex and formed by extensive promoter activity. Moreover, gene promoters are largely divergent and initiate transcription of reverse-oriented promoter upstream transcripts (PROMPTs). Although PROMPTs are commonly terminated early, influenced by early polyadenylation (pA) sites, promoters often cluster so that the divergent activity of one might impact another. Here, we find that the distance between promoters strongly correlates with the expression, stability and length of their associated PROMPTs. Adjacent promoters driving divergent mRNA transcription support PROMPT formation, but due to pA site constraints, these transcripts tend to spread into the neighboring mRNA on the same strand. This mechanism to derive new alternative mRNA transcription start sites (TSSs) is also evident at closely spaced promoters supporting convergent mRNA transcription. We suggest that basic building blocks of divergently transcribed core promoter pairs, in combination with the wealth of TSSs in mammalian genomes, provides a framework with which evolution  shapes transcriptomes.

overall_design: Mapping of paired 5’ and 3’ends of capped and polyadenylated RNAs from RRP40-depleted and eGFP control HeLa cells and using transcript isoform sequencing (TIF-Seq, see Pelechano et al. Nat Protoc 2014 (PMID: 24967623) and Pelechano et al. Nature 2013 (PMID: 23615609)).

first: Yun

last: Chen

first: Evgenia

last: Ntini

first: Nicola

last: Meola

first: Vicent

last: Pelechano

middle: I

first: Torben

last: Heick Jensen

first: Albin

last: Sandelin


title: Sex-Biased Gene Expression and Sequence Conservation in Pacific and Atlantic Salmon Lice (Lepeophtheirus salmonis)

city: Victoria

first: Ben

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

institute: The University of Victoria

summary: This study investigates sex-biased gene expression between populations of Atlantic and Pacific salmon lice, Lepeophtheirus salmonis. Two Atlantic L. salmonis populations were previously used for an array study (GSE56024) while a third dataset using Pacific L. salmonis was novel. Using all three populations, a consensus-based, meta-analysis approach was used to identify sex-biased and sex-specific genes.

overall_design:
Two separate experiments were conducted, one for Atlantic and one for Pacific salmon lice. As the Atlantic data has been previously published for other comparisons (GSE56024), only the Pacific data is uploaded here. Lice from three populations (2 in the Atlantic and 1 in the Pacific) were collected for in vitro bioassay analysis using emamectin benzoate. After 24hrs, lice were collected as per treatment protocol below. Males and females from all populations were compared separately before forming a consensus probe list of sex-biased genes concordantly expressed across all three populations.

Please note that each raw data file contains three or four 'block' data and each block data correspond to individual sample raw data. Therefore, each raw data file contains raw data for 3-4 samples (as indicated in the description field).

first: Jordan

last: Poley

last: Sutherland

first: Simon

last: Jones

first: Mark

last: Fast


title: miRNA expression data from pancreatic ductal adenocarcinoma (PDAC) cell line BxPC3 and its cisplatin-resistant derivative BxPC3-R

status: Public on May 01 2016

city: Atlanta

first: Roman

middle: F. N.

last: Mezencev

state: GA

address: 310 Ferst Dr

department: School of Biology

institute: Georgia Institute of Technology

summary:
Differential expression of miRNAs between parental and cisplatin-resistant PDAC cells was analyzed to elucidate the role of miRNAs in the acquired resistance of pancreatic cancer cells to cisplatin.
Cisplatin-resistant BxPC3-R cells were developed from the parental BxPC3 cell line by culturing them in medium with step-wise increasing concentration of cisplatin.

overall_design: Dataset includes 2 replicate cultures of BxPC3-R cells and 2 replicate cultures of BxPC3 cells

first: John

last: McDonald


title: Complex Balanced Translocation Disrupting TCF4 and Altering TCF4 Isoform Expression Segregates as Mild Autosomal Dominant Intellectual Disability

city: Bethesda

first: Barbara

last: Pusey

state: MD

address: 50 Center Drive

department: Undiagnosed Diseases Program

institute: NHGRI

summary:
Mutations of TCF4, which encodes a basic helix-loop-helix transcription factor, cause Pitt-Hopkins syndrome (PTHS) via multiple genetic mechanisms. TCF4 is a complex locus expressing multiple transcripts by alternative splicing and use of multiple promoters. We report a three-generation family segregating mild intellectual disability with an apparently balanced chromosomal translocation t(14;18)(q23.3;q21.2) that we characterized as a complex unbalanced karyotype 46,XY,der(14)del(14)(q23.3q23.3)t(14;18)(q23.3;q21.2)del(18)(q21.2q21.2) del(18)(q21.2q21.2)inv(18)(q21.2q21.2),der(18)t(14 ;18)(q23.3;q21.2) disrupting TCF4.
Using whole genome sequencing, transcriptome sequencing, qRT-PCR and nCounter analysis, we characterized the breakpoint junctions from derivative chromosomes and gene expression at the TCF4 locus. Our analyses revealed that family members segregating mild intellectual disability with the complex chromosome aberration had normal expression of genes along chromosomes 14 or 18 and no marked changes in expression of genes other than TCF4.
Affected individuals had 12-33 fold higher mRNA levels of TCF4 than did unaffected controls or individuals with PTHS. Increased levels of TCF4 transcript variants originating distal to the translocation breakpoint, not the fusion transcript generated by the derivative chromosome, contributed to this increased.
Although validation in additional patients is required, our findings suggest that the dysmorphic features and severe intellectual disability characteristic of PTHS is partially rescued by overexpression of short TCF4 transcripts encoding a nuclear localization signal, a transcription activation domain, and the basic helix-loop-helix domain.

overall_design: Examination of TCF4 Isoform expression comparison between mutant and control skin fibroblast tissues

first: Valerie

last: Maduro

middle: N

first: Praveen

last: Cherukuri

first: Cornelius

last: Boerkoel


title: microRNAs profiles of contrast-induced acute kidney injury rats

status: Public on May 14 2016

city: Shanghai China

first: linghong

last: shen

address: 1630 Dongfang Road

institute: Department of Cardiology, Renji Hospital                                  Shanghai Jiaotong University School of Medicine

summary: Contrast-induced acute kidney injury (CI-AKI) is typically defined by an increase in serum creatinine (SCr) after intravascular administration of contrast medium. Since creatinine is an unreliable indicator for acute changes in kidney function, an early biomarkers for CI-AKI diagnosis is important for initiating therapy.We assessed the hypothesis that circulating microRNAs (miRNAs) could be served as potential biomarkers to early detect CI-AKI.The rat model of acute kidney injury was developed as we previously described. We first detect miRNA profile of plasma and kidney tissue using Agilent microarray platform. 3 miRNA species with > 1.5-fold increase in plasma samples of CI-AKI rats, including miRNA-30a, miRNA-30e and miRNA-188, were selected as candidate miRNAs of potential biomarkers.

overall_design: 24 rats were randomly divided into 2 groups (CI-AKI group and control group), each with 4 subgroups (n=3). Peripheral blood and kidney samples were harvest at 8h after contrast medium/normal saline administration. Total RNA sample from each rat in the same subgroup was combined together as pooled sample for further test. The Agilent microarray platform was adapted to profile the miRNA spectra.

last: He

first: Ling-hong

last: Shen

first: Shi

middle: q

last: Sun

first: Tuo

last: Zhang


title: gene expression profiles in PC9 erlotinib resistance cells after erlotinib, HDAC inhibitor YF454A or combination treatment

status: Public on Apr 16 2016

city: Shanghai

first: Xiufeng

last: Pang

address: 500 Dongchuan Road

department: School of Life Sciences

institute: East China Normal University

summary:
To identify the potential mechanisms of enhanced activity of combined inhibition of erlotinib and YF454A, we conducted a microarray analysis on gene expression profiles in PC9 erlotinib cells.
We used Affymetrix GeneChip® Human Transcriptome Array 2.0 to  detail gene expression after indicated treatments and identified  the molecular mechanism during this process to facilitate further studies.

overall_design: PC9 erlotinib resistance cells were treated with vehicle control, erlotinib (5 µM), HDAC inhibitor YF454A (0.2 µM), or the combination of erlotinib and YF454A for 12 h. Samples were obtained from three independent biological replicates.RNA from each sample was labeled and hybridized using Affymetrix GeneChip® Human Transcriptome Array 2.0.

first: Guoliang

last: Chen

first: Weiwei

last: Yu

first: Mingyao

last: Liu


title: Expression profiling in grade I and grade II meningiomas and in normal control brain samples

status: Public on Apr 20 2016

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

summary:
Experiment: Establishment of expression profiles in grade I and grade II meningiomas and in normal control brain samples.
We extracted DNA from specimens and performed mutational analysis in meningiomas and extracted RNA that was processed and hybridized to Affymetrix microarrays.

overall_design:
Total RNA was extracted from 14 meningioma samples for expression profiling.
3 controls are normal brain tissue from the Affymetrix data resource center (http://www.affymetrix.com/support/technical/sample_data/gene_1_0_array_data.affx): Affymetrix_TisMap_Brain_01_v1_WTGene1, Affymetrix_TisMap_Brain_02_v1_WTGene1, Affymetrix_TisMap_Brain_03_v1_WTGene1. The RMA-normalized data for these samples are available in the supplementary file 'GSE77259_normalized_data_for_normal_brain_controls.txt'.

first: Hans

first: Sajjad

last: Karim


title: Nuclease footprints in sperm project past and future chromatin regulatory events

status: Public on May 04 2016

city: Durham

first: Graham

middle: David

last: Johnson

state: NC

address: 101 Science Drive

department: GCB

institute: Duke University

summary: Nuclear remodeling to an extreme condensed state is a hallmark of spermatogenesis. This is achieved by varied degrees of replacement of histones with protamines. Regions retaining nucleosomes may be of functional significance. To determine potential roles for somatic-like chromatin in the paternal gamete, sperm from wild type and transgenic mice harboring a single copy insert of the human protamine cluster were subjected to Micrococcal Nuclease (MNase)-seq. Nuclease footprints linked robust endogenous protamine transcription and transgene suppression to its chromatin environment. Murine footprints were enriched within regulatory regions and sequences expressed in the early embryo. These were highlighted by Ctcf footprints that were enriched within chromatin domain boundaries and sites bound in testes and ESCs. In contrast, Ctcf footprints were absent in human and bull sperm. The continuity of Ctcf binding through the murine germline may permit rapid reconstitution of chromatin organization following fertilization. This likely reflects its preparation for early zygotic genome activation and comparatively accelerated preimplantation embryonic development program observed in mouse as compared to human.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mononucleosomal sperm DNAs from wild type and transgenic mice were released with micrococcal nuclease or DNA fragmentation factor (DFF) and subjected to high-throughput sequencing. Testis RNAs from transgenic mice were subjected to high-throughput sequencing.

first: Meritxell

last: Jodar

first: Roger

last: Pique-Regi

first: Stephen

last: Krawetz


title: RNA Seq Comparison of midguts collected from Asian longhorned beetles larvae feeding on sugar maples and a nutrient-rich artificial diet

status: Public on Apr 22 2016

city: Lincoln

first: Erin

last: Scully

state: NE

address: 137 Keim Hall, UNL East Campus

institute: USDA-ARS Grain, Forage, and Bioenergy Research Unit

summary: The goal of this study was to compare RNA Seq profiles of Asian longhorned beetle larval guts feeding on two different substrates to identify key genes involved in woody tissue degradation, nutrient scavenging, and detoxification of host plant defensive compounds.

overall_design: RNA Seq profiles of four third instar larvae feeding on a nutrient rich artificial diet and on sugar maple trees were generating using the Illumina HiSeq 2000.


title: Differentially expressed genes after miRNA or siRNA transfection in human cancer cell lines II

status: Public on Apr 13 2016

city: Chiba

first: Naohiko

last: Seki

address: 1-8-1, Inohana

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (microRNAs or siRNAs) in human cancer, several cell lines (pancreatic cancer, esophageal cancer, bladder cancer, prostate cancer, renal cell carcinoma and lung squamous cell carcinoma) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (Panc-1, sw1990, TE8, TE9, A549, MRC-5, BOY, T24, PC3, C4-2, 786-O, A-498 and EBC-1) were treated with miRNAs (miR-375, miR-29a, miR-26a, miR-145-5p, miR-145-3p, miR-218, miR-320a), siRNAs (si-MMP11, si-LAMP1, si-LOXL2, si-PLOD2, si-UHRF1, and si-FOXM1).

first: Yusuke

last: Goto


title: New insights into the reproductive transcriptome profile of the Mediterranean fruit fly Ceratitis capitata

status: Public on Apr 26 2016

city: Göttingen

first: Ingrid

last: Curril

state: Niedersachsen

address: Justus-von-Liebig-Weg 11

department: Developmental Biology

country: Germany

institute: Georg-August-Universität Göttingen

summary:
Purpose: Use of RNAseq to identify crucial genes expressed in the reproductive tract of C. capitata
The medfly, Ceratitis capitata continues to pose a major threat to the agricultural sector in almost every continent. Promiscuous female medflies can oviposit up to 1000 eggs throughout their lifetime causing remarkable losses in crop viability.  Nowadays, there is an increasing demand for finding new improved solutions to counteract its invasive spreading capacity. To these regards, research that aims in understanding the reproductive biology of fruit fly pests by obtaining its genomic profiling can be of great contribution to this field.   In this study we have generated a De-novo assembly of the medfly reproductive tract transcripts. We used Transcriptomics via deep RNA-sequencing to identify the transcripts present in the sex organs (spermatheca, uterus and accessory glands) of sexually matured virgin and 24hr-freshly mated females as well as testes, and male accessory glands of C. capitata. In addition, differential expression changes between virgin and mated females could help elucidate crucial candidate genes that participate in the female physiological response to the male seminal input. Furthermore, in order to ensure pure and significant results of the transcriptomic analysis, we have included a negative control that includes gut and abdominal adipose tissue. The newly annotated genes from this investigation could furthermore contribute to the ongoing field of biological and genetic population control.

overall_design:
Sexually matured adult wildtype medflies of the following conditions/time points:
control: virgin female gastrointestinal tract control 100bp paired end reads
control: virgin female gastrointestinal tract control 50bp single read triplicates
treatment: Female Lower Reproductive tract from virgin-adult (1 day after pupa emersion) 100bp paired end reads
treatment: Female Lower Reproductive tract from virgin-adult (4 days after pupa emersion) 100bp paired end reads
treatment: Male Reproductive tract from virgin-adult (1 day after pupa emersion) 100bp paired end reads
treatment: Male Reproductive tract from virgin-adult (4 days after pupa emersion) 100bp paired end reads
treatment: Female Lower Reproductive from mated-adult (1 day after mating) 100bp paired end reads
treatment: Female Lower Reproductive from mated-adult (4 days after mating) 100bp paired end reads
treatment: Male Lower Reproductive tract from mated-adult (1 day after mating) 100 bp paired end reads
treatment: Male Lower Reproductive tract from mated-adult (4 days after mating) 100 bp paired end reads
treatment: Female Lower Reproductive tract from virgin-adult (4 days after pupa emersion) 50bp single reads triplicates
treatment: Female Lower Reproductive tract from mated-adult (1 day after mating) 50bp single reads triplicates
treatment: Male reproductive tract from mated-adult (1 day after mating) 50bp single reads triplicates
Total: 2 controls, 8 treatments, 21 sequencing runs
The first 9 samples of 100bp PE reads were used for the assembly and the rest of the samples (12 samples 50 bp SE) for differential expression analysis.

first: Georg

last: Oberhofer

first: Ernst

last: Wimmer


title: Exon level expression profiling of colorectal cancer tissue samples (77 samples)

status: Public on Apr 12 2016

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

institute: Institute for Cancer Research, Oslo University Hospital

summary: These colorectal cancer (CRC) samples have been analyzed by exon expression profiling to identify genes with overexpression of 3’ parts. By characterizing underlying transcript structures of such genes with a combination of rapid amplification of cDNA ends and deep-sequencing (RACE-seq), we identify and describe novel RNA-variants in CRC.

overall_design: We analyzed genome-wide expression at the exon-level using the Affymetrix Human Exon 1.0 ST platform. This set of CRC samples is a part of a larger series. Exon level expression values from a total of 202 CRCs and 21 normal colonic mucosa were used to detect samples that possess abnormal expression profiles. This submission includes 77 CRC samples. The remaining 125 CRC samples and 21 normal colonic mucosa samples are already deposited in GEO, accession numbers GSE24550, GSE29638, and GSE42690.

first: Ragnhild

last: Lothe


title: Expression data from gastric cancer and paried normal tissues

status: Public on Apr 07 2016

city: Hangzhou

first: Qinshu

last: Shao

state: ZheJiang

address: 158 Shangtang Road

institute: Zhejiang Provincial People’s Hospital

summary: Gastric cancer (GC) is one of the most common cancer worldwide. Specific and reliable molecular markers are limited; it is critical to identify new biomarkers for GC to aid in early diagnosis, treatment strategy, and prognosis evaluation. Microarray technology makes it possible to measure the expression levels of thousands of genes, and identifying meaningful and useful molecular targets from these large data.

overall_design: Total RNA was extracted from 10 pairs of GC tissue and adjacent non-tumor mucosa using TRIzol® reagent (Invitrogen, Carlsbad, CA, US) following the manufacturer's instructions. The RNA integrity number (RIN), detected by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US), was used to determine the RNA integrity. Total RNA meeting the specified quality criteria (RIN ≥ 7.0 and 28S/18S ≥ 0.7) were further purified using an RNase-Free DNase Set  (Qiagen, Hilden, Germany) and an RNeasy® Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Purified total RNA was then used for obtaining biotin-labeled cRNA  by applying the GeneChip® 3'IVT Express Kit (Affymetrix, Santa Clara, CA, US), according to the manufacturer's instructions. Then, the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, Santa Clara, CA, US) was used for performing the array hybridization and wash, with the use of a GeneChip® Hybridization Oven 645 (Affymetrix, Santa Clara, CA, US) and a GeneChip® Fluidics Station 450 (Affymetrix, Santa Clara, CA, US). All arrays were scanned using a GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with the default settings. Raw data were normalized by the MAS 5.0 algorithm in GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US). The significance analysis of microarray (SAM) was used to identify genes that were differentially expressed between the GC and normal tissues. Genes were considered to be differentially expressed when the Tumor versus Normal signal log ratio values were  ≥2 or ≤0.5.

first: Haibo

last: Yao

first: Jun

last: He

first: Yi

last: Jin


title: A coding sequence-embedded principle governs translational reading frame fidelity

city: Ithaca

first: Ji

last: Wan

state: NY

address: 303 Biotech 526 Campus Road

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: Upon initiation at an AUG start codon, the ribosome must maintain the correct reading frame for hundreds of codons in order to produce functional proteins. Although some sequence elements are able to trigger programmed ribosomal frameshifting (PRF), very little is known how the ribosome normally prevents spontaneous frameshift errors. Using high resolution ribosome profiling data sets, we discovered that the translating ribosome uses the 3’ end of 18S rRNA to scan the AUG-like codons after the decoding process. The internal mRNA:rRNA interaction not only contributes to predominant translational pausing, but also provides a post-decoding mechanism to safeguard the ribosome in the correct reading frame. Partially eliminating the AUG-like “sticky” codons in the reporter message leads to increased +1 frameshift errors. Remarkably, mutating the highly conserved CAU triplet of 18S rRNA globally changes codon “stickiness”. Further supporting the role of “sticky” sequences in reading frame maintenance, the codon composition of open reading frames is highly optimized across eukaryotic genomes by minimizing the appearance of AUG-like codons in the frame 2. These results suggest an important layer of information embedded within the protein coding sequences that instructs the ribosome to ensure reading frame fidelity during translation.

overall_design: Investigating the role of 18S rRNA in controlling translational reading frame fidelity

first: Xiangwei

last: Gao

first: Yuanhui

last: Mao

first: Leiming

last: Dong

first: Longfei

last: Jia

first: Xingqian

last: Zhang

first: Shu-Bing

last: Qian


title: Expression of genes in Runx2/Myc transgenic mouse thymus compared to control

status: Public on Apr 14 2016

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube Estate

institute: The University of Glasgow

summary: Retroviral insertional mutagenesis (RIM) is a powerful tool in cancer genomics. Transgenic mice expressing two potent collaborating oncogenes in the germline, Myc and Runx2, develop rapid onset tumours that can be accelerated and rendered polyclonal by neonatal infection with MoMLV. Deep sequencing of lymphomas from infected Runx2/Myc mice revealed a network of progression genes. Transcriptional analysis of basal expression levels in transgenic cells showed that the progression network showed strong evidence of clonal selection beyond gene expression level.

overall_design: We examined the gene expression profile of triplicate 10 day old thymus from CD2-Myc/CD2-Runx2 and C57/CBA mice to examine early gene changes in comparison to RIM targets in end stage tumours. We found no significant relationship between basal expression in the transgenic system and genes that were targets for retroviral integration.

first: Camille

last: Huser

first: Pawel

last: Herzyk

first: James

last: Neil


title: The signaling pathway involved in  wild type and 2D2-gut CD4+ T cell development

status: Public on Apr 01 2016

city: Kodaira, Ogawahigashi

first: Atsushi

last: Kadowaki

state: Tokyo

department: Immunology

institute: National Institute of Neuroscience, National Center of Neurology and Psychiatry

summary: To find the signalling pathway involved in WT/2D2 CD4+ gut T cell (CD4+ intraepithelial lymphocytes, CD4+IEL) differentiation, particulary to determine whether aryl hydrocarbon receptor (AHR) pathway is involved.

overall_design: Gene expression was analyzed ex vivo in CD4+ T cells that were sorted from Wild type-Gut / 2D2 mouse-Gut / Wild type-Spleen / 2D2 mouse-Spleen  (N=3 per group). The genes highly expressed in WT/2D2 Gut compared to WT/2D2 Spleen were selected by k-means clustering. AHR pathway related genes (IPA software) were further selected.

first: Takashi

last: Yamamura


title: Centromere misdivision promotes centromeric sequence changes, de novo centromere formation, and centromere expansion

status: Public on Apr 02 2016

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

summary: Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids.

overall_design: ChIP-seq was carried out with anti-CENH3 antibody using material 4DS and control (Chinese Spring, CS as short).

first: Fangpu

last: Han


title: The DNA methylation landscape of human melanoma (MIRA-Seq)

status: Public on Mar 31 2016

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

type: Methylation profiling by high throughput sequencing

summary: Melanoma genomes are often characterized by large numbers of sunlight-induced mutations. However, epigenetic alterations, in the form of aberrant DNA methylation patterns, are also abundant. Using MIRA-seq, we have carried out a comprehensive characterization of the DNA methylome in a series of metastatic melanoma samples and catalogued the methylation changes relative to normal melanocytes, the presumed cells of origin for these tumors. Individual melanoma tumors contained up to several thousand hypermethylated regions. We discovered 179 tumor-specific methylation peaks that were present in all (27/27) melanomas and may lend themselves as effective disease biomarkers, and 3124 methylation peaks were present in >40% of the tumors. We specifically examined the relationship between presence of the Polycomb mark, H3K27me3 in melanocytes and tumor-specific DNA methylation in melanoma. We found that 150 of the approximately 1,200 tumor-associated methylation peaks near transcription start sites (TSS) were H3K27me3-marked in melanocytes. Notably, DNA methylation in melanoma was specific for distinct H3K27me3 peaks rather than for H3K27me3-enriched regions with broad genomic coverage. Yet, there were also numerous H3K27me3 peak-associated TSS regions that were completely resistant to DNA methylation in tumors. Furthermore, a rather large group of genes became methylated in melanoma but lacked H3K27me3 in melanocytes. There was no relationship between presence of BRAF V600 mutations and the number of methylation peaks in individual tumors. Gene expression analysis showed a strong signature of upregulated immune response genes in melanomas presumably as a result of lymphocyte infiltration. Genes down-regulated in tumors were enriched for melanocyte differentiation and pigmentation factors. Overall, there was limited correlation between tumor-associated DNA methylation changes and changes in gene expression although distinct melanocyte differentiation genes including KIT, PAX3 and SOX10 became methylated and downregulated in melanoma.

overall_design: Using MIRA-Seq, DNA methylation profiles of 27 malignant melanomas and 3 primary cultured melanocyte samples were determined

first: Seung-Gi

first: Wenying

last: Xiong

first: Lu

last: Yang

first: Gerd

last: Pfeifer


title: miR-192-EGR1/HOXB9 regulatory network controls the angiogenic switch in cancer.

status: Public on Mar 21 2016

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: A deeper mechanistic understanding of tumor angiogenesis regulation is needed to improve current anti-angiogenic therapies, which thus far have only modestly improved patient survival. We present converging evidence from systems-based miRNA analyses of large-scale patient datasets along with in vitro and in vivo experiments that identify miR-192 as a key regulator of angiogenesis.

overall_design: Two groups of samples are included: 1.SKOV3ip1 cells treated with control miRNA. 2.SKOV3ip1 cells treated with miR-192. Gene expression profiles were compared between these two treatment groups.

first: Sherry

first: Anil

last: Sood

first: Ju-Seog

last: Lee


title: Genome-wide profiling of chicken DCs response to infectious bursal disease virus

status: Public on Mar 24 2016

city: nanjing

first: Jian

last: Lin

state: jiangsu

address: tongwei road N0.1

department: Life Science

institute: nanjing agricultural university

summary:
Background: Avian infectious bursal disease virus (IBDV) is a major poultry disease which leads to significant losses of poultry industry. Dendritic cells (DCs), the only bridge communicated the innate and acquired immunity, have the most important antigen presenting ability and can significantly influence the pathogenicity of viruses. To understand the interaction between IBDV and DCs, microarray was used to analyze the response of DCs infected by IBDV.

Results: Results showed that IBDV infection induced 479 up-regulated and 466 down-regulated mRNAs in chicken DCs. GO terms analysis suggested that transcription from RNA polymerase II promoter and RNA biosynthetic process were mainly enriched, whilst pathway analyses suggested that oxidative phosphorylation, T cell receptor and IL-17 signaling pathway might activated by IBDV infection. Moreover, we detected the microRNA (miRNA) and long non-coding RNA (lncRNA) alterations in IBDV-infected chicken DCs. Results identified 18 significant up- or down- regulated miRNAs and 441 significant up- or down-regulated lncRNAs in IBDV-stimulated DCs. Furthermore, we constructed 42 TF (transcription factors)-miRNA-mRNA interactions involving 1 TF, 3 miRNAs and 42 mRNAs in IBDV-stimulated DCs. Finally, we predicted the target genes of different expressed lncRNAs and constructed lncRNA-mRNA regulatory networks.

Conclusions: Altogether, our research suggested a mechanism to explain how IBDV infection triggered an effective immune response in chicken DCs.

overall_design: In the study presented here, cultured chicken bone marrow-derived dendritic cells (BMDCs) were randomly divided into control group and IBDV-stimulated group. Each group consisted of three wells of BMDCs from three chickens.

first: Jing

last: Xia

first: Keyun

last: Zhang

first: Qian


city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

institute: Oita university, Faculty of Medicine

type: Genome variation profiling by genome tiling array

summary: Genomic copy number aberrations of 11 gastric cancer cell lines were analyzed by 244k CGH array from Agilent Technologies. Based on this results, we separated the 11 cell lines into 2 groups, with and without copy number increase at chromosome 20q13

overall_design: We performed array comparative genomic hybridization to detect genomic copy number aberrations in 11 gastric cancer cell lines. Microarray images were analyzed by using Feature Extraction and DNA analytics softwares.

first: Shoichi

last: Fumoto

first: Tsuyoshi

last: Noguchi

first: Kazuyoshi

last: Yanagihara

first: Yuka

last: Hirashita

first: Chisato

last: Nakada

first: Naoki

last: Hijiya

first: Tomohisa

last: Uchida

first: Keiko

last: Matsuura

first: Ryoji

last: Hamanaka

first: Kazunari

last: Murakami

first: Masao

last: Seto

first: Masafumi

last: Inomata

first: Masatsugu

last: Moriyama


title: The DNA methylation landscape of human melanoma [ChIP-Seq]

first: Xiwei

last: Wu

overall_design: Examination of H3K27me3 histone modification in human normal melanocytes.

first: Seung-Gi

last: Jin

first: Wenying

last: Xiong

first: Lu

last: Yang

first: Gerd

last: Pfeifer


title: The DNA methylation landscape of human melanoma [RNA-Seq]

overall_design: Genome-wide gene expression analysis of 17 melanomas and 3 melanocyte samples


title: The DNA methylation landscape of human melanoma

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

overall_design: Refer to individual Series


title: Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis

status: Public on Mar 15 2016

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

institute: Hebrew University of Jerusalem

summary: We recently developed a high-resolution genome wide assay for mapping DNA excision repair named eXcision Repair-sequencing (XR-seq) (GEO accession: GSE67941) We have now used this assay to assay the effect of chromatin state on DNA repair. Here we report the results of a  time-course of the repair of the UV induced damages cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts [(6-4)PPs] in normal human skin fibroblasts. Comparison of this data to histone modification and DNA-seq maps (ENCODE) revealed initial repair of both damages is enriched in open and active chromatin states, whereas repair in heterochromatic and repressed chromatin states is relatively low and persists to later time points.

overall_design: We  performed XR-seq for two types of UV induced damages (CPD and (6-4)PP) at multiple time points after UV irradiation,  in normal NHF1, and CS-B (CS1ANps3g2, GM16095) fibroblast cell lines. Two biological replicates were performed for each experiment in which independent independent cell populations were UV treated and subjected to XR-seq. For assaying CPD repair, cells were irradiated with 10J/m2 and for assaying (6-4)PP cells were irradiated with 20J/m2.  Raw data for the 1h time points of (6-4)PP repair are the same as in GEO accession GSE67941).

first: S

first: J

last: Hu

last: Lieb

first: A

last: Sancar


title: Transcriptome analysis of Macrobrachium nipponense : genes and expression profile from hepatopancreas and muscle

status: Public on Mar 02 2016

city: huzhou

first: ding

last: zhili

address: xueshi road

institute: Huzhou University

summary: To identify genes involved in nutrition metabolism of Macrobrachium nipponense, two independent cDNA libraries from hepatopancreas and muscle were constructed through high-throughput next-generation sequencing techniques. A total of 112,548,142 and 90,140,774 high quality reads were generated in the two cDNA libraries, respectively. Clustering and assembly of these reads produced a nonredundant set of 98,560 unique sequences, with an average unigene length of 793 bp. The unigene sequences were subjected to GO, COG and KEGG functional classification. A large number of differentially expressed genes were recovered by comparison of the two tissues. The differentially expressed and their functions were predicted by KEGG pathway mapping. Furthermore, 17,971SSRs and 32,935 high-confidence SNPs were identified in the two EST datasets. This study lays the foundation for further research on gene function analysis in nutrition metabolism of M. nipponense.

overall_design: sample 1: hepatopancreas;  sample 2: muscle

first: Zhili

last: Ding

first: Jinyun

last: Ye


title: Pancreas-specific Sirt1-deficiency in mice compromises beta-cell function without development of hyperglycemia

status: Public on Mar 01 2016

city: Sydney

first: Jianmin

state: NSW

address: 370 Victoria Street Darlinghurst

department: Cancer Division

country: Australia

institute: Garvan Institute of Medical Research

summary:
Sirtuin 1 (Sirt1) has been reported to be a critical positive regulator of glucose-stimulated insulin secretion in pancreatic beta-cells. The effects on islet cells and blood glucose levels when Sirt1 is deleted specifically in the pancreas are still unclear.This study examined islet glucose responsiveness, blood glucose levels, pancreatic islet histology and gene expression in Pdx1-Cre;Sirt1(ex4F/F) mice that have loss of function and loss of expression of Sirt1 specifically in the pancreas. We found that in the Pdx1-Cre;Sirt1(ex4F/F) mice, the relative insulin positive area and the islet size distribution were unchanged. However, beta-cells were functionally impaired, presenting with lower glucose-stimulated insulin secretion. This defect was not due to a reduced expression of insulin but was associated with a decreased expression of the glucose transporter Slc2A2/Glut2 and of the Glucagon like peptide-1 receptor (Glp1r) as well as with a marked down regulation of endoplasmic reticulum (ER) chaperones that participate in the Unfolded Protein Response (UPR) pathway. Counter intuitively, the Sirt1-deficient mice did not develop hyperglycemia. Pancreatic polypeptide (PP) cells were the only other islet cells affected, with reduced numbers in the Sirt1-deficient pancreas.
This study provides new mechanistic insights showing that beta-cell function in Sirt1-deficient pancreas is affected due to altered glucose sensing and deregulation of the UPR pathway. Interestingly, we uncover a context in which impaired beta-cell function is not accompanied by increased glycemia. This points to a unique compensatory mechanism. Given the reduction in PP, investigation of its role in the control of blood glucose is warranted.

overall_design: To uncover other Sirt1-regulated mechanisms, we performed a gene expression microarray analysis comparing pancreata from the 6 month old Sirt1–deficient mice to their controls (n=3 per group).

first: Andreia

middle: V

last: Pinho

first: Mohammed

last: Bensellam

first: Elke

last: Wauters

first: Maxine

last: Rees

first: Marc

last: Giry-Laterriere

first: Amanda

last: Mawson

first: Le

middle: Q

last: Ly

first: Andrew

last: Biankin

first: D

last: Laybutt

first: Ilse

last: Rooman


title: Expression data from cleaved CD95L treated human Th17 and Treg cells.

status: Public on Mar 05 2016

city: Rennes

first: Patrick

last: Legembre

address: CRLCC Eugène Marquis, Rue Bataille Flandres Dunkerque, Bat. D

department: Chemistry Oncogenesis Stress Signalling

country: France

institute: Inserm U1242

summary: Th17 and Treg cells show a different infiltration and migrations pattern in inflamed skin from systemic lupus erythematosus patients. This distribution strongly correlates with the plasm levels of cleaved CD95L (cl-CD95L). To identify the mechanisms that underly this difference in migration, we used microarrays to identify differences in RNA expression induced by cl-CD95L treatment on Th17 and Treg cells from healthy donors.

overall_design: Total RNA was collected from Th17 and Treg cells cultured for 8h in RPMI medium supplemented with 8% FCS and treated with 100 ng/ml cleaved CD95L (treatment) or vehicle only (control) and hybridized on Affymetrix microarrays. Th17 and Treg cells were of obtained from buffy coats of healthy donors and sorted using the CD4+CD25+CD127dim/- Regulatory T Cell Isolation Kit II (Miltenyi biotec, Germany)  and the Human Th17 cell enrichment kit (Stemcell technologies, Canada) according to the manufacturers’ instructions. Cell enrichment was assessed with flow cytometry.

first: Doriane

last: Sanséau

last: Poissonnier

first: Marine

last: Malleter

first: Matthieu

last: Le Gallo

first: Nicolas

last: Levoin

first: Aubin

last: Penna

last: Blanco

first: Alain

last: Dupuy

first: Florence

last: Poizeau

last: Fautrel

first: Roselyne

last: Viel

first: Julien

last: Séneschal

first: Cécile

last: Contin

first: Thomas

last: Ducret

first: Anne-Marie

last: Vacher

first: Paul

last: Barrow

first: Robin

last: Flynn

first: Pierre


title: Hippocampal response to Hypobaric Hypoxia

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Sprague Dawley rats were exposed to Hypobaric Hypoxia for 1, 3 and 7 days followed isolation of Hippocampus. Microarray was performed utilizing RNA isolated from these samples. Each group included 5 animals.

overall_design: Agilent Rat Gene Expression 8X60K (AMADID: 028279) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Manish

last: Sharma

first: Gaurav

last: Kumar

first: Aastha

last: Chhabra

first: Dipti

last: Prasad


title: The gene expression pattern of mice fed the resveratrol-enriched rice DJ526 was very different from mice fed either resveratrol or Dongjin rice alone

status: Public on Mar 12 2016

city: Jeonju

first: Seong-Tshool

last: Hong

state: Chonbuk

address: Gungi-ro 20

department: Biomedical Sciences and Institute for Medical Science

institute: Chonbuk National University

summary: The gene expression profiling analyses by DNA chip showed that the gene expression pattern of mice fed resveratrol-enriched rice DJ526 was very different from mice fed either resveratrol or Dongjin rice alone, respectively, modifying expression of genes related to aging regulation, cell differentiation, extracellular matrix, neurogenesis, or secretion.

overall_design: (1) Ctrl (The control mice fed a NFD in which the carbohydrate source was corn starch and sucrose), (2) RS (resveratrol mice fed a NFD in which the carbohydrate source was corn starch and sucrose except containing resveratrol), (3) DJ (Dongjin mice fed a NFD in which the corn starch and sucrose were replaced with Dongjin rice), and (4) DJ526 (DJ526 mice fed a NFD in which the corn starch and sucrose were replaced with the resveratrol-enriched rice DJ526)

first: Hea-Jong

last: Chung


title: Landscape and dynamics of transcription initiation in P. falciparum

city: Heidelberg

first: Christophe

last: Chabbert

address: Meyerhofstrasse 1

institute: EMBL

summary: The lack of a comprehensive map of transcription start sites (TSS) across P. falciparum genome has hampered advances in decrypting the molecular mechanisms underlying regulation of gene expression in the malaria parasite. In eukaryotic model organisms, development of genome-wide approaches and next-generation sequencing technologies has contributed to a better understanding of the impact of local nucleotide composition on transcriptional regulation. Using such methods, we generated a single nucleotide-resolution map of transcription initiation events during P. falciparum intra-erythrocytic developmental cycle.

overall_design: Examination of transcription start site during the intra-erythorcytic development of the human parasite Plasmodium falciparum

first: Sophie

middle: H

last: Adjalley

first: Bernd

last: Klaus

first: Vicent

last: Pelechano

first: Lars

middle: M

last: Steinmetz


title: The retinoblastoma protein regulates hypoxia-inducible genetic programs, tumor cell invasiveness and neuroendocrine differentiation in prostate cancer cells

status: Public on Feb 24 2016

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

summary: Loss of tumor suppressor proteins, such as the retinoblastoma protein (Rb), results in tumor progression and metastasis. Metastasis is facilitated by low oxygen availability within the tumor that is detected by hypoxia inducible factors (HIFs). The HIF1 complex, HIF1α and dimerization partner the aryl hydrocarbon receptor nuclear translocator (ARNT), is the master regulator of the hypoxic response. Previously, we demonstrated that Rb represses the transcriptional response to hypoxia by virtue of its association with HIF1. In this report, we further characterized the role of Rb in HIF1-regulated genetic programs by stably ablating Rb expression with retrovirally-introduced short hairpin RNA in LNCaP and 22Rv1 human prostate cancer cells. DNA microarray analysis revealed that Rb regulates specific chromosomal gene clusters and loss of Rb in conjunction with hypoxia leads to dysregulation of HIF1-regulated genetic programs that increase cell invasion and promote neuroendocrine differentiation. For the first time, we have established a direct link between hypoxic tumor environments, Rb inactivation and progression to late stage metastatic neuroendocrine prostate cancer. Understanding the molecular pathways responsible for progression of benign prostate tumors to metastasized and lethal forms will aid in the development of more effective prostate cancer therapies.

overall_design: RNAs derived from human LNCaP cells stably infected with either scrambled control shRNA or a shRNA directed to RB1. Cells were exposed to either 24 h hypoxia (1% O2) or maintained under normoxic conditions. Biological triplicates were tested and compared.

first: Timothy

last: Beischlag

first: Michael

middle: E

last: Cox


title: Cytosolic splice isoform of Hsp70 nucleotide exchange factor Fes1 is required for the degradation of misfolded proteins in yeast

status: Public on Feb 29 2016

city: Stockholm

first: Claes

last: Andréasson

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholm University

summary: Cells maintain proteostasis by selectively recognizing and targeting misfolded proteins for degradation. In Saccharomyces cerevisiae, the Hsp70 nucleotide exchange factor Fes1 is essential for the degradation of chaperone-associated misfolded proteins by the ubiquitin-proteasome system. Here we show that the FES1 transcript undergoes unique 3' alternative splicing that results in two equally active isoforms with alternative C-termini, Fes1L and Fes1S. Fes1L is actively targeted to the nucleus and represents the first identified nuclear Hsp70 nucleotide exchange factor. In contrast, Fes1S localizes to the cytosol and is essential to maintain proteostasis. In the absence of Fes1S, the heat-shock response is constitutively induced at normally non-stressful conditions. Moreover, cells display severe growth defects when elevated temperatures, amino acid analogues or the ectopic expression of misfolded proteins, induce protein misfolding. Importantly, misfolded proteins are not targeted for degradation by the ubiquitin-proteasome system. These observations support the notion that cytosolic Fes1S maintains proteostasis by supporting the removal of toxic misfolded proteins by proteasomal degradation. This study provides key findings for the understanding of the organization of protein quality control mechanisms in the cytosol and nucleus.

overall_design: 4 strains (WT, fes1Δ, fes1ΔS, fes1ΔL) were sequenced in triplicates from independent RNA isolations.

first: Naveen

middle: K

last: Gowda

first: Jayasankar

last: Kaimal

first: Anna

last: Masser

first: Wenjing

last: Kang

first: Marc

middle: R

last: Friedländer


title: Transcriptome analysis of two clonally-derived ICC progenitor cell lines [RNA-seq]

status: Public on Feb 22 2016

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: Interstitial cells of Cajal (ICC) are electrical pacemakers and mediators of neuromuscular neurotransmission in the gastrointestinal tract. Studies in organotypic cultures of intact gastric muscular wall tissues identified Kit(low)Cd44(+)Cd34(+)Insr(+)Igf1r(+) cells as local ICC progenitors (Lorincz et al., Gastroenterology 2008;134:1083-1093). Subsequently, conditionally immortalized Kit(low)Cd34(+) cells were isolated by immunomagnetic and fluorescent cell sorting and serial cloning from the gastric muscular wall of homozygous, 14-day-old H-2Kb-tsA58 mice and shown to share other phenotypic characteristics with in-situ ICC precursors (2xSCS70 cells; Bardsley et al., Gastroenterology 2010;139:942-952). 2xSCS70 cells were also found to express the ICC marker Ano1, to be able to extensively self-renew in the absence of the SV40 tsA58-TAg when cultured in NeuroCult® Neural Stem Cell Proliferation Medium (NSCPM; STEMCELL Technologies) and to differentiate into Kit(+) ICC both in vitro and in vivo. Wild-type cells with Kit(low)Ano1(+)Cd44(+)Cd34(+)Insr(+)Igf1r(+) phenotype (2xSCS2F10 cells) were prospectively isolated from primary cultures of dissociated gastric muscular wall tissues from 7-day-old C57BL/6J mice by serial cloning following 150-day expansion in NSCPM containing 5% cell-free chick embryo extract (CEE; Accurate Chemical). Long-term culturing of both cell lines was associated with further decline in Kit expression while expression of Ano1 and other markers of ICC precursors was maintained. Following spontaneous transformation, both 2xSCS70 and 2xSCS2F10 cells grafted into nude mice gave rise to tumors containing Kit(+)cells and otherwise resembling gastrointestinal stromal tumors (GIST), which originate from the ICC lineage (Bardsley et al., Gastroenterology 2010;139:942-952). This study utilized RNA-sequencing to complement the companion microarray study in non-transformed 2xSCS70 and 2xSCS2F10 cells.

overall_design: Libraries were made from total RNA isolated from ICC progenitor cell lines using the Illumina TruSeq mRNA Sample Preparation Kit v2 and sequenced on the Illumina HiSeq 2000 platform.


title: Expression analysis of DNMT3A mutant-transduced hematopoetic stem/progenitors

status: Public on Feb 10 2016

city: Tokyo

first: Junji

last: Koya

address: 7-3-1, Hongo, Bunkyo-ku

institute: The University of Tokyo

summary: Despite the impact of DNMT3A mutation in acute myeloid leukemia has been emphasized, the precise molecular mechanisms in leukemogenesis are largely unknown. Here we show that, in murine transplantation experiments, recipients transplanted with DNMT3A mutant-transduced cells exhibit aberrant hematopoietic stem cell (HSC) accumulation. Differentiation-associated genes are down-regulated without accompanying changes in methylation status of their promoter-associated CpG islands in DNMT3A mutant-transduced stem/progenitor cells. DNMT3A mutant also promotes monoblastic transformation in vitro in combination with HOXA9. Molecularly, DNMT3A mutant interacts with polycomb repressive complex 1 (PRC1), leading to transcriptional silencing of PU.1. Suppression of PRC1 impairs aberrant HSC accumulation and monoblastic transformation. Taken together, our results highlight the functional role of DNMT3A mutation, forming the basis for leukemia development.

overall_design: GFP-labeled empty vector, DNMT3A wild-type (WT), R882H-transduced LSK cells derived from transplanted mice were utilized for compared the expression profiles (3 sorted empty vector-transduced LSK cells, 3 sorted DNMT3A WT-transduced LSK cells, and 3 sorted DNMT3A R882H-transduced LSK cells. Total RNA was extracted by TaKaRa NucleoSpin RNA XS according to the manufacturer’s protocol. Amplification and biotin labeling of fragmented cDNA was carried out from 3.67 ng of total RNA by using NuGen Ovation Pico WTA System V2 (NuGEN) and SureTag Complete DNA Labeling Kit (Agilent). Each 2 μg of cDNA were hybridized to the Agilent SurePrint G3 Mouse Gene Expression 8x60K (Agilent) using Gene Expression Hybridization Kit (Agilent). After scanning, the signal intensity for each feature was measured by Agilent Feature Extraction (Agilent).

first: Mineo

last: Kurokawa


title: Transcriptome analysis of two clonally-derived ICC progenitor cell lines


title: Comparison of gene expression between wild-type and Osterix1-Cre:Hdac3 CKO BMSC-derived osteoblasts

status: Public on Jan 31 2016

first: Asha

last: Nair

address: 200 1ST ST SW

summary:
Bone marrow stromal cells (BMSC) were isolated from femurs and tibias of littermate wildtype and CKO mice.  Cells were plated in osteogenic culture medium
(alphaMEM, 20% FBS, 1% antibiotic/antimycotic, 1% non-essential amino acids, 50 ug/mL ascorbic acid, 10 mM beta glycerophosphate, 10^-7 M dexamethasone) and cultured for 7 days prior to RNA isolation.

overall_design: Total RNA isolated from osteogenic cultures of BMSC grown for 7 days

first: Jennifer

last: Westendorf

first: Meghan

last: McGee-Lawrence


title: Genome-wide profiling of 2 month vs >6 month old muscle Treg cells

status: Public on Jan 12 2016

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We report age-related gene expression of Treg cells isolated from injured muscle and spleen. Male C57BL/6 Foxp3-GFP reporter mice were injured intramuscularly with cardiotoxin. Tregs were sorted directly into Trizol from injured muscle and spleen 4 days post-injury.

overall_design: Gene expression profiling of muscle and splenic Tregs from 2- vs >6-month old mice (biological duplicate for each).

first: Wilson

last: Kuswanto

first: David

middle: P

last: Zemmour

first: Diane

last: Mathis


title: Genome-wide profiling of muscle Treg cells from IL-33 treated mice

summary: We report gene expression of Treg cells isolated from injured muscle in IL-33 vs PBS treated mice. Male Foxp3-GFP C57BL/6 reporter (2 months old) mice were injured intramuscularly with cardiotoxin/rIL-33 (0.3 ug/muscle). Tregs were sorted directly into Trizol from injured muscle 4 days post-injury.

overall_design: Gene expression profiling of muscle Tregs from IL-33 vs PBS injured mice.

first: Dalia

last: Burzyn

first: Liang

last: Yang


title: Analysis of gene expression signatures in brown adipose tissue (BAT) following acute activation of AgRP neurons

city: Cologne

first: Peter

last: Frommolt

address: Joseph-Stelzmannstr. 26

institute: CECAD

summary:
We have found that acute activation of AgRP-neurons lead to inhibition of insulin-stimulated glucose uptake into BAT. Based on this finding, we asked whether this effect was accompanied by acute changes in gene expression, which could point to the mechanism(s) underlying the impaired insulin sensitivity.
In summary, our data suggest that activation of AgRP-neurons actuely reprograms gene expression in BAT towards a myogenic profile.

overall_design: The arcuate nucleus of 4 mice expressing channelrhodopsin 2 in AgRP-neurons through Cre-mediated recombination (ChR2-AgRP) and 4 Cre-negative controls (ChR2-fl/WT, Ctrl), were stimulated with blue laser light for one hour, total RNA from BAT was isolated and subjected to a microarray-based gene expression analysis.

first: Sophie

last: Steculorum

first: Johan

last: Ruud

first: Ismene

last: Karakasilioti

first: Jens

middle: C

last: Brüning


title: Transcriptome in control, Fzd3 and Celsr3 mutant embryonic mouse cortex

status: Public on Jan 30 2016

city: Brussels

first: Andre

last: GOFFINET

address: Avenue Mounier 73

department: Neuroscience

institute: University of Louvain

summary: We compared the transcriptome in E16.5 embryonic mouse cortex isolated by microdissection, in control (+/+) mice and in mice with mutation in frizzled3 (Fzd3) and Celsr3.

overall_design: Triplicate RNA samples prepared for each genotype

last: Goffinet

first: Fadel

last: Tissir


title: Role of ST2 expession in regulatory Tcells on muscle regneration

status: Public on Jan 10 2016

summary: We describe the effects of Treg ST2 expression on muscle regeneration.  We compare regneration from cryo-injured tibialis anterior muscle from Foxp3-Cre/ST2-flox vs Foxp3-Cre mice 8 days post-injury. These analyses from whole muscle provide insight into the role of muscle Tregs in the context of regeneration.

overall_design: The tibialis anterior muscle from male Foxp3-Cre/ST2 flox or Foxp3-Cre/ST2 WT C57BL/6 mice (2 months old) were cryo-injured using a liquid nitrogen chilled metal probe for 8 seconds. 8 days post-injury whole muscle was harvested and snap frozen in liquid nitrogen. Whole muscle was then homogenized directly in TriZol and gene expression profiling was performed on Affymetrix Mouse Gene 1.0 ST Arrays.

first: Andrew

last: Rhoads


title: Role of IL33 on muscle regneration in aging

summary: We compare the effect of IL-33 vs PBS on muscle regneration from 22-month old mice 8 days post-injury. These analyses from whole muscle provide insight into the role of IL-33 on regeneration in the context of aging.

overall_design: The tibialis anterior muscle from male C57BL/6 mice (22 months old) were cryo-injured using a liquid nitrogen chilled metal probe for 8 seconds. Mice received 2 ug of rIL-33 via intraparitoneal injection the day prior and the day following cryoinjury. 8 days post-injury whole muscle was harvested and snap frozen in liquid nitrogen. Whole muscle was then homogenized directly in TriZol and gene expression profiling was performed on Affymetrix Mouse Gene 1.0 ST Arrays.


title: Antibody performance in ChIP-sequencing assays: From quality scores of public datasets to quantitative certification

status: Public on Jan 07 2016

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

institute: IGBMC

summary: We have established a certification system for antibodies to be used in chromatin immunoprecipitation assays coupled to massive parallel sequencing (ChIP-seq). This certification comprises a standardized ChIP procedure and the attribution of a numerical quality control indicator (QCi) to biological replicate experiments. The QCi computation is based on a universally applicable quality assessment that quantitates the global deviation of randomly sampled subsets of ChIP-seq dataset with the original genome-aligned sequence reads. Comparison with a QCi database for >28,000 ChIP-seq assays were used to attribute quality grades (ranging from ‘AAA’ to ‘DDD’) to a given dataset. In the present report we used the numerical QC system to assess the factors influencing the quality of ChIP-seq assays, including the nature of the target, the sequencing depth and the commercial source of the antibody. We have used this approach specifically to certify mono and polyclonal antibodies obtained from Active Motif directed against the histone modification marks H3K4me3, H3K27ac and H3K9ac for ChIP-seq. The antibodies received the grades AAA to BBA (www.ngs-qc.org). We propose to attribute such quantitative grading of all antibodies attributed with the label “ChIP-seq grade”.

overall_design: The NGS-QC team has setup a certification procedure for Antibodies dedicated to ChIP-seq applications based on (1)a highly reproducible pipeline for performing ChIP-seq assays including the use of an automated liquid handling platform (TECAN EVO75) for ChIP and sequencing library preparation steps and (2) the use of the NGS-QC Generator tool for providing a ChIP-seq quality grade and to evaluate other parameters like the Optimal sequencing depth, the degree of reproducibility among biological replicates and the comparison of the quality grades of the certified antibody with datasets retrieved in the public domain.  This quality certification structure makes possible to assign a measured Quality Stamp to ChIP-seq grade Antibodies.

first: Marco-Antonio

first: Pierre-etienne

last: Cholley

first: Matthias

last: Blum

first: Benjamin

last: Billore

first: Hinrich

last: Gronemeyer


title: Pretreatment with Gamma-Secretase Inhibitor Prevents Tumor-Like Overgrowth in Human iPSC-Derived Transplant for Spinal Cord Injury

status: Public on Jan 06 2016

city: Shinjyuku-ku, Tokyo

first: Toshiki

last: Okubo

address: shinanomachi 35

department: Orthopaedics surgery

institute: Keio university school of medicine

summary: Cell cycle- and more mature neuronal marker-related genes increased by > 2-fold change in both the GSI groups compared to the control group.

overall_design: To analyze gene expression profiles in hiPSC-NS/PCs treated with or without Gamma-secretase inhibitor.

first: Akio

last: Iwanami

first: Jun

last: Kohyama

first: Masaya

last: Nakamura

first: Hideyuki

last: Okano


title: Microarray analysis of the self-pruning related transcriptome in sweet orange (Citrus sinensis) spring shoots

status: Public on Jan 05 2016

city: WuHan

first: jin

middle: zhi

last: zhang

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

institute: Huazhong Agricultural University

summary: Transcriptome changes were also examined at three stages of SAM self-pruning utilizing microarray. Combining results from different stages, 1,573 differentially expressed genes were identified; the extensive repertoire of genes associated with programmed cell death, cell wall biosynthesis and metabolism strongly suggests that abscission layers activate both catabolic and anabolic wall modification pathways during self-pruning process.

overall_design: Three independent citrus RNA samples (Three days before self-pruning, begin self-pruning and seven days after self-pruning) were hybridized with microarrays separately

first: Jin-Zhi

last: Zhang

first: Chun-Gen

last: Hu


title: Functional dissection of Drosophila melanogasterSUUR protein influence on H3K27me3 profile

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

summary: In eukaryotes, heterochromatin replicates late in S phase of the cell cycle and contains specific covalent modifications of histones. SuURmutation found in Drosophila makes heterochromatin replicate earlier than in wild type and reduces the level of repressive histone modifications. SUUR protein was shown to be associated with moving replication forks, apparently through the interaction with PCNA. The biological process underlying the effects of SUUR on replication and composition of heterochromatin remains unknown.

overall_design: Examination of H3K27me3 histone modification in Drosophila embryos in presence or absence of SuUR mutation.

first: Olga

last: Posukh

first: Stepan

last: Belyakin

first: Petr

last: Laktionov

middle: A

first: Dmitry

last: Koryakov