title: Grape berry developmental series comparing pruning treatments from a vineyard in Clare Valley, South Australia (CLA-05)

city: Glen Osmond

first: Mark

middle: Raymond

last: Thomas

state: SA

address: PO Box 350

institute: CSIRO

summary:
Changes in gene expression during berry development during a grape growing season were analysed. The effect on gene expression of different viticultural practises during grape berry development was investigated in this study by comparing two pruning methods (spur versus machine).
Grape berries were collected and pooled on a weekly basis to obtain a developmental series comprised of 17 developmental stages from flowering until harvest across the grape growing season for both spur and machine pruned vines. Gene expression patterns during development and between pruning treatments were obtained.
Keywords: Time course, developmental series and treatments

overall_design: Seventeen consecutive developmental stages were analyzed for gene expression changes using the Affymetrix one colour array platform. The developmental stages were numbered 1 to 17. Two biological replicates were collected for each developmental stage. Biotin labeled probes were prepared from the extracted RNA from each of the pooled berry samples and hybridized to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridization station was randomized using the AlgDesign package from R.

middle: R

first: Christopher

last: Davies

first: Pat

last: Iocco


title: Leukemia inhibitory factor via the toll-like receptor 5 signaling pathway involves aggravation of cachexia induced by human gastric cancer-derived 85As2 cells in rats

status: Public on Nov 14 2018

city: Inashiki-gun

first: Kiyoshi

last: Terawaki

state: Ibaraki

address: 3586 Yoshiwara, Ami-machi

country: Japan

institute: Tsumura & Co.

summary: Cancer cachexia is highly prevalent in gastric cancer patients and is characterized by decreased food consumption and body weight. We previously created a rat model of cancer cachexia using MKN45cl85 and 85As2 cells derived from human gastric cancer. The 85As2 cells induced cachexia more potently than MKN45cl85 cells did. To clarify the mechanism underlying the difference in the cachexia-inducing ability of these cells, we conducted a DNA microarray analysis, with a focus on cell proliferation and the production of leukemia inhibitory factor (LIF), a cachexia-inducing factor. The plasma human LIF levels of 85As2-induced cachexic rats increased in parallel with the worsening of symptoms whereas the plasma levels of MKNcl85 were low. 85As2 cells displayed more genetic changes than MKN45cl85 cells did, which were related to Toll-like receptor (TLR) 4//5 signaling. Stimulation of both the cells with TLR4 (lipopolysaccharide) or TLR5 (flagellin) agonists did not affect proliferation. However, in 82As2 cells, LIF production was significantly increased by stimulation with TLR5, which was suppressed by an inhibitor of interleukin-1 receptor-associated kinase-1/4, which are important factors in the TLR5 signaling pathway. In conclusion, it is possible that the increase in LIF production through the activation of the TLR5 signaling pathway contributes to the cachexia-inducing ability of 85As2 cells.

overall_design: Gene expression in MKN45cl85 and 85As2 cells was measured. MKN45cl85 cells were orthotopically grafted into mice, and peritoneal cavity cells were collected from specimens exhibiting peritoneal metastasis. These cells were then cultured and xenografted repeatedly. This established another cell line was 85As2. MKN45cl85 and 85As2 cells were cultured in a 10 cm dish until they were semi-confluent. Total RNA was extracted for DNA microarray analysis. Three RNA samples from cells cultured on different days were prepared.

first: Yohei

last: Kashiwase

first: Yumi

last: Sawada

first: Kanako

last: Miyano

first: Yoshikazu

last: Higami

first: Kazuyoshi

last: Yanagihara

first: Masahiro

last: Yamamoto

first: Yasuhito

last: Uezono


title: The effect of cell culture on age-related transcriptomic changes in dermal fibroblasts

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: During aging, stromal functions are thought to be impaired, yet little is known whether this stems from molecular and cellular changes of fibroblasts, a major component of stroma. Using population- and single-cell whole transcriptomics, and long-term lineage tracing, we studied alterations in murine dermal fibroblasts during physiological aging under different dietary regimes known to affect longevity. We show that the identity of aged fibroblasts becomes undefined, with the distinct fibroblast states present in young skin no longer clearly demarcated. In addition, old fibroblasts not only reduce the expression of genes involved in the formation of the extracellular matrix, but intriguingly, also gain adipogenic traits, paradoxically becoming similar to neonatal pro-adipogenic fibroblasts. These age-related alterations are sensitive to systemic changes in metabolism: long-term caloric restriction prevents them in old fibroblasts in a reversible manner, whereas a high-fat diet potentiates them in young fibroblasts. Finally, inhibition of the master regulator of adipogenesis, PPARgamma, attenuates fibroblast aging in vivo, providing potential anti-aging therapeutic alternatives to caloric restriction.

overall_design: Dermal fibroblasts were isolated from four young (2-months-old) and four old (18-months-old) female C57/Bl6 mice. For sample collection two young and two old mice were sacrificed per day (N=4).From each mouse 5000 fibroblasts were immediately profiled and 5000 fibroblasts were profiled after culturing.

first: Marion

last: Salzer

first: Salvador

last: Aznar-Benitah


title: The FGF1/CPP-C chimera protein protects against intestinal adverse effects of Carbon-ion radiotherapy without exacerbating pancreatic carcinoma.

city: Chiba

first: Atsuko

last: Ishikawa

state: Chiba

address: Anagawa 4-9-1

department: Research Center for Charged Particle Therapy

institute: National Institute of Radiologocal Sciences

summary: In order to screen for molecules contributing to the effects of FGF1/CPP-C on radiation-induced intestinal damage, the total RNA expression profile of the irradiated jejunum was obtained using a DNA microarray analysis after Carbon-ion irradiation with the FGF1/CPP-C pretreatment.

overall_design: The total RNA expression profile of the irradiated jejunum was obtained using a DNA microarray analysis 4 h after Carbon-ion irradiation with the 12-h FGF1/CPP-C pretreatment.

first: Fumiaki

last: Nakayama

first: Mitsuko

last: Kawano

first: Taichi

last: Miuta

first: Mayumi

last: Fujita

first: Sachiko

last: Koike

first: Kaori

last: Imadome

first: Takeshi

last: Yasuda

first: Toru

last: Imamura

first: Takashi

last: Imai


title: Genetic basis for coordination of meiosis and sexual structure maturation in Cryptococcus neoformans

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

country: China

institute: the institute of microbiology chinese academy of sciences

type: Expression profiling by high throughput sequencing

summary: In the human fungal pathogen Cryptococcus neoformans, sexual mating is considered to benefit its infections through meiosis-driven hyper-virulent variants and infectious meiotic spores. How meiotic cycle and mating differentiation program are genetically and developmentally integrated to safeguard successful meiotic sporulation remains poorly known. In C. neoformans, sporulation occurs following two parallel events, meiosis and differentiation of specialized cell termed basidium. To reveal the gene circuits specifically orchestrating basidial maturation and meiosis, we performed high-coverage stand-specific RNA-sequencing analysis to monitor gene induction timing through unisexual differentiation and reveals a co-regulation of these two events by a shared regulatory program. Our findings indicated that the regulatory coupling of meiosis and basidial development may serve as a determinant underlying production of infectious meiospores in C. neoformans.

overall_design: 12 samples contain wild type at five various time courses (6, 12, 24, 48 and 72 hrs) during unisexual development and pum1 overexpression strain at 24hrs post mating stimulation with two replicates.

first: Linxia

last: Liu

first: Guang-Jun

last: He

first: Lei

last: Chen

first: Jiao

last: Zheng

first: Yingying

first: Lan

last: Shen

first: Xiuyun

last: Tian

first: Erwei

last: Li

first: Ence

last: Yang

first: Guojian

last: Liao

first: Linqi

last: Wang


title: Transcriptional effects of Deoxynivalenol on intestinal porcine epithelial cells (IPEC-J2) under low glucose condition

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

summary: in vitro microarray study of transcriptional changes of jejunal cells

overall_design:
three samples per experimental group were used for expression profiling
ANOVA

first: Constanze

last: Nossol

first: Michael

last: Oster


title: The effect of caloric restriction on the transcriptome of dermal fibroblasts during aging

first: Antoni

last: Berenguer-LLergo

overall_design: 9-months-old female mice were either fed a normal diet ad libitum for 9 months (Old ND group), a normal diet for 2 months followed by 30% caloric restriction for 7 months of (Old CR group), or a 30% caloric restriction for 7 months followed by a normal diet for 2 months (Old CR-ND group). Young mice (4-weeks-old) were fed ND ad libitum for 4 weeks (Young ND group). For sample collection three mice from different groups were sacrificed per day. n=5 (biological replicates)

first: Marion

last: Salzer

first: Salvador

last: Aznar-Benitah


title: The effect of high fat diet on the transcriptome of murine dermal fibroblasts

overall_design: 2-months-old female mice were fed for 6 months with a high fat diet or control diet. All mice were sacrificed on the same day. N=4


title: Grape berry developmental series comparing irrigation treatments in a vineyard in Wingara, Victoria, Australia (WIN-05)

status: Public on Nov 22 2018

first: Mark

last: Thomas

department: Plant Industry

country: Australia

summary:
Changes in gene expression during berry development during a grape growing season were analysed. The effect on gene expression of different viticultural practises during grape berry development was investigated in this study by comparing two irrigation methods (standard versus prolonged deficit irrigation).
Grape berries were collected and pooled on a weekly basis to obtaining a developmental series comprising of 17 developmental stages from flowering until harvest across the grape growing season for both standard and prolonged deficit irrigated vines. Gene expression patterns during development and between pruning treatments were obtained.
Keywords: Time course, developmental series and treatments

overall_design: Seventeen consecutive developmental stages were analysed for gene expression changes using the Affymetrix one colour array platform. The developmental stages were numbered 1 to 17. Two biological replicates were collected for each developmental stage. Biotin labeled probes were prepared from the extracted RNA from each of the pooled berry samples and hybridised to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridisation station was randomised using the AlgDesign package from R.

first: Christopher

last: Davies

first: Pat

last: Iocco


title: The effect of topical PPARG inhibitor (GW9662) treatment on the transcriptome of old dermal fibroblasts

overall_design: The backskin of four 12-months-old mice was treated topically 3 times per week with 300ul Acetone containing 150nmoles GW9662 or with 300ul Acetone alone (as a control) for 6 months. For sample collection one animal from each group was sacrificed the same day. n=4


title: Transcriptome analysis of fibroblast subpopulations isolated from neonatal murine dermis.

overall_design: CD26+ papillary, Dlk1+ reticular, Sca1+ pre-adipogenic and Sca1+/Dlk1+ pre-adiogenic fibroblasts were FACS isolated from three newborn (P2) female littermates. N=3


title: N6-methyladenosine demethylation by the fat mass and obesity-associated gene (FTO) defines tyrosine kinase inhibitor resistance in leukemia

city: C

first: E

last: F

state: D

address: B

country: USA

institute: A

summary: The discovery of activating mutations in receptor tyrosine kinases (RTKs) leads to clinical testing of RTK inhibitors (TKIs). However, the rapid acquisition of resistance limits TKI effectiveness. Here we establish TKI-resistant cells that propagate in the absence of RTK signaling. Relative to sensitive cells, TKI-resistant cells display decreased N6-methyladenosine (m6A), a ubiquitous and reversible modification on RNA, but upregulated fat mass and obesity-associated gene (FTO), an m6A demethylase. Notably, the naïve leukemia cell populations are heterogeneous with respect to FTO levels. Cells with higher intrinsic and transient FTO expression demonstrate reduction of m6A methylation and TKI sensitivity with higher tumorigenic. Genetic or pharmacological dysfunction of FTO increases m6A abundance sensitizing resistant cells to TKIs. Mechanistically, FTO-mediated m6A demethylation promotes mRNA stability and protein translation rate, upregulating oncogenes that are indispensable for survival and proliferation. Our findings therefore establish a role of FTO-dependent m6A demethylation for TKI-resistance, offering a therapeutic window for incorporating m6A modulators in counteracting acquired TKI resistance.

overall_design: We establish nilotinib resistance in K562 cell line, and explored the molecular and functional characteristics of resistant cells. To elucidate mechanisms by which leukemia cells overcomes nilotinib resistance, we performed gene microarray (HumanHT-12v4 Expression BeadChip)in K562 cells resistant to nilotinib, a second-line TKI to cure imatinib-refractory patients.


title: The transcriptome of murine dermal fibroblasts

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

overall_design: Refer to individual Series


title: How Lactobacillus plantarum Shapes its Transcriptome in Response to Contrasting Habitats

city: BARI

first: pasquale

last: filannino

address: Via Amendola, 165/A

department: Dipartimento di Scienze del Suolo

country: Italy

institute: Università degli Studi di Bari “Aldo Moro”

summary: Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here, we demonstrated how L. plantarum regulates and shapes its transcriptome in response to contrasting habitats. Firstly, multivariate clustering analysis of transcriptional data (RNA-Seq), complemented with metabolomics and phenomics, grouped the strains according to the habitats of origin. Subsequently, selected strains from each habitat switched to repeated cultivation on MRS medium and transcriptomes homogenized into a unique cluster. Adaptation to this common medium mainly relied on activation of genes for phage- and prophage-related proteins and transposases. Finally, the comparison of growth across model media and with respect to MRS medium showed that 44% of the overall 3,112 gene transcripts changed depending on the specific habitat. Regulation and shaping of transcriptomes mainly concerned carbohydrate acquisition, pyruvate catabolism, proteolytic system and amino acid, lipid and inorganic ion transport and metabolism, with contrasting responses for contrasting habitats. Pathways reconstruction demonstrated how the large genome size of L. plantarum imparts transcriptome and metabolic flexibility as the basic mechanism for a nomadic lifestyle.

overall_design: We isolated presumptive autochthonous L. plantarum strains from nine different habitats: intestines from A. mellifera L. worker bees and Drosophila melanogaster, feces from omnivore and vegan healthy volunteers, table olives, tomatoes, pineapples, sourdoughs and cheeses. Isolation and cultivation was on nine model media

first: Maria

last: De Angelis

first: Marco

last: Gobbetti

first: Raffaella

last: Di Cagno

first: Pasquale

last: Filannino


title: Transcriptional effects of Deoxynivalenol on intestinal porcine epithelial cells (IPEC-J2)


title: Heterogeneous drug resistance in and antifungal naïve chronic infection

city: Riverside

first: Jason

last: Stajich

state: CA

address: 900 University Ave

department: Microbiology and Plant Pathology

institute: University of California-Riverside

summary: Purpose: We compared the expression profile of three fluconazole resistant clinical isolates to two fluconazole sensitive clinical isolates, from the same patient, all containing mutation in the trancription factor Mrr1, to define the Mrr1 regulon in Candida lusitaniae.

overall_design: Mehods: Overnight cultures grown in YPD were diluted into YNBG10 and grown at 30 C with shaking to mid-exponential phase, diluted into prewarmed medium then grown to mid-exponential phase before harvesting RNA.

first: Elora

last: Demers

first: Amy

last: Biermann

first: Sawyer

last: Masonjones

first: Alex

last: Crocker

first: Alix

last: Ashare

first: Deborah

last: Hogan


title: MicroRNA and mRNA regulatory network in EGFR-mutated lung adenocarcinoma

status: Public on Nov 13 2018

city: Tokyo

first: Sophia

last: Subat

address: 3-8-31 Ariake, Koto-ward,

institute: Japanese Foundation for Cancer Research

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


title: Expression data for participants in iWITH study at screening visit

city: Bethesda

first: Sai

last: Kanaparthi

state: MD

address: 7500 Old Georgetown Rd

department: BiG

institute: Immune Tolerance Network

summary:
A cross sectional study using data collected at the time of liver biopsy, the final eligibility assessment for participation in iWITH (NCT01638559), an immunosuppression withdrawal trial.
Microarrays were used to understand the gene expression profile differences among the three histological clusters (Cluster 1, Cluster 2 and Cluster 3)

overall_design: RNA samples (n=151) were extracted from cryopreserved liver tissue samples using TRIzol and hybrid-ized onto Affymetrix Human Genome U219 96-array plates.  We performed quality control using AffyPLM and excluded samples with a Normal-ized Unscaled Standard Error >1.05, resulting in 133 evaluable arrays.

first: Alberto

last: Sanchez-Fueyo

first: Sandy

last: Feng


title: Functional validation of microRNAs targeting genes of DNA double-strand break repair to radiosensitize non-small lung cancer cells

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

institute: University of Padova

summary:
DNA-Double strand breaks (DSBs) generated by radiation therapy represent the most efficient lesions to kill tumor cells, however, the inherent DSB repair efficiency of tumor cells can cause cellular radioresistance and impact on therapeutic outcome. Genes of DSB repair represent a target for cancer therapy since their down-regulation can impair the repair process making the cells more sensitive to radiation. In this study, we analyzed the combination of ionizing radiation (IR) along with microRNA-mediated targeting of genes involved in DSB repair to sensitize human non-small cell lung cancer (NSCLC) cells. MicroRNAs are natural occurring modulators of gene expression and therefore represent an attractive strategy to affect the expression of DSB repair genes. As possible IR-sensitizing targets genes we selected genes of homologous recombination (HR) and non-homologous end joining (NHEJ) pathway (i.e. RAD51, BRCA2, PRKDC, XRCC5, LIG1). We examined these genes to determine whether they may be real targets of selected miRNAs by functional and biological validation. The in vivo effectiveness of miRNA treatments has been examined in cells over-expressing miRNAs and treated with IR. Taken together, our results show that hsa-miR-96-5p and hsa-miR-874-3p can directly regulate the expression of target genes. When these miRNAs are combined with IR can decrease the survival of NSCLC cells to a higher extent than that exerted by radiation alone, and similarly to radiation combined with specific chemical inhibitors of HR and NHEJ repair pathway.

This SuperSeries is composed of the SubSeries listed below.


title: miRNA  expression profiling of gamma-irradiated A549 cells at 24 h after irradiation.

summary: We analyzed the combination of ionizing radiation (IR, 2.0 Gy) along with microRNA-mediated targeting of genes involved in DSB repair to sensitize human non-small cell lung cancer (NSCLC) cells.

overall_design: We evaluated the extent of miRNA response of NSCLC cells upon irradiation by performing miRNA expression profiling on total RNA extracted at 24h after irradiation. Analyses were carried out in A549 cells that proved to be radioresistant in terms of clonogenic survival when irradiated with the 2 Gy dose, which represents the dose delivered daily in conventional fractionated radiation therapy protocols.

first: Celeste

last: Piotto

last: Biscontin

first: Caterina

last: Millino

first: Maddalena

last: Mognato


title: miRNA  expression profiling of gamma-irradiated A549 cells at 4 h after irradiation

overall_design: We evaluated the extent of miRNA response of NSCLC cells upon irradiation by performing miRNA expression profiling on total RNA extracted at 4h after irradiation. Analyses were carried out in A549 cells that proved to be radioresistant in terms of clonogenic survival when irradiated with the 2 Gy dose, which represents the dose delivered daily in conventional fractionated radiation therapy protocols.


title: Transcriptional response of Acinetobacter baumannii to hydrogen peroxide and role of mumR and oxyR in regulating this response

city: Nashville

first: Lillian

last: Juttukonda

state: TN

address: 1161 21st Avenue South

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University

summary:
Acinetobacter baumannii is a Gram-negative opportunistic pathogen that causes multiple infections, including pneumonia, bacteremia, and wound infections. Due to multiple intrinsic and acquired drug-resistance mechanisms, A. baumannii isolates are commonly multi-drug resistant and infections are notoriously difficult to treat. Therefore, it is important to identify mechanisms used by A. baumannii to survive stresses encountered during infection as a means of identifying new drug targets. In this study, we determined the transcriptional response of A. baumannii to hydrogen peroxide stress using RNASequencing. Upon exposure to hydrogen peroxide, A. baumannii differentially transcribes several hundred genes. In this study, we also determined the transcriptional profile of A. baumannii strains with the transcriptional regulators mumR or oxyR genetically inactivated and identified transcriptional differences between these strains and wild-type A. baumannii in response to hydrogen peroxide stress. In doing this, the function of A. baumannii OxyR in hydrogen peroxide stress resistance and regulation of genes required for hydrogen peroxide detoxification was defined. Moreover, the
contribution of the uncharacterized regulator MumR to hydrogen peroxide stress resistance was also explored. This work reveals the transcriptome of an important human pathogen in the presence of hydrogen peroxide stress.

overall_design: Transcriptional profiling of A. baumannii strains with genetic deletions of transcriptional regulators mumR and oxyR in the presence and absence of hydrogen peroxide stress

middle: J

first: Erin

last: Green

first: Eric

middle: P

last: Skaar


title: Comparative analysis of transcriptome profiles between wild-type Arabidopsis and two ABA deficit mutants aba3-1 and aba2-2 in osmotic stress conditions

city: Yokohama

first: Shunsuke

last: Watanabe

state: Kanagawa

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

department: Center for Sustainable Resource Science

institute: RIKEN

summary: Arabidopsis ABA3 is an enzyme involved in the synthesis of the sulfurated form of the molybdenum (Mo) cofactor (MoCo), which is required for the enzymatic activity of so-called Mo enzymes such as aldehyde oxidase (AO) and xanthine dehydrogenase (XDH). It has been reported that AO and XDH are essential for the biosynthesis of the bioactive compounds, ABA and allantoin, respectively. However, aba3 mutants often exhibit pleiotropic phenotypes that are not explained by defects in ABA and/or allantoin biosynthesis, leading us to hypothesize that ABA3 regulates additional metabolic pathways. To reveal the currently unidentified functions of ABA3 we compared transcriptome and metabolome of the Arabidopsis aba3 mutant with those of wild type and a typical ABA-deficient mutant aba2. We found that endogenous levels of anthocyanins, members of the flavonoid group, were significantly lower in the aba3 mutant than in the wild type or the aba2 mutant under oxidative stress. In contrast, mutants defective in the AO and XDH holoenzymes accumulated significantly higher levels of anthocyanins when compared with aba3 mutant under the same conditions. Our findings shed light on a key role of ABA3 in the ABA- and allantoin-independent accumulation of anthocyanins during stress responses.

overall_design: wild-type Col-0, aba3-1 and aba2-2 after two differential osmoic stress (acute and prolonged stress)

first: Mitsunori

last: Seo


title: Gene expression analysis of miR-210 over-expressing flies at ZT0.

summary: MicroRNAs (miRNAs) are a novel class of small RNAs which act as modulators of gene expression either by inhibiting the translation or by inducing the degradation of their target mRNAs. Several studies suggest a role for miRNAs as regulators of the circadian clock in mammals and Drosophila. Based on computational predictions of target mRNAs of clock (or clock related) genes, we have selected the miR-210 as a putative regulator of the period clock gene. We demonstrated that flies over-expressing this miRNA in the canonical clock neurons show an impaired locomotor activity pattern in both light-dark (LD) and constant darkness conditions (DD). Moreover, the projections of the Pigment Dispersing Factor (PDF)-expressing clock neurons in the optic lobe are abnormal showing peculiar “star” shaped body cells. The microarray analysis performed in the adult fly brain, revealed that this miRNA is affecting indirectly the expression of some circadian genes (ie: pdf, npf, cry, tim, pdp1) but not the period gene, and directly genes like echinus and RhoGAp92B. The in-vivo down regulation of echinus indeed can be associated with a severe impairment of the locomotor activity of flies, while the GTPase RhoGAP92B, important for the regulation of the cellular shape of neurons, could be involved in the morphological development of the PDF-expressing  neurons.

overall_design: Gene expression profiling was carried out on controls (w;tim-GAL4 (UAS)/+) and miR-210 overexpressing flies (w;tim-GAL4(UAS)/UAS-miR-210) by using the Drosophila custom platform (Agilent Technologies). Total RNA was obtained from approximately 25 flies brains for each genotype. Four biological replicates were analyzed for controls and miR-210 overexpressing samples respectively for a total of 8 microarray experiments.

first: Paola

last: Cusumano

first: Federica

last: Sanfrelli

first: Rodolfo

last: Costa


title: Expression data of lamina propria macrophages from LysMCre and LysMCre;Arntfl/fl mice with DSS-induced acute colitis

status: Public on Nov 12 2018

city: Philadelphia

last: Simon

state: PA

address: 421 Curie Blvd. BRBII/II, Room 438

institute: University of Pennsylvania

summary: Mice with myeloid ARNT deficiency (LysMCre;Arntfl/fl mice) exhibit defective resolution of DSS-induced acute colitis compared to LysMCre mice. This microarray is carried out to compare the phenotype of lamina propria macrophages from the two cohorts, and to identify factors that are disrupted by myeloid ARNT deficiency and can potentially contribute to the defective resolution of acute colitis.

overall_design: LysMCre mice were used as control animals with intact Arnt alleles in myeloid populations. LysMCre;Arntfl/fl mice were the experimental animals with conditionally deleted Arnt in myeloid cells. Five female LysMCre mice and four female LysMCre;Arntfl/fl mice were co-housed and subjected to DSS-induced colitis (3% dextran sodium sulfate (DSS) in drinking water for 5 days, followed by 3 days on regular drinking water). Lamina propria macrophages (CD45+, CD11b+, F4/80+) were isolated by flow sorting on Day 8.

last: Lin

first: M

middle: C


title: Gene expression analysis of miR-210 over-expressing flies at ZT0 and ZT12

summary: Single microRNAs are usually associated with hundreds of putative target genes that can influence multiple phenotypic traits in Drosophila, ranging from development to behaviour. We investigated the function of Drosophila miR-210 in circadian behaviour by misexpressing it within circadian clock cells. Manipulation of miR-210 expression levels in the PDF (pigment dispersing factor) positive neurons affected the phase of locomotor activity, under both light-dark conditions and constant darkness. PER cyclical expression was not affected in clock neurons, however, when miR-210 was up-regulated, a dramatic alteration in the morphology of PDF ventral lateral neuron (LNv) arborisations was observed. The effect of miR-210 in shaping neuronal projections was confirmed in vitro, using a Drosophila neuronal cell line. A transcriptomic analysis revealed that miR-210 overexpression affects the expression of several genes belonging to pathways related to circadian processes, neuronal development, GTPases signal transduction and photoreception. Collectively, these data reveal the role of miR-210 in modulating circadian outputs in flies and guiding/remodelling PDF positive LNv arborisations and indicate that miR-210 may have pleiotropic effects on the clock, light perception and neuronal development.


title: The effect of aging on the transcriptome of murine dermal fibroblasts

first: Antoni

last: Berenguer-LLergo

summary: During aging, stromal functions are thought to be impaired, yet little is known whether this stems from molecular and cellular changes of fibroblasts, a major component of stroma. Using population- and single-cell whole transcriptomics, and long-term lineage tracing, we studied alterations in murine dermal fibroblasts during physiological aging under different dietary regimes known to affect longevity. We show that the identity of aged fibroblasts becomes undefined, with the distinct fibroblast states present in young skin no longer clearly demarcated. In addition, old fibroblasts not only reduce the expression of genes involved in the formation of the extracellular matrix, but intriguingly, also gain adipogenic traits, paradoxically becoming similar to neonatal pro-adipogenic fibroblasts. These age-related alterations are sensitive to systemic changes in metabolism: long-term caloric restriction prevents them in old fibroblasts in a reversible manner, whereas a high-fat diet potentiates them in young fibroblasts. Finally, inhibition of the master regulator of adipogenesis, PPARgamma, attenuates fibroblast aging in vivo, providing potential anti-aging therapeutic alternatives to caloric restriction.

overall_design: Dermal fibroblasts were isolated from four young (2-months-old) and four old (18-months-old) mice. For sample collection one young and one old mouse were sacrificed per day. N=4

first: Marion

last: Salzer

first: Salvador

last: Aznar-Benitah


title: Expression data from Arabidopsis seedlings expressing a synthetic oxygen sensor device

city: Pisa

first: Francesco

last: Licausi

address: Via Mariscoglio 34

department: Institute of Life Sciences

institute: Scuola Superiore Sant'Anna

summary: Gene expression was compared between 7-day old seedlings expressing two effector modules of an oxygen sensor device,consisting of the Saccharomyces cerevisiae Gal4 activation domain (AD) fused to the human HIF-CODD and the Gal4 DNA binding domain (BD) fused to the human pVHL, and seedlings expressing the previously described effector modules in addition to the sensory module constituted by the human PHD3 gene under control of constitutive promoters

overall_design: Seedlings were individually genotyped by PCR to identify double and triple overexpressors,  before RNA extraction and hybridization on Affymetrix microarrays

first: Beatrice

last: Giuntoli

first: Sergio

last: Iacopino


title: Construction and analysis of miRNA library in gold-colored mutant leaves of Ginkgo biloba L.

status: Public on Nov 11 2018

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

type: Non-coding RNA profiling by high throughput sequencing

summary: High-throughput RNA, sRNA and degradome sequencing were performed to identify a large number of miRNAs in  G. biloba leaf to provide useful information for uncovering the regulatory networks of color formation in G. biloba leaves.

overall_design: sRNA sequencing in leaves of G. biloba

first: Weixing

last: Li


title: KFTX paclitaxel (PTX)-resistant ovarian cancer cells, KFTXlow PTX-resistant ovarian cancer cells and KFlow PTX-sensitive ovarian cancer cells expression profilies

status: Public on Nov 10 2018

city: Yonago City

first: Takafumi

last: Nakamura

address: 86 Nishi-cho

department: Department of Biomedical Science

institute: Tottori University

summary: Oncolytic vaccinia virus (OVV) has demonstrated appropriate safety profiles for clinical development. Although OVV was designed to kill cancer cells efficiently, sensitivity to OVV varies in individual cancers. Here, we found that OVV was much more efficient in KFTX paclitaxel (PTX)-resistant ovarian cancer cells, compared to that in KFlow PTX-sensitive cells. Microarray analysis showed that urothelial carcinoma-associated 1 (UCA1) upregulation contributed to both enhanced PTX resistance and OVV spread.

overall_design: OVV spread was much more efficient in KFTX cells than KFlow and KFTXlow cells. However the spread in KFTXlow cells was not comparable with that in KFTX cells. These cell lines were compared to identify host factors which enhanced OVV spread.

first: Kosuke

last: Horita

first: Hajime

last: Kurosaki

first: Motomu

last: Nakatake

first: Nozomi

last: Kuwano

first: Tetsuro

last: Oishi

first: Hiroaki

last: Itamochi

first: Sho

last: Sato

first: Hiromichi

last: Kono

first: Mai

last: Ito

first: Kosei

last: Hasegawa

first: Tasuku

last: Harada


title: Gene expression analysis of miR-210 over-expressing flies at ZT12.

first: Cristiano

last: De Pitta

overall_design: Gene expression profiling was carried out on controls (w;tim-GAL4 (UAS)/+) and miR-210 overexpressing flies (w;tim-GAL4(UAS)/UAS-miR-210) by using the Drosophila 2.0 custom platform (Agilent Technologies). Total RNA was obtained from approximately 25 flies brains for each genotype. Four biological replicates were analyzed for controls and miR-210 overexpressing samples respectively for a total of 8 microarray experiments.

first: Paola

last: Cusumano

first: Alberto

last: Biscontin

first: Federica

last: Sanfrelli

first: Rodolfo

last: Costa


title: MeCP2 regulates genome-wide gene expression through recognition of H3K27me3 [NanoString]

city: Gwangju

first: Wooje

last: Lee

address: 309, Pilmun-daero, Dong-gu

department: Cellular and Molecular Medicine

country: South Korea

institute: Chosun University

summary: MeCP2 plays a multifaceted role in gene expression regulation and chromatin organization. Interaction between MeCP2 and methylated DNA to regulate gene expression is well established. However, the widespread MeCP2 distribution suggests its additional interactions with chromatin. Here we show, by both biochemical and ChIP-seq analyses, that MeCP2 directly binds to nucleosome subunit proteins and is recruited to distinct chromatin regions where H3K27me3 is enriched. We further observed that the impact of MeCP2 on transcriptional changes is correlated with histone post-translational modification patterns. Our findings indicate that MeCP2 can be recruited to genomic loci via indirect binding and that interaction between MeCP2 and histone proteins plays a significant role in gene expression regulation.

overall_design: Transcriptional levels of WT or Mecp2 KO OE tissues were measured using pre-made sets of panel, nCounter Mouse Neuropathogy Panel Kit (XT-CSO-MNROP1-12, NanoString Technologies) containing 770 genes. The measurements were performed in biological duplicates.

first: Qizhi

last: Gong


title: Identification of genes related with carcass fatness in pigs based on RNA-seq results

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

summary:
Purpose: RNA-seq method was applied to select genes expressed in fat tissue and pinpointed genes potentially associated with fatness traits in pigs.
Methods: The RNA-seq analysis was performed on fat tissue collected from 16 Pulawska pigs (8 pigs per two groups - with high and low backfat thickness) maintained at the same environmental and feeding condition. The total RNA was isolated using by TriReagent and 300ng was used to  cDNA libraries preparation.  The NGS sequencing was performed on HiScan SQ (Illumina) in 90 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Sus scrofa reference genome. Differentially expressed genes were detected by DESeq2. The RNA-seq results were validated using by qPCR.
Results: In the group of pigs characterized by thicker subcutaneous fat, 166 genes with increased expression were identified, including genes involved in biological processes associated with negative regulation of long-chain fatty acid transport (GO: 0010748) (IRS2, THBS1, AKT2), regulation of metabolic lipids ( GO: 0019216) (EEF1A2, IRS2, ACACA, SIK1, ADGRF5, IDH1, FGF2, PDE3B, FASN, AKT2, CYR61, CHD9, ME1, SCD), cellular response to hormonal stimuli (GO: 0032870) (IRS2, ACACA, SIK1 , GHR, NR4A1, PDE3B, PTGER2, AKT2, AACS, ADCY6, KAT2B, RHOQ, FOS). Genes involved in the signaling pathway responsible for the activation of gene expression by SREBF (R-SSC-2426168) (ACACA, FASN, CHD9, SCD ) and the insulin signaling pathway also were identified (RHOQ, SOCS3, IRS2, AKT2, PDE3B, PYGM, FASN, ACACA).
Conclusions: The presented results allowed to pinpointed the interesting, candidate genes related with fat content in carcasses in pigs, which can be analyzed in future in the term of using in breeding practice as genetic markers.  The study was financed from funds of the project -BIOSTRATEG, the decision number BIOSTRATEG2/297267/14/NCBR/2016.

overall_design: The subcutaneous fat transcriptome sequencing was performed for 16 samples collected form Pulawska breed, using Illumina HiScan SQ in 90 single-end cycles and in 4 technical repetitions.

first: Katarzyna

last: Piórkowska

last: Ropka-Molik

first: Mirosław

last: Tyra

last: Żukowski

first: Artur

last: Gurgul


title: Pituitary transcriptomic changes dependent on feed conversion in pigs

summary:
Purpose: RNA-seq method was applied to select genes expressed in feed conversion in pigs  and pinpointed genes potentially associated with this feature.
Methods: The whole pituitary samples were collected from 16 Puławska pigs (8 pigs per two groups - with high and low feed conversion) maintained at the same environmental and feeding condition. The RNA-seq analysis was performed in 90 single-end cycles on HiScanSQ platform (Illumina) and differentially expressed genes (DEGs) were determined using Deseq2 software. Validation was performed for 10 randomly selected genes  using real-time PCR method.
Results: The study showed that in pigs characterized by better feed conversion 274 genes were differentially expressed. Genes showed decreased expression encode proteins associated with cholesterol metabolism (APOA1, CH25H, APOE) and regulation of hormone levels (POMC, CTSZ, ADM, AGTR1, SOX8, AGT, CPT1, APOA1, GJA1, MYRIP, CYP1B1, NR1D1). Four genes showed over the 10-fold decrease of expression (CRYM, ISM1 and WNK4), where the CRYM protein binds thyroid hormone for regulatory and developmental roles and WNK4 regulates the balance between NaCl reabsorption and K(+) secretion. In turn, genes showed an increase of expression in the pituitary of pigs having better feed conversion encode proteins were related to cellular response to corticotropin-releasing hormone stimulus (NR4A1, NR4A2, NR4A3) and regulation of type B pancreatic cell proliferation (BIRC5, NR4A3, NR4A1).
Conclusions: The present study indicates new genes potentially related to feed conversion, which is one of the most economically important traits in pig breeding. The selected genes should be investigated in future in the terms of their association with fattening traits. The study was financed from funds of the project -BIOSTRATEG, the decision number BIOSTRATEG2/297267/14/NCBR/2016.

overall_design: Thepituitary transcriptome sequencing was performed for 16 samples collected form Pulawska breed, using Illumina HiScan SQ in 90 single-end cycles and in 4 technical repetitions.


title: Characteristics of long non-coding RNAs in the pancreas of rats with acute pancreatitis

city: Shanghai

first: Jing

last: Lin

state: State...

address: Shanghai

institute: Red House Hospital

summary: This study aimed to describe the microarray-based differential expression profile of mRNAs and lncRNAs in acute experimental pancreatitis and identify candidate biomarkers for the diagnosis, prognosis, and treatment of AP.

overall_design: A rat model of AP was generated with retrograde pancreatic ductal injection of sodium taurocholate, and the pancreas was harvested for microarray detection. The biological functions of differentially expressed genes noted from microarray data were assessed by bioinformatics analysis.

first: Shijin

last: Xia


title: The transcriptomic profile of porcine anterior pituitary cells is influenced by adiponectin

status: Public on Nov 09 2018

city: Olsztyn

first: Kamil

last: Dobrzyn

state: Warminsko-Mazurskie

address: Oczapowskiego, 1A

department: Department of Animal Anatomy and Physiology

institute: University of Warmia and Mazury

summary: Adiponectin is thought to be involved in the regulation of metabolic homeostasis and reproductive processes. Adiponectin controls carbohydrate and lipid metabolism by regulating the fatty acid oxidation process, increasing insulin sensitivity and decreasing plasma triglyceride levels. Adiponectin also plays an important role in the modulation of female reproductive functions, both directly and by influencing the secretory functions of the higher branches of the hypothalamic-pituitary-gonadal axis. The main aim of this study was to determine the effect of adiponectin on global gene expression and on differentially expressed genes (DE-genes) under the influence of the studied hormone in porcine anterior pituitary (AP) cells.

overall_design: We analyzed samples obtained from 4 individuals (n=4). Obtained from the anterior pituitary culture cells were divided for two groups: controls [without treatment] and adiponectin treated ones. The concentration of adiponectin in the culture medium was 10 μg/ml. In vitro cells cultures were cultivated with treatments for 24 hours.

first: Karol

last: Szeszko

first: Nina

last: Smolinska

first: Marta

last: Kiezun

first: Edyta

last: Rytelewska

last: Kisielewska

first: Marlena

last: Gudelska

first: Tadeusz

last: Kaminski


title: Microarray upon ZMYND8 knockdown in MCF7 cells

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: ZMYND8, a chromatin reader/effector protein, knockdown in MCF7 cells

first: Moitri

last: Basu

first: Isha

last: Sengupta

first: Md

middle: W

last: Khan

first: Dushyant

middle: K

last: Srivastava

first: Partha

last: Chakrabarti

first: Siddhartha

last: Roy

first: Chandrima

last: Das


title: Global gene expression changes in canine CD4+ peripheral T-cell lymphoma

city: Fort Collins

first: Anne

last: Avery

state: CO

address: 1619 Campus Delivery Colorado State University

department: Microbiology, Immunology, Pathology

institute: Colorado State University

summary: We evaluate differential gene expression in 6 cases of canine CD4+ peripheral T-cell lymphoma (PTCL) compared to sorted CD4+ lymphocytes from the lymph nodes of healthy dogs.Lymph node aspirates from 6 dogs submited for routine diagnostics and diagnosed with CD4+ PTCL by flow cytometry were selected for RNA-seq. Patients were naïve to treatment at the time of sample submission. Aspirates from selected cases had a purity of greater than 88% neoplastic cells. Neoplastic cells were identified by the following immunophenotype: CD4+CD3+CD5+/-CD45+MHCIIlo. Hierarchical clustering of samples resulted in distinct separation of control lymphocytes and PTCL cases with intermixing of PTCL from Boxer and non-Boxer dogs. Top enriched pathways are involved in G-coupled protein receptor signaling, extracellular matrix remodeling and vascular development, inflammatory response and immune signaling, and mitotic activity.  This study provides the global gene expression analysis of aggressive canine T-cell lymphoma using RNAsequencing.

overall_design: RNAsequencing of 6 canine CD4+ peripheral T-cell lymphoma samples compared to 3 sorted normal CD4+ control lymphocytes.

first: Lauren

last: Harris


title: The in vitro effect of orexin A on the porcine myometrial transcriptomic profile during early-implantation period

first: Kamil

last: Dobrzyn

summary: Orexins belong to the group of metabolism regulating factors connected mainly with the nervous system. Both biologically active neuropeptides, orexin A (OXA) and orexin B (OXB)  are products of the proteolytic cleavage of common 130 amino-acid precursor – prepro-orexin (PPO). In the reproductive system orexins has been found to act not only on the endocrine, but also auto- and paracrine manner. In the present study we focused on the effect of OXA treatment on the global gene expression in the porcine myometrium during the most dynamic phase of the early pregnancy – the implantation period (days 15 to 16 of gestation).

overall_design: We analized samples obtained from 4 individuals (n=4). Obtained from the uterine horns tissue explants were divided for two groups: controls [without treatment] and orexin A treated ones. The concentration of orexin A in the culture medium was 10 µM. In vitro tissue cultures were cultivated with treatments for 24 hours.

last: Szeszko

first: Katarzyna

first: Joanna

last: Wyrebek

first: Kinga

last: Bors


title: Gene profiling-based phenotyping for identification of cellular parameters that contribute to fitness, stress-tolerance and virulence of Listeria monocytogenes variants

city: Wageningen

first: Jeroen

middle: Steven

last: Koomen

address: Bornse Weilanden 9

country: Netherlands

institute: Wageningen University

summary: Microbial population heterogeneity allows for a differential microbial response to environmental stresses and can lead to the selection of stress resistant variants. In this study, we have used two different stress resistant variants of Listeria monocytogenes LO28 with mutations in the rpsU gene encoding ribosomal protein S21, to elucidate features that can contribute to fitness, stress-tolerance and host interaction using a comparative gene profiling and phenotyping approach. Transcriptome analysis showed differential expression of 319 genes of which 116 genes were upregulated and 114 genes were downregulated in both rpsU variants. Upregulated genes included a major contribution of SigB-controlled genes such as intracellular acid resistance-associated glutamate decarboxylase (GAD) (gad3), genes involved in compatible solute uptake (opuC), glycerol metabolism (glpF, glpK, glpD), and virulence (inlA, inlB). Downregulated genes in the two variants involved mainly genes involved in flagella synthesis and motility. Phenotyping results of rpsU variants matched the gene profiling data including enhanced freezing resistance conceivably linked to compatible solute accumulation, higher glycerol utilisation rates, and better adhesion to Caco 2 cells presumably linked to higher expression of internalins. Also, bright field and electron microscopy analysis confirmed reduced flagellation of the variants. The activation of SigB-mediated stress defence offers an explanation for the multiple-stress resistant phenotype in rpsU variants.

overall_design: Two comparisons were performed: WT over variant 14 (biological duplicate, and Cy5-Cy3 dye-swapped)  and WT over variant 15 (biological triplicate, and Cy5-Cy3 dye-swapped). All strains were grown in BHI at 30 degrees C, shaken at 160 rpm, harvested at OD600 between 0.4-0.5

first: Heidy

middle: M

last: den Besten

first: Karin

middle: I

last: Metselaar

first: Marcel

middle: H

last: Tempelaars

first: Lucas

last: Wijnands

last: Zwietering

first: Tjakko

last: Abee


title: Microarray upon ZMYND8 knockdown in Hela cells

first: madavan

last: vasudevan

summary: ZMYND8, a chromatin reader/effector protein, knockdown in Hela cells

first: Santanu

last: Adhikary

first: Sulagna

last: Sanyal

first: Moitri

last: Basu

first: Isha

last: Sengupta

first: Sabyasachi

last: Sen

last: Srivastava


title: Expression data from GFP- or GFP Satellite alpha-transfected human retinal pigment epithelia cell line ARPE19

status: Public on Nov 08 2018

city: Guangzhou

first: Lili

last: Gong

state: Guangdong

address: Jinsui Road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: Oxidative stress (OS) and inflammation play pivotal roles in retinal pigment epithelium (RPE) degeneration and age-related macular degeneration (AMD) pathogenesis. Interleukin 17 (IL17) signaling is a founding pathway regulating inflammatory response, the IL17 ligand has been shown to induce RPE degeneration and is emerging as a potential target for AMD treatment. However, the regulation and function of IL17 receptors are largely unexplored in RPE cells under OS. Here, we identified that IL17RA was significantly upregulated in the presence of OS both in human and mouse RPE cells. We found that OS upregulates expression of reprogramming factor Kruppel-like factor 4 (KLF4), which directly binds to the IL17RA promoter and activates IL17RA transcription, therefore inducing RPE proinflammatory response. Furthermore, our results reveal that KLF4 isoform 2, but not the canonical KLF4 isoform1, is the major isoform in RPE cells that activates IL17RA transcription. Finally, we demonstrate that mRNA level of IL17RA was positively correlated with that of KLF4 isoform2 in AMD patients. Together, our data demonstrates a new regulatory mechanism of IL17RA by KLF4 upon OS exposure, which is likely to play a role in AMD pathogenesis.

overall_design: ARPE19 cells were transfected with GFP plasmid. Then cells were treated without (H2O2 0H) or with (H2O2 3H)  10 mU/ml glucose oxidase for 3h. Each treatment was performed in triplicates. Untreated ARPE (H2O2 0H) was considered as control group.


title: Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Ovarian Pathology and Granulosa Cell Epigenome and Transcriptome Alterations: Ancestral Origins of PCO and POI

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: Previous studies have shown that exposure to a number of environmental toxicants can promote the epigenetic transgenerational inheritance of ovarian disease, including decreases in the primordial follicle pool of oocytes that are similar to what is seen in POI, and increases in ovarian cysts that are similar to what is seen in PCOS. In the current study, transgenerational changes to the epigenome of ovarian granulosa cells are characterized in F3 generation rats after ancestral vinclozolin or DDT exposures compared to controls. In purified granulosa cells from 20 day old F3 generation females 164 differentially methylated regions (DMRs) (p<1e-06) were found in the F3 generation vinclozolin lineage, and 293 DMRs (p<1e-06) in the DDT lineage, compared to controls.

overall_design: Pregnant F0 generation female rats were transiently exposed with vinclozolin, DDT or control vehicle (dimethylsulfoxide, DMSO) from days 8-14 of gestation. The in utero exposed offspring, F1 generation rats, were bred to produce the F2 generation, and similarly F2 generation animals were bred to produce the transgenerational F3 generation. No sibling or cousin crosses were used to avoid inbreeding artifacts. Only the F0 generation rats received the experimental treatments. Granulosa cells were harvested from the ovaries of super-ovulated F3 generation females at 20-22 days of age. Granulosa cells were isolated and analyzed so as to characterize DNA methylation.

first: Eric

last: Nilsson

first: Rachel

last: Klukovich

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck

first: Yeming

last: Xie

first: Wei

last: Yan


title: Integrated transcriptome and hormone profiling highlight the role of multiple phytohormone pathways in wheat resistance against fusarium head blight

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

summary: Multiple molecular tools and assays were deployed to compare the resistant variety Sumai3 with three regionally adapted Canadian cultivars, Stettler, Muchmore and FL62R1. Macroscopic and microscopic disease evaluation established the relative level of Type II FHB resistance of the four varieties and revealed that the F. graminearum (Fg) infection process displayed substantial temporal differences among organs. The rachis was found to play a critical role in preventing Fg spread within spikes. Large-scale, organ-specific RNA-seq at different times after Fg infection demonstrated that diverse defense mechanisms were expressed faster and more intensely in the spikelet of resistant varieties. The roles of plant hormones during the interaction of wheat with Fg was inferred based on the transcriptomic data obtained and the quantification of the major plant hormones. Salicylic acid and jasmonic acid were found to play predominantly positive roles in FHB resistance, whereas auxin and ABA were associated with susceptibility, and ethylene appeared to play a dual role during the interaction with Fg.

overall_design: The four genotypes were subjected to challenge by the pathogenic fungus Fusarium graminearum or with 10 μl ddH2O as a mock treatment. Samples inoculated with Fg were taken at 1, 2, 3 days post inoculation (dpi) from spikelets and 2, 3, 4 dpi from rachis. Samples treated with water were harvested at 2 days post treatment from spikelets and rachis.

first: Lipu

last: Wang

first: Youlian

last: Pan

first: Pierre

last: Fobert


title: Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Prostate Pathology and Stromal-Epithelial Cell Epigenome and Transcriptome Alterations: Ancestral Origins of Prostate Disease

summary: The incidence of prostate disease is increasing, and some of this increase may be attributable to ancestral exposure to environmental toxicants and epigenetic transgenerational inheritance mechanisms. The goal of the current study was to determine the effects that exposure of gestating female rats to vinclozolin has on the epigenetic transgenerational inheritance of prostate disease, and to characterize by what molecular epigenetic mechanisms this has occurred. Results indicate that there were changes in DNA methylation in both cell types.

overall_design: Gestating female rats (F0 generation) were exposed to vinclozolin by daily injections during E8-E14 of gestation. F1 generation offspring were bred to produce the F2 generation, which were bred to produce the transgenerational F3 generation. Prostate epithelial and stromal cells were isolated from F3 generation from 20-day old rats, prior to the onset of disease, and used to obtain DNA for analysis. MeDIP-seq was used to characterize the methylation present in the cells.


title: Hippo kinases Mst1 and Mst2 sense and amplify IL-2R−STAT5 signaling in Treg cells to establish stable regulatory activity

city: Memphis

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
Interleukin-2 (IL-2) and downstream transcription factor STAT5 are important for maintaining regulatory T (Treg) cell homeostasis and function. Tregs can respond to low levels of IL-2, but the mechanisms by which STAT5 is activated during partial IL-2 deficiency remain uncertain. We identified the serine-threonine kinase Mst1 as a signal-dependent amplifier of IL-2−STAT5 activity in Tregs. Tregs had high Mst1 and Mst2 (Mst1−Mst2) activity that was crucial to prevent tumor resistance and autoimmunity. Mechanistically, Mst1−Mst2 sensed IL-2 signals to promote the STAT5 activation necessary for Treg cell homeostasis and lineage stability, and maintain the highly suppressive phophorylated-STAT5+ Treg cell subpopulation. Unbiased quantitative proteomics revealed an association of Mst1 with the cytoskeletal DOCK8−LRCHs module that shaped activity Rho-family GTPase Rac activity, which in turn mediated STAT5 activation in Tregs. Collectively, IL-2−STAT5 signaling critically depends upon Mst1−Mst2 functions to maintain a stable Treg cell pool and immune tolerance.
We used microarrays to compare the global transcription profiles of WT and Mst1/Mst2-null Treg cell populations

overall_design: In total 9 samples were analyzed: Treg cells (WT, n = 5; Mst1/Mst2-null, n = 4).

first: Hao

last: Shi

first: Chaohong

first: Hongbo

last: Chi


title: Mucispirillum schaedleri interferes with Salmonella Typhimurium virulence factor expression

city: Munich

first: Bärbel

last: Stecher

address: Pettenkoferstr. 9a

department: Max von Pettenkofer Institute

institute: Ludwig Maximilian University of Munich

summary: We used transcriptomics to investigate how Mucispirillum schaedleri ASF 457 interferes with the gene expression of Salmonella Typhimurium in the cecum of gnotobiotic mice

overall_design: RNA-Seq of the gut microbiota from 8 gnotobiotic mice harboring either (I) Salmonella (4 replicates) or (II) Salmonella and Mucispirillum schaedleri ASF 457 (4 replicates).

first: Simone

last: Herp

first: Sandrine

last: Brugiroux

first: Debora

last: Garzetti

first: Diana

last: Ring

first: Lara

last: Jochum

first: Markus

last: Beutler

first: Claudia

last: Eberl

first: Saib

last: Hussain

first: Steffi

last: Walter

first: Roman

middle: G

last: Gerlach

first: Hans

last: Ruscheweyh

last: Huson

first: Mikael

middle: E

last: Sellin

first: John

middle: F

last: Baines

first: Philipp

last: Rausch

first: Marijana

last: Basic

first: André

last: Bleich

first: David

last: Berry


title: Epigenetic Transgenerational Inheritance of Testis Pathology and Sertoli Cell Epimutations: Generational Origins of Male Infertility

first: Michael

last: Skinner

summary: Environmental toxicant induced epigenetic transgenerational inheritance has been shown to affect testis pathology and sperm count. Sertoli cells have an essential role in spermatogenesis by providing physical and nutritional support for developing germ cells. The current study was designed to further investigate the transgenerational epigenetic changes in the rat Sertoli cell epigenome that are associated with the onset of testis disease.

overall_design: Gestating female F0 generation rats were transiently exposed to the toxicants DDT (dichlorodiphenyltrichloroethane) or vinclozolin. The F1 generation offspring were bred to generate the F2 generation which were then bred to the transgenerational F3 generation. The DNA was obtained from purified Sertoli cells isolated from 20-day testis of transgenerational F3 generation rats. Transgenerational alterations in DNA methylation were observed in the Sertoli cells.

first: Ingrid

last: Sadler-Riggleman

first: Rachel

last: Klukovich

first: Eric

last: Nilsson

first: Daniel

last: Beck

first: Yeming

last: Xie

first: Wei

last: Yan


title: Transcriptional profiles of decidualized cultured WT vs NELF-B cKO Uterine stromal cells

status: Public on Nov 07 2018

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Pausing of RNA polymerase II (Pol II) during early transcription, mediated by the negative elongation  factor (NELF) complex, allows cells to coordinate and appropriately respond to signals by modulating  the rate of transcriptional pause release. Promoter proximal enrichment of Pol II occurs at uterine genes  relevant to reproductive biology; thus, we hypothesized that pausing might impact endometrial response by  coordinating hormonal signals involved in establishing and maintaining pregnancy.We deleted the NELF-B  subunit in themouse uterus using PgrCre (NELF-B UtcKO).Resulting females were infertile.Uterine response  to the initial decidual stimulus of NELF-B UtcKOwas similar to that of control mice; however, subsequent full  decidual response was not observed. Cultured NELF-B UtcKO stromal cells exhibited perturbances in extracellular  matrix components and also expressed elevated levels of the decidual prolactin Prl8a2, as well as  altered levels of transcripts encoding enzymes involved in prostaglandin synthesis and metabolism. Because  endometrial stromal cell decidualization is also critical to human reproductive health and fertility, we used  small interfering to suppressNELF-B or NELF-E subunits in cultured human endometrial stromal cells, which  inhibited decidualization, as reflected by the impaired induction of decidual markers PRL and IGFBP1.  Overall, our study indicatesNELF-mediated pausing is essential to coordinate endometrial responses and that  disruption impairs uterine decidual development during pregnancy.

overall_design: 3 replicates each of WT and NELF-B UtcKO uterine stroma cells cultured for 24 hours with estradiol and progesterone to induce decidualization

first: Sylvia

last: Hewitt

first: Rong

last: Li

first: Nyssa

last: Adams

first: Wipawee

last: Winuthayanon

first: Katherine

last: Hamilton

first: Lauren

last: Donoghue

first: Sydney

middle: L

last: Lierz

first: Marleny

last: Garcia

last: Lydon

first: Francesco

last: DeMayo

first: Karen

last: Adelman

first: Kennest

middle: S

last: Korach


title: Altered expression of the Cdk5 activator-like protein, Cdk5α, causes neurodegeneration, in part by accelerating the rate of aging.

city: Bethesda

first: Kory

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

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

overall_design: Refer to individual Series


title: Characteristic regulation of Lbp and Sod3 gene expression in peri-implant connective tissue of rats

city: Chiyoda-ku

first: Hodaka

last: Sasaki

address: 2-9-18, Kandamisaki-cho

department: Dept. of Oral and Maxillofacial Implantology

institute: Tokyo Dental College

summary: The mucosal penetration area formed by implant placement is critical problems of dental implant treatment, because epithelial barrier is broken and it can become a source of inflammation. To clarify the influence and risk caused by dental implant treatment in peri-implant soft tissue, we compared gene expression profile of peri-implant soft tissue and oral mucosal tissue with microarray analysis.

overall_design: Upper first molars of 5-week-old rat was extracted, and titanium alloy implants were placed only in the left extraction socket for peri-implant connective tissue (PICT) group. Four weeks after surgery, samples were harvested only peri-implant soft tissue by laser microdissection (LMD). For periodontal connective tissue (PCT) was harvested from 9-week-old mice by LMD. For oral mucosa connective tissue (OMCT), upper first molar of 5-week-old rat was extracted and harvest wounded area of connective tissue after 4 weeks by LMD.

first: Takafumi

last: Kobayashi


title: Pre-neural serotonin influences late embryonic development and behavior patterns in zebrafish. Expression data from 2 and 4 dpf zebrafish larvae.

city: Woods Hole

first: Evgeny

middle: G.

last: Ivashkin

state: MA

address: 7 MBL St.

department: Josephine Bay Paul Center

institute: Marine Biological Laboratory

summary:
The presence of serotonergic system during early pre-neural development is conserved amongst all studied invertebrate and vertebrate animals. Previously, we discovered that early embryonic pre-neural serotonin relays physiological and behavioral information from mother to progeny in an invertebrate model system. However, the question of whether the similar logic might apply during vertebrate development remains unanswered. Thus, we took advantage of zebrafish model system to address this based on the systematic investigation of composition and function of early pre-neural serotonergic system in fish. As a result, we characterized the presence, distribution and activity of molecules involved in serotonin synthesis and transport at pre-neural and neural stages of development. Then, we experimentally revealed the existence of delayed developmental and behavioral effects resulting from the manipulations of pre-neural (zygote, blastula and gastrula) serotonergic system. In particular, the delayed effects included differences in the synthesis of serotonin in early serotonergic neurons in the central nervous system as well as in behavioral alterations in zebrafish larvae. At the same time, the effects resulting from manipulations of pre-neural serotonin appeared highly specific and did not coincide with any major abnormalities. Similar manipulations of the serotonergic system at later neural stages did not show similar effects, thus, demonstrating that transduction of a serotonergic signal is not based on the general level of retained serotonin but on its availability in the specific cells. Accordingly, gene expression analysis demonstrated specific changes in response to the elevation of early pre-neural serotonin, which included the delayed and pre-mature onsets of different gene expression programs. Taken together, our results introduce a novel function of early pre-neural serotonergic system in a vertebrate embryo – tuning and fine control of specific mechanisms at later neural developmental stages that result in a mild variation of an adaptive spectrum.
We used microarrays to identify the aftermath of early pre-neural serotonin increase and decrease.

overall_design: Injections of embryos were performed at the using Eppendorf FemtoJet microinjector. We co-injected serotonin of reserpine with lysine-fixable TRITC-conjugated fluorescent dextran (Molecular Probes, USA). Total RNA was extracted from 30-40 2 and 4 dpf zebrafish larvae from each experimental group. Total RNA from each sample was used for the synthesis of cDNA, which was hybridized to 902007 Affymetrix® Zebrafish Gene 1.0 ST Array with Ambion WT terminal labeling and hybridization protocol. Experiments and controls were done in biological duplicates.

first: Andrey

last: Zinovyev

first: Igor

last: Adameyko


title: gene expression when silencing RBMS3  in ovarain cancer cell line SKOV3

status: Public on Nov 06 2018

first: Geyan

last: Wu

address: Zhongshan Er Road

institute: Sun Yet-sen universtiy

summary:
The development of resistance to platinum-based chemotherapy remains the unsurmountable obstacle in cancer treatment and consequently leads to tumor relapse. This study aims to investigate the mechanism by which loss of RBMS3 induced chemoresistance in epithelial ovarian cancer (EOC).

Experimental design: Fluorescence in situ hybridization and immunochemistry were used to determine deletion frequency and expression of RBMS3 in 15 clinical EOC tissues and 150 clinicopathologically characterized EOC specimens. The effects of RBMS3 deletion and CBP/β-catenin antagonist PRI-724 in chemoresistance were examined by clone formation and Annexin V assays in vitro, and by intraperitoneal tumor model in vivo. The mechanism by which RBMS3 loss sustained activation of miR-126-5p/β-catenin/CBP signaling and the effects of RBMS3 and miR-126-5p competitively regulating DKK3, AXIN1, BACH1 and NFAT5 was explored using CLIP-seq (PRJNA484809),  RIP, electrophoretic mobility shift and immunoblotting immunofluorescence assays.

Results: Loss of RBMS3 in EOC was correlated with the overall and relapse-free survival. Genetic ablation of RBMS3 significantly enhanced, whereas restoration of RBMS3 reduced, the chemoresistance ability of EOC cells both in vitro and in vivo. RBMS3 inhibited β-catenin/CBP signaling through directly associating with and stabilizing multiple negative regulators, including DKK3, AXIN1, BACH1 and NFAT5, via competitively preventing the miR-126-5p-mediated repression of these transcripts. Importantly, co-therapy of CBP/β-catenin antagonist PRI-724 induced sensitization of RBMS3-deleted EOC to platinum therapy.

Conclusions: Our results demonstrate that genetic ablation of RBMS3 contributes to chemoresistance and PRI-724 may serve as a potential tailored treatment for patients with RBMS3-deleted EOC.

overall_design: Gene expression in ovarian cancer cell line SKOV3 was measured in control cells and RBMS3 KO cells.  Two independent experiments were performed  for each experiment.


title: Gene expression of yeast fermentor culture after circadian temperature entrainment

city: Groningen

first: Jasper

last: Bosman

state: Groningen

address: Zernikeplein 11

department: Bioinformatics

institute: Hanzehogeschool

summary:
This gene expression experiment aimed to discover circiadian clock genes in yeast cells grown in a 1L fermentor culture
Yeast were entrained for a period of time after the culture was released to a freerun (see growth protocol below). Samples were taken from fermenter cultures (1 × 109 yeast cells) every 3 hours over the first day of constant conditions (free-run), starting 1h before the temperature transition from 21°C to 28°C

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: 9 Samples were taken from a fermenter culture every 3 hours over the first day of constant conditions (free-run), starting 1h before the temperature transition from 21°C to 28°C

first: Zheng

last: Eelderink-Chen

first: Martha

last: Merrow


title: Identification of common highly expressed genes of Salmonella Enteritidis by in silico prediction of gene expression and in vitro transcriptomic analysis

first: Devendra

last: Shah

state: Washington

address: #402, Bustad Hall

department: Veterinary Microbiology and Pathology

institute: Washington State University

summary: We report the use of RNA-Seq technique to identify  common highly expressed genes in pathogenic poultry-associated field strains of S. Enteritidis grown in LB-salt broth (300mM NaCl) and low-phosphate/low -magnesium/low-pH LPM broth at avian body temperature (42°C).

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: Characterization and comparison of transcriptome of three S. Enteritidis strains previously identified as high-pathogenic

first: Kim

last: Chiok


title: miRNome dynamics during flower development in Arabidopsis

city: Berlin

first: Dijun

last: Chen

address: Philippstr. 13 (House 22)

department: Plant Cell and Molecular Biology

institute: Humboldt University

summary: Flower development is a dynamics process in which floral organs are produced from pools of stem cells residing in meristems (Smyth et al., 1990). In order to obtain a high resolution map of the changes of miRNA gene expression during this process thus to provide insights into specific expression patterns and their underlying gene regulatory networks, an inducible system which allows us to obtain synchronized flowers (Wellmer et al., 2006) was used to collect seedlings as well as  stage-specific floral tissues at four stages (stages 0, 2, 4 and 8) for transcriptome profiling by miRNA-seq .

overall_design: We used the AP1-GR system to conduct RNA-seq experiments at different stages of flower development. Samples were generated from tissue in which the AP1-GR protein was induced using a treatment of 1 uM DEX to the shoot apex. The material was collect before treatment and 2, 4 and 8 days after treatment. Experiments were done in two or three biological replicates.

first: Kerstin

last: Kaufmann


title: Global transcriptomic response of modified Bacillus anthracis over expressing protective antigen

first: Ashish

last: Sharma

address: 14 Service Rd West Building 14A Room 176 MS-5522

department: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

institute: National Institute of Health

summary: In this study we focused on understanding the effect of over expression of recombinant protective antigen (rPA) on the Bacillus anthracis metabolism and genes expression with the purpose of improving the production of this recombinant toxin in particular and recombinant proteins in general. To achieve this goal  controlled growth  of the B. anthracis ames strain transformed with pYS5 (PA producer) plasmid encoding protective antigen and the corresponding empty vector pSW4 (non-producer) were performed and protein production, bacterial growth characteristics  and gene transcription pattern were analyzed. Controlled condition batch runs were performed for both strains and samples from early log (OD 3), log (OD 10) and late log (OD 16) phase were used for gene expression profiling. We found that most of the genes belonging to transport, TCA, glycolysis, PPP and amino acid biosynthesis were up-regulated in the lag phase samples which help the cell coping with the increased requirements of nutrient and energy for rPA expression. These pathways are down-regulated in the log and latelog phase as cellular stress response onsets, which is reflected in the decreased specific growth rate.

overall_design: Time point mRNA profiling of Bacillus anthracis ames strain BH500 transformed with pYS5 (PA producer) and the corresponding empty vector pSW4 (non-producer).

first: A

first: J

last: Shiloach

first: S

last: Leppla

first: Andrei

last: Pomerantsev


title: Gene expression profiles of normal and injured podocytes induced by immunotoxin.

city: Isehara

first: Masahiro

last: Okabe

address: 143 Shimokasuya

institute: Tokai University School of Medicine

summary: Podocyte injury is a key event for progressive renal failure. We previously established a mouse model of inducible podocyte injury (NEP25) and demonstrated relentless progression of glomerular injury toward sclerosis. To further investigate molecular events, we performed polysome analysis of intact and injured podocytes utilizing the NEP25 and RiboTag transgenic mice. We show here the expression profiling of normal podocytes and podocytes injured by immunotoxin.

overall_design: RiboTag mice were crossed with Nphs1-Cre mice (designated as Nphs1-RiboTag mice) and podocyte RNA was isolated from podocyte specific polysomes. RNA of Glomerular cells was also obtained from Nphs1-RiboTag mice. Nphs1-RiboTag mice were crossed with NEP25 mice (designated as Nphs1-RiboTag-NEP25). Nphs1-RiboTag-NEP25 mice was injected with LMB2 to induce podocyte injury and podocyte RNA was isolated 4 and 7 days later.

first: Masaru

last: Motojima

first: Yoichi

last: Miyazaki

first: Ira

last: Pastan

first: Takashi

last: Yokoo

first: Taiji

last: Matsusaka


title: New miRNA signatures herald human NK cell subsets at different stages of differentiation: involvement of miR-146a-5p in the regulation of KIR expression

city: Genova

first: annalisa

last: barla

state: GE

address: via Dodecaneso 35

department: DIBRIS

institute: Università degli Studi di Genova

summary:
Natural killer cells are cytotoxic innate lymphoid cells that play an important role for early host defenses against infectious pathogens and surveillance against tumor growth and metastasis. In humans, NK cells may be divided in various subsets on the basis of the relative expression of the CD56 molecule and of the low-affinity FcγRIIIA CD16. In particular, the two main NK cell subsets are represented by the CD56bright CD16-/dull and the CD56dull CD16bright NK cells. A number of experimental evidences indicate that CD56bright and CD56dull NK cells represent different maturative stages of the NK cell developmental pathway.
In an effort to identify NK cell miRNA signatures that may contribute to the NK cell-specific maturation program, we determined the miRNA profile of human NK cell subpopulations derived from peripheral blood samples of healthy donors.
We identified multiple miRNAs that are differentially expressed in CD56bright CD16- and CD56dull CD16bright NK cells. Among these, we found a few miRNAs with a consistent differential expression in the two NK cell subsets, and with an intermediate expression in the CD56brightCD16dull NK cell subset, representing a transitional step of maturation of NK cells. Our data have been confirmed by both quantitative real-time PCR and multivariate analysis.
These analyses allowed us to establish the existence of a miRNA signature able to discriminate the two main NK cell subsets, regardless of their surface phenotype.
In addition, by analyzing the putative targets of representative miRNAs we show that miR-146a-5p, that displays a significant up-regulation in CD56bright as compared to CD56dull NK cells, may be involved in the regulation of killer Ig-like receptor (KIR) expression.
These findings may contribute to a better understanding of the physiologic significance of miRNAs in the regulation of NK cell development/function. In addition, our results suggest that miR-146a-5p targeting, resulting in KIR down-regulation, may be exploited as a tool to generate/increment the effect of NK KIR-mismatching against HLA class I+ tumor cells and thus to improve the NK-mediated anti-tumor activity.

overall_design: 20 samples from 10 different healthy donors: from each donor CD56bright (CD16-) and CD56dull  (CD16+) NK cells subsets were isolated and analyzed

first: Emanuela

last: Marcenaro

first: Simona

last: Candiani


title: Establishment of stably expandable induced myogenic stem cells by defined factors

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

summary: Numerous studies have been conducted to improve the supply of myogenic stem cells for patients with muscle disease, including Duchenne muscular dystrophy. Collecting muscle samples from patients in order to obtain myoblasts or satellite cells is very invasive. Thus, a new method for obtaining myogenic stem cells is required. Here, we established stably expandable induced myogenic stem cells (iMSCs) with defined factors. The iMSCs showed high expression levels of Pax7, Myf5, and MyoD. Also, the iMSCs differentiate into myotubes which are multinucleated fiber. Additionally, the iMSCs differentiated into myotubes, which are multinucleated fibers. We confirmed its myogenic differentiation capacity in mdx mice by detecting dystrophin-positive cells in iMSCs-injected TA muscles. The iMSCs showed higher proliferation capacity than MDSCs in both in vitro and vivo. This study suggests the possibility to apply directly converted expandable myogenic stem cells to muscle disease patients.

overall_design: Gene expression of iMSC and sort-iMSC was anaylyzed. MEF and MDSC were used as control. Each group has two samples.

first: Kyu-Shik

last: Jeong

first: Eun-Joo

last: Lee

first: Meeyul

last: Hwang

first: Myeong-Mi

first: Yong-Deuk

first: Myeong-Jin

first: Ahmed

last: Elfadl

first: Daehee


title: Transcriptomics of gut microbiome of high fat diet mice supplemented with mannose.

city: La Jolla

first: Vandana

last: Sharma

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

summary:
Purpose: Using a C57BL6/J mouse model of diet-induced obesity, we observed that mannose supplementation of high fat diet-fed mice prevents weight gain, lowers adiposity, reduces liver steatosis, and improves glucose tolerance and insulin sensitivity. Mannose increases Bacteroidetes to Firmicutes ratio of the gut microbiota, a signature previously associated with the lean phenotype. These beneficial effects of mannose are observed when supplementation is started early (3 weeks post weaning) but are lost when started later in life (8 weeks post weaning). We profiled transcriptomes of gut microbiota from high fat diet mice supplemented with or without mannose to understand the functional differences of supplementation at 3 weeks post weaning and 8 weeks post weaning.
Method: Mice were weaned on high fat diet (HFD) or high fat diet with 2% mannose in drinking water (HFDM). RNA from each mouse for each diet group was isolated individually using Ambion RiboPure Bacteria kit (ThermoFisher Scientific). 1 mg cecal RNA each from 8 mice/diet group was pooled to generate 1 pool/diet for library preparation. The quality of total RNA was assessed by the Agilent Bioanalyzer Nano chip (Agilent Technologies). Total RNA was Ribo-depleted using Ribo-Zero Gold rRNA kit (Epidemiology) (Illumina). RNA-Seq library was constructed from the recovered non-ribosomal RNAs using Truseq Stranded total RNA library preparation kit (Illumina) as per the instructions. Multiplexed libraries were pooled and single-end 50-bp sequencing was performed using an Illumina Hiseq 1500.
Results: The comparison of transcriptome profiles of mice supplemented with mannose at 3 weeks post weaning and 8 weeks post weaning shows mannose reduced transcript abundance for glycosyl hydrolases and carbohydrate metabolism when supplied at 3 weeks post weaning.
Conclusion: The beneficial effects of mannose in responsive mice (3 weeks post weaning) are at least in part due to reduced energy harvest by gut microbes.

overall_design: RNASeq was done for HFD and HFDM samples for sets at 3 as well as 8 weeks post weaning. Differential transcript abundance was calculated for HFDM vs HFD for both sets (3 and 8 weeks post weaning) and functional comparisons were drawn.

first: Scott

middle: N

last: Peterson


title: Expression data in BEAS-2B cells and HCT116 cells incubated with copper(II) for different times

city: Buenos Aires

first: Christian

middle: Martin

last: Saporito-Magriña

state: Buenos Aires

address: Junin 956

department: Fisicoquímica y Química Analítica

country: Argentina

institute: Facultad de Farmacia y Bioquimica UBA

summary:
Copper induced stress is known to involve an enhanced oxidant production. This event could be accompanied by an antioxidant response. However, additional processes transcriptionally regulated might participate in the protective response against the metal ions.
We used microarrays to detail the global programme of gene expression due to the copper overload and outline the cell processes mostly involved in the toxicity of the metal ions in two cell lines,  BEAS-2B cells and HCT116 cells.

overall_design:
BEAS-2B cells and HCT116 were plated at 60-80% confluence and they were incubated with 800 µM CuSO4  and 1400 µM CuSO4  respectively, dissolved in DMEM for 0, 2, 4, 6, 12 and 18 hours. At the end of the corresponding incubation time cells were harvested  for RNA extraction and hybridization.
time course

first: Christoph

last: Borner

first: Melanie

last: Börries

first: Geoffroy

last: Andrieux


title: Signiture microRNA expression patterns identified in Williams syndrome

city: Kyoto

first: Ryo

last: Kimura

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

institute: Kyoto University Graduate School of Medicine

summary: Williams Syndrome (WS) is a rare neurodevelopmental disorder caused by heterozygous deletions in a chromosome 7q11.23 region typically encompassing 26-28 genes. WS patients exhibit a wide spectrum of symptoms, including cardiovascular disease, intellectual disability, visuospatial deficits and hypersociability a behavioral profile that contrasts with autism spectrum disorder (ASD). However, the relationship between neuropsychiatric phenotypes and dysregulated gene networks caused by the 7q11.23 deletion is unknown. We report results from a large-scale integrated transcriptome analysis of peripheral blood in clinically evaluated subjects with WS, ASD and matched controls. We identified significantly differential expressed genes in WS as compared with ASD or controls, even after removing genes spanning the 7q11.23 region. Using weighted gene co-expression network analysis (WGCNA), we found that three co-expression modules were upregulated in WS, and were significantly associated with the intermediate phenotypes such as anxiety and attention problems. Notably, these three co-expression modules were only composed of genes located outside of 7q11.23 critical region. One module was associated with immune systems and B cell proliferation. Its top hub gene, BCL11A, is implicated in ASD and chromatin modification. Another module was enriched with genes associated with astrocytes and oligodendrocytes, and the third module was associated with RNA processing and neurons.MicroRNA (miRNA) profiling revealed differentially expressed miRNAs whose targets were enriched in each co-expression module associated with WS. These results identify genes and potential driver miRNAs, located outside of 7q11.23 critical region, that are novel candidates for mediating the neuropsychiatric phenotypes in WS.

overall_design: We profiled miRNA expression  from 35 WS patients and 31 controls using peripheral blood.

first: Masatoshi

last: Hagiwara


title: Estrogen-like activity in cell signaling of Sparassis crispa-Extraction (SCE)

city: Shinjuku-ku

first: kayoko

last: Kawaguchi

state: Tokyo

department: Pediatric Cardiology

institute: Tokyo Women'Medical University

summary: Comparing the expression profiles of the genes in response to 17β-estradiol (E2) and SCE (10 μg/ml,100 μg/ml, SCE-EtOAc).

overall_design: Two-condition experiment, E2 or each SCE vs. control cells. Three biological replicates for E2.

first: Kawaguchi

last: Kayoko

first: Yoshiyuki

last: Furutani

first: Toshio

last: Nakanishi

first: Ryoiti

last: Kiyama


title: Differential gene expression of Andrographis paniculata and andrographolide enriched andrographis paniculata extract in liver cells

city: Pune

first: Saroj

last: Ghaskadbi

email: ssg@unipune.ac.in, sghaskadbi@gmail.com

state: Maharashatra

address: Ganeshkhind

department: Department of Zoology

institute: SPPU

summary: Andrographis paniculata Nees and its major compound andrographolide is known to exhibit a pleothera of activities. Active component enriched extracts are known to provide various beneficial effects, and therefore it was interesting to investigate whether increased amount of major compound alters gene expression. To acheive this,  HePG2 cells treated with Andrographis paniculata extract (AP) and andrographolide enriched –extract (AP20) were subjected to microarray analysis to check their effect on global gene expression.

overall_design: HepG2 Cells were treated with AP and AP20 extract (0.01%) in triplicates for 24 hrs. A “biological average” was obtained from these three replicates and total RNA was isolated from the pooled cell extract and was used microaray study.

first: Swati

last: Khole

first: Smriti

last: Mittal

first: Nidhi

last: Jagadish

first: Sharmilli

last: Chettiar

first: Vivek

last: Singh

first: Aarti

last: Desai

first: Abhijeet

last: Kulkarni

first: Vijay

last: Gadgil

first: Vilas

last: Sinkar


title: The transcriptome of the marine copepod Temora longicornis under heat stress and recovery

status: Public on Nov 05 2018

city: Gent

first: Ilias

last: Semmouri

state: Oost-Vlaanderen

address: Coupure Links 653

department: Faculty of Bio engineering

country: Belgium

institute: UGent

summary: Our manuscript aimed to use RNA sequencing technology to study the transcriptomics responses and mechanisms of this species to temperature fluctuations. We focused on both a short term and a more sustained exposure to heat stress. We report significant effects of temperature on the gene expression of Temora.

overall_design: Eight replicates were kept for four days at 14 °C and the other eight were acclimatized to 17 °C over the course of 24 h and kept at this temperature for the remaining three days. Subsequently at day four, four randomly selected replicates were moved for 24 hours to 17 °C from the 14 °C group and vice versa. This resulted in four treatment groups (1) a group exposed to 14°C for five days, (2) a group exposed to 17°C for five days (below referred to as the 'sustained exposure' group), (3) a group exposed to 14°C for four days and then to an additional acute exposure of 17°C (below referred to as 'acute exposure' group), and (4) a group exposed to 17°C for three days and then to an additional recovery exposure of 14°C (below referred to as 'recovery exposure' group). Only 3 replicates for each treatment group were sequenced.

first: Jana

last: Asselman

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: Deforce

first: Colin

middle: R

last: Janssen

first: Karel

middle: A

last: De Schamphelaere


title: Mapping the differential distribution of the cohesin subunit Scc1 in Trypanosoma brucei brucei.

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin immunoprecipitation of genomic loci in Trypanosoma brucei where Scc1 is deposited. This was achieved by deletion of one Scc1 allele and N-terminal tagging of the second Scc1 allele with a Ty1-tag. During the ChIP experiment, the DNA was crosslinked and cells were permeabilized with digitonin. DNA was fragmented by sonication with a Covaris instrument. DNA bound to Ty1-Scc1 was pulled down by using a BB2 anti-Ty1 antibody. Cross links are reversed and the DNA was purified and prepared for Illumina sequencing.

overall_design: Experiment was done in triplicates, each with an input control. As a control, an input sample was included for each ChIP experiment.

first: Laura

last: Müller

first: T

last: NSiegel


title: Microarray analysis of gene expression after suppression of PBRM1 or KDM5C in 786-O VHL+/+ or VHL-/- cells

city: New Haven

first: Qin

last: Yan

state: CT

address: 310 Cedar St

department: Pathology

institute: Yale University

summary:
1. PBRM1 loss elicited very similar transcriptional changes as KDM5C loss;
2. PBRM1 loss, and to a lesser extent KDM5C loss, elicited greater transcriptional response in VHL-/- cells than that in VHL+/+ cells.

overall_design: PBRM1 or KDM5C were suppressed by shRNA in 786-O cells VHL+/+ or VHL-/- before gene expression in triplicates was compared.

first: Lili

last: Liao

first: Zongzhi

last: Liu

first: Jie

first: Xiaohua

last: Niu

first: Yaomin

last: Xu

first: Haifeng

last: Yang


title: human ESC-MSCs: IFN-γ-nontreated, IFN-γ-treated for 1 day, IFN-γ-treated for 3 days

status: Public on Nov 03 2018

city: Hangzhou

first: Hua

state: Zhejiang

address: #866 Yu Hang Tang Rd

department: Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province

institute: School of Medicine,Zhejiang University

summary: Transcriptional and lncRNA profiling of human embryonic stem cells derived mesenchymal stem cells within or without IFN-γ treatment

overall_design: hESC-MSCs treated with IFN-γ for 0day, 1day and 3days for microarray analysis.  3 Biological replicates for each group

first: Yafei

last: Wang


title: A dual sRNA in  Staphylococcus aureus is induced in response to glucose decrease

status: Public on Nov 02 2018

city: Strasbourg

first: Stefano

last: Marzi

address: 2 allée Konrad Roentgen

department: UPR9002 - IBMC

country: France

institute: CNRS

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

overall_design: Refer to individual Series


title: Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns

city: Utrecht

first: Abel

last: Vertesy

address: Uppsalalaan 8

institute: Hubrecht Institute

summary:
To advance our understanding of the genetic programs that drive cell and tissue specialization, it is necessary to obtain a comprehensive overview of gene expression patterns. Here, we have used spatial
transcriptomics to generate high-resolution, anteroposterior gene expression maps of C. elegans males and hermaphrodites. To explore these maps, we have developed computational methods for discovering region- and tissue-specific genes.
We have found extensive sex-specific gene expression differences in the germline and sperm and discovered genes that are specifically expressed in the male reproductive tract. These include a group of uncharacterized genes that encode small secreted proteins that are required for male fertility. We conclude that spatial gene expression maps provide a powerful resource for identifying tissue-specific gene functions in C. elegans. Importantly, we found that expression maps from different animals can be precisely aligned, enabling transcriptome-wide comparisons of gene expression patterns.

overall_design: Spatial transcriptomics by RNA-tomography (TomoSeq) on 20um sections

first: Annabel

last: Ebbing

first: Marco

last: Betist

first: Bastiaan

last: Spanjaard

first: Jan

middle: P

last: Junker

first: Eugene

last: Berezikov

first: Alexander

last: van Oudenaarden

first: Hendrik

middle: C

last: Korswagen


title: Dynamic alteration of cancer stem cell regulators in glioblastoma through radiation-induced mesenchymal transition

city: Birmingham

first: Mutsuko

last: Minata

state: Alabama

address: 1824 6th Ave. S

department: Neurosurgery

institute: University of Alabama at Birmingham

summary: To identify function and functional targets of CD109, we compared the gene expression profiles of human GSCs with or without shCD109

overall_design: CD109 expression in 2 kinds of Glioma stem cells (GSCs) was silencing using lentiviral shCD109 infection. The cells were incuvated with Lentivirus and polybrene.

first: Ichiro

last: Nakano

first: Krishna

last: Bhat

first: Alessandra

last: Audia

first: Dongquan

last: Chen


title: The effect of RsaI on global gene expression in S. aureus

summary: The virulon of Staphyloccocus aureus is controlled by intricate connections between transcriptional and post-transcriptional regulators including proteins and small non coding RNAs (sRNAs). Most of the sRNAs regulate gene expression through base-pairings with mRNAs. Here, we have determined the transcriptome of RsaI sRNA of S. aureus.

overall_design: Global overview of RsaI impact on gene regulation, a comparative transcriptomic analysis was performed on total RNAs extracted from the WT HG001 strain, the isogenic HG001∆rsaI mutant strain, and the same mutant strain complemented with a plasmid expressing RsaI under the control of its own promoter

first: Isabelle

last: Caldelari

first: Pascale

last: Romby


title: MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus RsaI sRNA targetome

summary: The virulon of Staphyloccocus aureus is controlled by intricate connections between transcriptional and post-transcriptional regulators including proteins and small non coding RNAs (sRNAs). Most of the sRNAs regulate gene expression through base-pairings with mRNAs. Here, we have applied and adapted the MS2-affinity purification approach coupled to RNA sequencing (MAPS) to determine the targetome of RsaI sRNA of S. aureus.

overall_design: Affinity purification of in vivo regulatory complexes coupled with high throughput RNA sequencing methodology or MAPS standing for MS2 affinity purification coupled to RNA


title: Next-generation sequence analysis of the submerged Iris tectorum in plant culture and in plant-algae co-culture

first: Qifa

last: Zhou

address: Yuhangtang Rd

institute: Zhejiang University

summary: We conducted a culture experiment by deeply submerging plants in swine wastewater in culturing Iris tectorum and co-culturing Iris tectorum and Dictyosphaerium sp., and found that the plants grew sub-normal in the plant-microalgae co-culture while the plants were dead after 21 days in the plant culture. We generated a comprehensive RNA-seq dataset from the submerged Iris tectorum leaves in both the plant culture and the plant-microalgae co-culture, aiming at providing information on the response mechanisms of the plants to waterlogging stress. Besides raw reads of the RNA-seq dataset, we used DEseq2 algorithms to detect the differently expressed genes in the plants between the different cultures. Additionally, we performed the plant disease resistance gene analysis for all the differentially expressed genes.

overall_design: The  plants were cultured alone or co-cultured with the microalgae (3 replicates each)

first: Zhou

last: Qifa

first: Cheng

last: Qilu