title: Tumor-associated macrophages regulate the gene expression profiles of pancreatic cancer cells both under normoxia and hypoxia

status: Public on May 07 2018

first: Huilin

last: Ye

address: No.107 YanJiang West Road

department: Sun Yat-sen Memorial Hospital

institute: Sun Yat-sen University

summary: Pancreatic cancer is a devastating and intractable disease with highly lethal rate, which is equal to incidence of the disease.It is well established that tumor microenvironment plays a pivotal role in tumor progression and metastasis.Tumor-associated macrophages (TAMs) are frequently found in close proximity with pancreatic cancer cells, but it is uncertain whether they are involved in pancreatic cancer progression.TAMs around the cancer regions usually exert their tumor-supporting functions by the secretion of cytokines and inflammatory mediators.In this study, we aim to investigate that whether tumor-associated macrophages regulate the gene expression profiles of pancreatic cancer cells both under normoxia and hypoxia.

overall_design: We investigated the differential expression profiles of mRNA in PANC-1 pancreatic cancer cells between four groups: the PANC-1-alone control group under hypoxia (HPC groups), the PANC-1-cocultured TAMs group under hypoxia (HPM groups),  the PANC-1-alone control group under normoxia (NPC groups) and the PANC-1-cocultured TAMs group under normoxia (NPM groups).The data of each group are collected from independent experiments in triplicate.Transcriptomic analysis was carried out using a microarray (Arraystar Human mRNA Gene Expression Microarrays V3; Agilent Technology, Santa Clara, USA), which targets 34487 Entrez protein-coding genes.

first: Rufu

last: Chen


title: Differential Gene Expression Patterns in Vein Regions Susceptible and Resistant to Neointimal Hyperplasia

status: Public on May 08 2018

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

country: USA

institute: University of Utah

summary: Arteriovenous hemodialysis graft (AVG) stenosis results in thrombosis and AVG failure, and develops chiefly as a consequence of neotinimal hyperplasia (NH) formation in the graft-venous anastomosis region. Of note, the juxta-anastomotic vein regions are relatively resistant to NH. AVG stenosis has not been resolved partly due to our limited understanding of the molecular processes involved in the pathophysiology. We hypothesized that the gene expression profiles of the NH prone and NH-resistant regions will be different after graft placement, and analysis of their genomic profiles may yield therapeutic targets to address AVG stenosis. To test this hypothesis we evaluated the global genomic profiles of the graft-venous anastomosis (NH-prone) and juxta-anastomotic (NH-resistant) vein regions in a porcine model of AVG stenosis using a porcine microarray. Gene expression changes in these two distinct vein regions, relative to the gene expression in un-operated veins, were examined at an early (5 days) and later (14 days) time period following graft placement. Global genomic changes were much greater in the NH-prone region than in the NH-resistant region at both time points. In the NH-prone region, genes related to regulation of cell proliferation and osteo/chondrogenic vascular remodeling were most enriched among the significantly up-regulated genes at day 5 and day 14, respectively. At both time points, genes related to muscle phenotype were significantly down-regulated. These results provide insights into the spatial and temporal genomic modulation underlying NH formation in AVG, and suggest potential therapeutic strategies to prevent and/or limit AVG stenosis.

overall_design: Gene expression in a porcine model of arteriovenous hemodialysis graft stenosis was measured at 5 and 14 days after graft placement in four independent experiments, using different biological replicates for each experiment. Measurements were taken at the anastomosis, downstream of the anastomosis, and from the external jugular vein as a control.

first: Sun

middle: H

last: Kwon

first: Li

last: Li

first: Christi

middle: M

last: Terry

first: Yan-Ting

last: Shiu

first: Philip

middle: J

last: Moos

middle: A

first: Donald

middle: K

last: Blumenthal

first: Alfred

last: Cheung


title: Next Generation Sequencing to determine the fundamental mechanisms of Tribolium castaneum larvae to cope with hypoxia

status: Public on May 09 2018

city: Shanghai

first: Xueqing

last: Geng

state: Shanghai

address: Dongchuan Road 800#

department: School of Agriculture and Biology

country: China

institute: Shanghai JiaoTong University

type: Expression profiling by high throughput sequencing

summary: We used high-throughput sequencing technology to determine the fundamental mechanisms of Tribolium castaneum to cope with hypoxia. Totals of 12,524,554 useful reads from the control group and 14,193,339 useful reads from the treatment group were generated after Q20 filtering. A total of 16,524 unigenes had been annotated. More than 300 transcripts showed differential expression between the control and hypoxia group, with a fold change ≥1.5 and p value <0.05. Of the 333 identified DEGs, 154 were downregulated and 179 were upregulated. Altered expression of 9 genes was confirmed with qRT–PCR, demonstrating the qRT-PCR data matched the RNA-seq results well. Finally, our results indicated that limiting the available oxygen to T. castaneum increased glycolysis and inhibited the Krebs cycle, and that accumulated pyruvic acid was preferentially converted to lactic acid via anaerobic metabolism. This study advances the field of pest control and makes it possible to develop more efficient strategies for hermetic storage.

overall_design: Examination of gene expression in Tribolium castaneum larvae after 12 h hypoxia treatment, compared with normoxic ones

first: Lei

last: Wang


title: miRNA expression in H460 cells treated with sulforaphane

status: Public on May 05 2018

city: guangzhou

middle: qian

last: qian

institute: Southern Medical University

summary: H460 cells treated with vehicle or sulforaphane (SFN) for 48 hours were used to acquire expression profiles of a total of 1891 unique miRNAs. We aimed at identifying the differentially expressed miRNAs between cells treated or untreated with SFN.

overall_design: In the study presented here, total RNAs of H460 cells treated with vehicle or sulforaphane (SFN) for 48 hours were extracted, labeled with Hy3TM and hybridized on the miRCURYTM LNA Array.

first: Qianqian

first: Guanghui

last: Xiao


title: Collaborative repressive action of the antagonistic ETS transcription factors Pointed and Yan fine-tunes gene expression to confer robustness in Drosophila [Agilent]

city: Chicago

first: Jemma

middle: L.

last: Webber

state: IL

address: 929 E 57th Street

department: Ben May Department for Cancer Research

institute: University of Chicago

summary: Purpose: To understand how gene expression changes in yan and pnt mutant embryos

overall_design: A custom expression array was designed on the Agilent GE 8x15K platform. Probes were designed using the Earray software by Agilent to represent putative Yan target genes. RNA was extracted froms stage 11 wildtype, yan null or pnt null embryos with TRIzol following manufacturer's protocol and purified using an RNeasy Mini Kit from Qiagen. Total RNA was labeled and hybridized according to standard protocol using the Quick Amp One-Color Labeling Kit from Agilent. Triplicate experiments were performed for each genotype.

first: Jie

last: Zhang

first: Ilaria

last: Rebay


title: Gene expression differences of mammary tumors after treatment

city: East Lansing

first: Jing-Ru

last: Jhan

state: MI

address: 567 Wilson Rd BPS 2120

department: Physiology

institute: Michigan State University

summary: Current therapeutic outcomes for breast cancer underscore the complexity of treating a heterogeneous disease. Indeed, studies have shown that differences in gene expression among patients with the same subtype of breast cancer are correlated with the response to treatment. This strongly suggests that there is an urgent need to treat breast cancer with a personalized approach. Here we employed cell signaling pathway signatures predict pathway activity in subtypes of MMTV-Myc mammary tumors.  We then split tumors into subsets and developed individualized combinatorial treatments for two subtypes with distinct pathway activation patterns.  In this treatment, we focus on papillary subtype-specific treatment, targeting Myc, Stat3, and Akt pathways. We compared gene expression differences after treatment.

overall_design: Tumor mice receiving vehicle- or drug-treatment for 21 days. Total RNA was collected. 3 for vehicle treatment. 3 for drug treatment.

first: Eran

middle: R

last: Andrechek


title: Gene expression analysis of cancer-associated fibroblasts (CAFs) from the murine breast cancer model MMTV-PyMT after perturbing the expression of Dickkopf-3 (DKK3)

city: London

first: Fernando

last: Calvo

state: London

address: 237 Fulham Road

department: Cancer Biology

country: United Kingdom

institute: The Institute of Cancer Research

summary: Immortalized (hpv-E6) murine fibroblasts isolated from normal mammary glands and carcinoma stages (CAFs) from the MMTV-PyMT model (FVB/N background) were used in this analysis. CAFs were transfected with two independent RNAi targeting Dickkopf-3 (DKK3) or control RNAi and changes in whole-genome gene expression were evaluated by microarray. In addition, the effect of stable ectopic expression of DKK3 in normal fibroblasts (which normally do not express DKK3) was also evaluated. Analysis demonstrated the role of DKK3 in controlling specific transcriptional programs in CAFs.

overall_design: CAFs were seeded in subconfluency and transfected with control (siCtr) or two independent RNAi targeting DKK3 (siDKK3#2 and siDKK3#3) on duplicate. Normal fibroblasts (NFs) ectopically expressing empty vector (null) or DKK3 were also seeded in subconfluency (duplicates). After 48 h, total RNA was isolated and processed for gene expression analyses as suggested by the manufacturer. Standard expression analysis data (SST-RMA) was used for the analysis.

first: N

last: Ferrari

first: F


title: Epigenomics of Glycine max

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Cytosine methylation is a base modification that is often used by genomes to store information that is stably inherited through mitotic cell divisions. Most cytosine DNA methylation is stable throughout different cell types or by exposure to different environmental conditions in plant genomes. Here, we profile the epigenomes of ~100 Glycine max lines to explore the extent of natural epigenomic variation. We also use these data to determine the extent to which DNA methylation variants are linked to genetic variations.

overall_design: 100 MethylC-seq, 102 RNA-seq, 102 small RNA-seq of Glycine max.

first: Scott

last: Jackson


title: Trancriptional profiling of rat bladder after daily administration of Pioglitazone and Rosiglitazone in vivo (mRNA)

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

summary: The purpose of the study was to investigate the nongenotoxic carcinogenic effect of Pioglitazone. Pioglitazone is a PPARgamma agonist and is known to cause bladder tumours in male rats and an increase in the incidence of bladder cancer in humans has been observed in patients treated with Pioglitazone.  Pioglitazone is not considered genotoxic or carcinogenic in mice and tumours are only observed in male rats suggesting a nongenotoxic mechanism of tumorigenesis. A suggested hypothesis is urinary calculi formation and subsequent irritation, hyperplasia and metaplasia. Rosiglitazone was used as reference compound as this PPARgamma agonist does not cause changes in the bladder but cause lipoma/liposarcoma in rats.

overall_design: Sprague-Dawley rats were dosed for 3 time periods: 3, 28 or 90 days. The animals (10/sex/group) were dosed orally with vehicle (0.5 % methylcellulose), Pioglitazone (16 and 63 mg/kg/day)) or Rosiglitazone (10 mg/kg/day). Bladder urothelium was isolated from 5 animals/sex/group and further processed for transcriptional profiling.

first: Michael

last: Römer

first: Nina

last: Ostenfeldt

first: Dorthe

middle: B

last: Toft

first: Karen

last: Wegener

first: Tulipan

last: Zollinger

first: Remi

last: Terranova

first: Joanne

last: Quinney

first: Cliff

last: Elcombe


title: Trancriptional profiling of rat bladder after daily administration of Pioglitazone and Rosiglitazone in vivo (miRNA)

overall_design: Sprague-Dawley rats were dosed for 3 time periods: 3, 28 or 90 days. The animals (10/sex/group) were dosed orally with vehicle (0.5 % methylcellulose), Pioglitazone (13 and 63 mg/kg/day) or Rosiglitazone (10 mg/kg/day). Bladder urothelium was isolated from 5 animals/sex/group and further processed for transcriptional profiling.


title: Gene expression signatures for specific Akt inhibitor afuresertib treatment in malignant pleural mesothelioma (MPM) cell lines

status: Public on May 03 2018

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

institute: Kinjo Gakuin University

summary: To investigate the effect of afuresertib on gene expression, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to suppress the cell proliferation of MPM cell lines.  MSTO-211H and ACC-MESO-4 cells were treated with afuresertib (10 μmol/L) for 24 h in vitro.

overall_design: MSTO-211H and ACC-MESO-4 cells were treated with afuresertib for 24 h in vitro.

first: Md

last: Wahiduzzaman


title: Paternal TCDD Exposure Alters the Placental Epigenome

city: Nashville

first: Kaylon

last: Bruner-Tran

state: TN

address: 1161 21st Avenue South

institute: Vanderbilt University Medical Center

type: Methylation profiling by genome tiling array

summary: Preterm birth (PTB), spontaneous parturition prior to 37 weeks gestation, is the leading cause of neonatal mortality.  We previously demonstrated that developmental exposure of male mice (F1 animals) to the environmental endocrine disruptor 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) was associated with reduced sperm quantity/quality in adulthood and their control mating partners frequently delivered preterm.   Reproductive defects persisted in the F2 and F3 descendants and mating partners also exhibited an enhanced risk of spontaneous PTB.  Reproductive changes in the F3 males, the first generation without direct TCDD exposure, suggest epigenetic alterations occurred in the male germline.  Importantly, the sperm epigenome impacts development of the placenta, a tissue which is known to influence the timing of parturition. Therefore, we conducted an epigenetic microarray analysis of control and F1 male derived placentae obtained on E18.5 of pregnancy.

overall_design: DNA from 3 control placentae was compared to 5 placentae from females mated to F1 males.  Each placenta was from a different pregnancy.  Decidua was removed.

middle: L

first: Tianbing

last: Ding


title: Expression data from 10 DPA fibers

city: anyang

first: Man

last: Wu

state: henan

address: huanghe street

institute: CAAS

summary:
Upland cotton (Gossypium hirsutum L.) is the most important fiber crop, and its lint yield improvement is impeded due to its narrow genetic base and the lack of understanding of the genetic basis of yield.  Backcross inbred lines (BILs) or near-isogenic lines (NILs) in the same genetic background differing in lint yield, developed through advanced backcrossing, provide an important genomic resource to study the molecular genetic basis of lint yield.
We used a microarray-based comparative transcriptome analysis on developing fibers at 10 days post-anthesis (DPA) between a high-yield (HY) group and a low-yield (LY) group each with three BILs were selected from a BIL population between G. hirsutum and G. barbadense, and identified differentially expressed genes (DEGs) during this process.

sample_organism:
Gossypium barbadense
Gossypium hirsutum

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Fibers were selected at rapidly elongation stages of fiber development for RNA extraction and hybridization on Affymetrix microarrays. A high-yield (HY) group and a low-yield (LY) group each with three BILs were selected from a BIL population between G. hirsutum and G. barbadense. We identified a number of yield and yield component QTL- co-localizing DEGs and developed several DEG-based SSCP-SNP markers for the traits, thereby providing a set of candidate genes for molecular breeding and the genetic manipulation of lint yield in cotton. Three BILs (i.e., NMGA-026, NMGA-017 and NMGA-144, designated HY1, HY2, and HY3, respectively) were high-yielding (HY); and three other BILs (i.e., NMGA-066, NMGA-095 and NMGA-023, designated LY1, LY2 and LY3, respectively) were low-yielding (LY).

first: Jinfa

last: Zhang

first: Shuxun

last: Yu


title: Affymetrix SNP array data for Cryptomeria japonica samples [Axiom_Cj70K_v2]

city: Hitachi

first: Kentaro

last: Mishima

state: Ibaraki

address: 3809-1 Juochoishi

department: Breeding Department

institute: Forest Tree Breeding Center

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Japanese cedar (Cryptomeria japonica) is an allogamous coniferous species that relies on wind-mediated pollen and seed dispersal, and it is one of the most important forestry tree species in Japan. For accelerating breeding, we collected massive SNPs based on ESTs from several organs using NGS, and thus carried out QTL, GWAS and GS based on high-density linkage maps.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on SNPs based on EST from several organ and several sample.
Affymetrix 70K arrays Cj 70k_v2 was performed for 478 individuals.


title: Effect of Wakame Containing Diets on Hepatic Gene Expressions in Rat

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: Wakame is an edible seaweed that is a common constituent in the Japanese diet. Previous studies showed that wakame consumption is associated with prevention of metabolic syndrome; however, the molecular mechanisms of this protective effect are poorly understood. To determine if the expression of hepatic genes is affected by the ingestion of brown seaweed, Undaria pinnatifida (wakame), rats were fed diets containing 0, 0.1, or 1.0 g/100 g dried wakame powder for 28 days. Administration of 1% wakame significantly decreased total serum total cholesterol levels. Hepatic gene expression was investigated using DNA microarray analysis. Microarray analysis showed that wakame suppresses the lipogenic pathway by downregulating SREBF-1. Moreover, bile acid biosynthesis and gluconeogenesis are promoted by upregulation of the PPAR signaling pathway, which leads to a reduction in the accumulation of cholesterol and promotion of β-oxidation. These results provide useful genetic information about various biochemical processes by which wakame regulates energy metabolism.

overall_design: Male Sprague Dawley (SD) rats aged 4 weeks were housed in a temperature-controlled room with a 12-h light-dark cycle (lights on at 08:00 and off at 20:00). Animals were allowed free access to drinking water and were fed a diet prepared according to the recommendations of the American Institute of Nutrition (AIN-93G). After acclimatization to the environment and to investigators for 1 week, rats were fed purified experimental diets. Rats were divided into three groups (n = 6, 3 rats/cage) and fed one of the following synthetic diets: control diet containing 7% fat, 20% casein, 52.9% corn starch, 5% cellulose, 1% vitamins, 3.5% minerals, or wakame diet, consisting of the control diet supplemented with the indicated amount of wakame powder. Animals were fed these diets for 28 days. Food intake was measured every 2–3 days on a per-cage basis. On the final day of the experiment, livers were excised from each animal and submerged in RNALater (Life Technologies, Carlsbad, CA, USA) overnight at 4°C and then stored at -80 °C until RNA isolation. Total RNA was used for microarray analysis.  All animal experiments were approved by the Animal Care Committee of Oriental Yeast Co., Ltd. and followed the Committee Guidelines for the Care and Use of Laboratory Animals (11009).

first: Keiko

last: Yoshinaga

first: Hikari

last: Izumi

first: Kaz

last: Nagaosa

first: Tomoko

last: Ishijima

first: Takahisa

last: Nakano

last: Abe


title: Transcriptomic studies in the development and ripening of strawberry fruits

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

country: Spain

institute: University of Cordoba

summary: Strawberry is an ideal model for studying the molecular biology of the development and ripening of non-climacteric fruits. By using a custom-made and high quality oligo microarray platform done with over 32000 probes including all of the genes actually described in the strawberry genome, we have analyzed the expression of genes during the development and ripening in the receptacles of these fruits.

overall_design: A custom-made oligo microarray (60-mer length) platform (FraGenomics 35k) containing a total of 35234 singletons corresponding to those sequences published in the strawberry genome project (http://www.strawberry.org). For each sequence, 4 different oligos were printed per block and four blocks were printed per data set. We have analyzed three control samples green fruits, a three samples red fruits.

first: Juan

last: Muñoz-Blanco

first: Laura

last: Medina-Puche

first: Antonio

last: Rodríguez-Franco

first: Rosario

last: Blanco-Portales


title: Affymetrix SNP array data for Cryptomeria japonica samples [Axiom_Cj70K_v1]

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on SNPs based on EST from several organ and several sample.
Affymetrix 70K arrays Cj 70k_v1 was performed for 473 individuals.


title: Global transcriptional responses to a long-term treatment of bile salts in Bifidobacterium longum BBMN68

status: Public on May 04 2018

city: BeiJing

first: Xiong

last: Yao

address: No. 17, Tsinghua East Road, Haidian District

institute: China Agriculture University

summary:
Purpose：Bifidobacteria are common inhabitants of the human gastrointestinal tract. In order to colonize in the gut, it is important to adapt to the physiological concentrations of bile salts. The global response to bile in B. longum BBMN68, isolated from a healthy centenarian in the Bama County of the Guangxi Zhuang Autonomous Region in China, has been investigated through RNA-seq transcriptomics sequencing in our previous work. However, a long-term bile salts treatment is more suitable to simulate the human gastrointestinal tract environment. The goals of this study are to invstigated the global response to a long-term treatment of bile salts in B. longum BBMN68.
Methods: Samples from BBMN68 cultured with or without 0.75 g liter-1 ox-bile for 24 hours were sequenced on an  Illumina Hiseq platform. Three independent biological replicates were produced including 6 samples in total.
Results: Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 11-13 million total mapped reads per sample.

sample_organism: Bifidobacterium longum subsp. longum BBMN68

overall_design: mRNA from Bifidobacterium longum BBMN68, cultured in MRSc anaerobically at 37℃ with or without 0.075% oxgall for 24h, was sequnced  in triplicate, using Illumina Hiseq platform

first: Yanling

last: Hao


title: Affymetrix SNP array data for Cryptomeria japonica samples

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

overall_design: Refer to individual Series


title: Comparative Analysis of Irradiated and Unirradiated Pelophylax nigromaculatus Skin Transcriptome

city: Suzhou

first: Li

last: Zhong

state: Jiang Su

address: No.199 Renai Road,Industrial Park,

institute: Suzhou University

summary: The goal of this study was to compare the skin transcriptomes of non-irradiated and 30 Gy irradiated  Pelophylax nigromaculatus and to find the polypeptide sequences that were changed before and after irradiation. Skin mRNA profiles of  non-irradiated and 30Gy irradiated Pelophylax nigromaculatus were generated by deep sequencing,using Illumina HiSeq.The sequenced sequences were assembled into transcripts, and the transcripts were hierarchically clustered using the Corset program. Subsequent analysis was performed using the clustered sequences as references:CDS prediction, SNP and InDel analysis, gene expression level analysis, SSR analysis, RNA-seq overall quality assessment, differential expression analysis, differential gene GO enrichment analysis and KEGG enrichment analysis.Through differential analysis, 875 down-regulated mRNAs and 536 up-regulated mRNAs were identified, and 271 significant changes in peptides were found through the rank sum test, which provided the basis for the next study.

first: Shuyu

last: Zhang


title: Gene expression and alllele inheritence in xiphophorus spontaneous melanoma in backcross BC1 interspecies animals  in Xiphophorus maculatus Skin

status: Public on May 01 2018

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

summary: RNA-Seq of spontaneous melanoma in Xiphophorus interspecies hybrids, and paired normal skin samples from the same melanoma-bearing animals were performed.

sample_organism: Xiphophorus maculatus x Xiphophorus hellerii

overall_design: Gordan-Kosswig cross of X. maculatus-X. hellerii interspecies backcross were made. At age of 9 month, melanoma-bearing animals were identified and dissected. RNA from tumor/skin samples were isolated and sequenced for allelel inheritence analysis and overall gene expression profiling.

first: William

last: Boswell

first: Markita

last: Savage

first: Mikki

first: Ronald

last: Walter


title: Expression data from rat insulinoma INS-1 cells under glucotoxic condition

city: Miki-cho

first: Yasunori

last: Sugiyama

state: kagawa

address: ikenobe 2393

department: Department of Life Science

institute: Kagawa University

summary:
Glucotoxicity of INS-1 cells stimulation by chronic high glucose.
We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of up and down-regulated genes during this process.

overall_design: INS-1 cells cultured with chronic high glucose for RNA extraction and hybridization on Affymetrix microarrays.


title: Acute HSF1 depletion induces cellular senescence through activation of the MDM2-p53-p21 pathway in human diploid fibroblasts

city: Maebashi

first: Tsukasa

last: Oda

state: Gunma

address: Showa-machi, 3-39-15

department: IMCR

institute: Gunma University

summary: Heat shock transcription factor 1 (HSF1) regulates the expression of a wide array of genes, controlling expression of heat shock proteins (HSPs) and cell growth. Although acute depletion of HSF1 induces cellular senescence, the underlying mechanisms are poorly understood. Here, we report that HSF1 depletion-induced senescence (HDIS) of human diploid fibroblasts (HDFs) was independent of HSP-mediated proteostasis, but dependent on activation of the p53-p21 pathway, partly because of increased expression of dehydrogenase/reductase 2 (DHRS2), a putative MDM2 inhibitor. We observed that HDIS occurred without decreased levels of major HSPs or increased proteotoxic stress in HDFs. Additionally, an inhibitor of HSP70 family proteins increased proteotoxicity and suppressed cell growth, but failed to induce senescence. Importantly, we found that activation of the p53-p21 pathway due to reduced MDM2-dependent p53 degradation was required for HDIS. Furthermore, we provide evidence that increased DHRS2 expression contribute to p53 stabilization and HDIS. Collectively, our observations uncovered a molecular pathway in which HSF1 depletion-induced DHRS2 expression leads to activation of the MDM2-p53-p21 pathway required for HDIS.

overall_design: hTERT-immortalized human fibroblasts expressing doxycycline-inducible shRNA targeting HSF1 were treated with DOX for 0, 1, 3, 7 days and gene expression was measured.

first: Takayuki

last: Yamashita


title: Transcriptome of Acacia cornigera extrafloral nectaries

status: Public on May 02 2018

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

summary: Nectaries are the glands responsible for nectar secretion. In the tree Acacia cornigera, extrafloral nectaries produce nectar primarily consumed by mutualistic ant colonies.  To understand the genetic programming underlying nectar production, and in particular the connection of the jasmonic acid pathway with the mutualistic ants, extrafloral nectaries tissue was collected at ten time points and conditions, with RNA being isolated and subjected to Illumina RNA-seq analysis.

overall_design: Samples from Acacia cornigera extrafloral nectaries were taken in May, 2014, in Puerto Escondido, Oaxaca, Mexico, and stored in liquid nitrogen before further processing.  The first six sample types are from different times of day (9am, noon, 2pm, 3pm, and 8am), the last four sample types are under different conditions perturbing the condition of mutualistic ant colonies (Pseudomyrmex ferrugineus).  Samples were in triplicate but not all replicates passed quality control steps.  Exfloral nectaries were pooled in RNAlater™ solution (Ambion, Austin, TX) on ice, and stored at 4°C prior to RNA extraction. Each biological replicate was represented by nectaries pooled from different individual plants. RNA was extracted from nectaries by mechanical disruption, with a microcentrifuge pestle, and using the RNAqueous®-Micro scale RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for barcoded library creation and Illumina HiSeq 2500 sequencing. Twenty-four TruSeq RNA v2 libraries were created and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. Pooled libraries generated over 800 M reads and the average quality scores were above Q30.

first: Clay

last: Carter

first: Martin

last: Heil


title: miRNAs associated with ALG-1 and ALG-2 in adult C. elegans

city: La Jolla

first: Amy

last: Pasquinelli

state: CA

address: 9500 Gilman Drive

department: Biological Sciences

institute: University of California, San Diego

summary: Investigated the specific miRNAs that are assocaited with ALG-1 and ALG-2 in adult (D5) C. elegans. ALG-1 and ALG-2 were IP-ed from D5 collected C.elegans, RNA was isolated and used for small RNA sequencing. Two biological replicates were used.

overall_design: Examined the miRNAs associated with ALG-1 and ALG-2 in D5 by immunoprecipitation and small RNA sequencing

first: Laura

last: Chipman

first: A

middle: E


title: Genome-wide identification and characterization of novel lncRNAs in Ginkgo biloba leaves

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: To explore the overall long noncoding RNA (lncRNA) involved in major developmental stages of Ginkgo biloba leaves , we deeply sequenced samples of leaves from different developmental stages (from April to October) using strand-specific RNA sequencing (ssRNA-seq) menthod. We obtained 27.44 Gb raw data and identified 1323 novel lncRNAs. We also categorized the novel lncRNAs as intergenic, intronic, antisense and sense based on their location on theGinkgo biloba genome. Furthermore, lncRNAs targeted protein-coding genes were predicted and functional annotated. In addition, we constructed a network of interactions between ncRNAs (miRNAs, lncRNA) and mRNAs. Our results suggest that the identified novel lncRNAs are important in modulating development process of Ginkgo biloba, and provide a rich resource for further research on the function of these novel lncRNAs.

overall_design: seven developmental stages of  leaves

last: Wang


title: Toxic effects and foundation of proton radiation on the early-life stage of zebrafish development

city: Beijing

first: Baoquan

last: Zhao

address: Taiping road,27

institute: Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences

summary:
Zebrafish is an ideal model for the toxicity studies on medicines and environmental genetic toxicants.Different development defects were observed in zebrafish embryos exposed to -ray and heavy ion (carbon or iron) irradiation
We used microarrays to detail the gene expression situation after radiation.

overall_design: Proton beam irradiation was carried out at the terminal of the heavy ion accelerator facility at Peking University. The proton beam energy was 8 MeV/u, and the dose rate was 7.5 Gy/min.To detect the gene expression, three experimental groups were established as follows: zebrafish embryos collected from wild type breeding pairs, pooled, and allowed to develop for 24 h. One group of, 60 embryos was withdrawn to serve as the non-irradiated control (CK). To investigate the radiation response, two other groups of, 60 embryos each were withdrawn and irradiated with 12 (IR1) or 15 Gy (IR2) of protons. Embryos in all three groups were then allowed to grow and develop at 28.5 ◦C using standard maintenance protocols.

first: Xiaoman

last: Li

first: Xiaodan

last: Zha


title: Evaluation of gene expression changes in tcs08 single and double mutants in the pneumococcal strain TIGR4

city: Greifswald

first: Sven

last: Hammerschmidt

state: MV

address: Felix-Hausdorff-Str. 8

department: Molecular Genetics and Infection Biology

country: Germany

institute: University of Greifswald

summary: In order to elucidate the regulatory role of pneumococcal TCS08, a transcriptomic approach was performed using microarray from bacterial cultures in chemical defined medium of single and double tcs08 mutants. A total of 159 genes presenting significant expression changes were selected for further evaluation and discussion. These 159 genes were classified accordingly to their biochemical function.

overall_design: response regulator 08, histidine kinase 08 and a rr08-hk08 mutants were generated in a pneumococcal TIGR4 background. Each individual mutant strain and its wild-type were cultivated in chemically defined medium until early-log phase and collected for RNA isolation in triplicate

first: Alejandro

last: Gómez-Mejia

first: Gustavo

last: Gámez

first: Stephanie

last: Hirschmann

first: Viktor

last: Kluger

first: Hermann

last: Rath

first: Sebastian

last: Böhm

first: Franziska

last: Voss

first: Niamatullah

last: Kakar

first: Lothar

last: Petruschka

first: Gerhard

last: Burchhardt

first: Birgit

last: Rietow

first: Uwe

last: Völker

first: Reinhold

last: Brückner

first: Ulrike

last: Mäder


title: Gene expression from the whole blood of rheumatoid arthritis patients and normal controls.

city: Cambridge

first: Ty

last: Thomson

state: MA

address: 1 Alewife Center

institute: Selventa

summary: 21 samples were collected from 15 RA and control patients with matched microarray and RNA-seq data.  The data was collected to examine the effects of RNA-seq data normalization, read number, and the use of gene sets with the aim of determining the effect of these factors on correlation to microarrays and predictive performance of multivariate models.  DAS28 scores are provided for RA patients.

overall_design: 21 samples were collected from 15 people, 10 rhuetmoid arthritis (RA) patients and 5 normal controls.  6 biological replicates were taken from the RA patients.

first: Reynald

last: Lescarbeau


title: Gene expression data from kidney and liver of systemic Iah1-knockout mouse

city: Nagoya

first: Misato

last: Kobayashi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University


title: Transcriptome of mouse thymic and thyroid epithelial cells

city: Freiburg

first: Ana

last: Izcue

address: Am Stübeweg 51

institute: Max Planck Institut of Immunobiology and Epigenetics

summary: We have compared the transcriptional profiles from two epithelial cell types to find genes specifically expressed in thymic medullary epithelial cells. Epithelial cells from thyroid and thymic medulla from C57BL/6 mice were sorted and their transcriptional profiles compared. Cells were gated as viable, Epcam+ CD45- for thyroid and viable, Epcam+ CD45- UEA+ for thymic medulla.

overall_design: Overall design: Three independent replicates were analysed per group. For Thyroid epithelial cells: 20 thyroids per replicate were minced in RPMI and digested with collagenase and DNAse. Supernatants were stained with Epcam and CD45 for FACSsort; Fluorogold was used to exclude dead cells. Thymic epithelial cells: thymi were minced, digested with collagenase, dispase and DNAse. Supernatants were stained with Epcam, CD45 and UEA for FACSsort; Fluorogold was used to exclude dead cells. Replicates 1 and 2 were from 6 pooled thymi each; replicate 3 was from 2 pooled thymi.

first: Maria

last: Brack


title: Development of molecular markers linked to powdery mildew resistance gene Pm4b by combining SNP discovery from transcriptome sequencing data with bulked segretant analysis (BSR-seq) in wheat

first: pei

middle: pei

last: WU

address: Zhongguancun South Street

institute: Chinese Academy of Agricultural Sciences

type: Genome variation profiling by high throughput sequencing

summary: Powdery mildew resistance gene Pm4b, originating from Triticum perscicum, is effective against the prevalent Blumeria graminis f. sp. tritici (Bgt) isolates from certain regions of wheat production in China. The lack of tightly linked molecular markers with the target gene prevents the precise identification of Pm4b during the application of molecular marker-assisted selection (MAS). The strategy that combines the RNA-seq technique and the bulked segregant analysis (BSR-seq) was applied in an F2:3 mapping population (237 families) derived from a pair of isogenic lines VPM1/7*Bainong 3217 F4 (carrying Pm4b) and Bainong 3217 to develop more closely linked molecular markers. RNA-seq analysis of the two phenotypically contrasting RNA bulks prepared from the representative F2:3 families generated 20,745,939 and 25,867,480 high-quality read pairs, and 82.8% and 80.2% of them were uniquely mapped to the wheat whole genome draft assembly for the resistant and susceptible RNA bulks, respectively. Variant calling identified 283,866 raw single nucleotide polymorphisms (SNPs) and InDels between the two bulks. The SNPs that were closely associated with the powdery mildew resistance were concentrated on chromosome 2AL. Among the 84 variants that were potentially associated with the disease resistance trait, forty-six variants were enriched in an about 25 Mb region at the distal end of chromosome arm 2AL. Four Pm4b-linked SNP markers were developed from these variants. Based on the sequences of Chinese Spring where these polymorphic SNPs were located, 98 SSR primer pairs were designed to develop distal markers flanking the Pm4b gene. Three markers, Xics13, Xics43 and Xics76, were incorporated in the new genetic linkage map, which located Pm4b in a 3.0 cM genetic interval spanning a 6.7 Mb physical genomic region. This region had a co-linear relationship with Brachypodium distachyum chromosome 5, rice chromosome 4, and sorghum chromosome 6. Seven genes associated with disease resistance were predicted in this collinear genomic region, which included protein kinases of PKc_like super family, C2 domain protein, peroxidase activity protein, Mlo family protein, and catalytic domain of the serine/threonine kinases (PKc_like super family). The markers developed in the present study facilitate identification of Pm4b during its MAS practice.

overall_design: Development linked markers of Pm4b

first: Peipei

last: Wu

first: Hongjie

last: Li


title: A stromal niche regulate CSCs in Wnt-Met mammary gland tumors

status: Public on Apr 23 2018

city: Berlin

first: Giovanni

last: Valenti

address: Robert-Roessle-Strasse 10

department: Cancer

institute: Max Delbrueck Center for Molecular Medicine

summary:
CSCs may be regulated by extrinsic signals provided by specialized microenvironments, or niches, which sustain CSC expansion.
We investigated the role of cancer associated fibroblasts (CAFs) in the regulation of CSCs using a genetically engineered mouse model of basal-like breast cancer driven by combined activation of Wnt/β-catenin and HGF/Met signaling (Wnt-Met mice). We found that CAFs secrete soluble factors that promote the expansion of the population of self-renewing cells that generate mammospheres and enhance the capacity of CSCs to form invasive 3D structures. Using transcriptional profiling, we identified a network of paracrine interactions between CAFs and CSCs that regulate reciprocal functions.

overall_design: We sorted CAFs, CSCs and TECs from Wnt-Met mammary gland tumors and fibroblasts from control mammary glands (COFs). We performed microarray analysis on RNA samples isolated from sorted cells to evaluate gene differentially expressed between CAFs and COFs, CSCs and TECs, and potential interactions that CAFs and CSCs establish in Wnt-Met mammary gland tumors

first: Walter

last: Birchmeier


title: Phenotypic analysis of conventional knockout mice lacking a protein responsible for ossification of the posterior longitudinal ligament

city: Kurume

first: Michiyo

last: Tsuru

state: Fukuoka

address: 67 Asahimachi

department: Orthopardic Surgery

institute: Kurume Universuty

summary:
We found disease-specific proteins from serum proteomics of ossification of posterior longitudinal ligament, and made knockout mice.
We discovered protein peculiar to a disease in serum of the ossification of posterior longitudinal ligament  (OPLL), and, as a result of producing knockout mouse, we checked spinal ligament ossification and combination of diabetes and thought that it was a typical mouse and analyzed the sequence of the kidney organization.

overall_design: Proteomics analysis carried out OPLL of the wild mouse that the ossification of the ligament was confirmed when glucose and urine glucose showed a mouse to the high value from a knockout

first: Kensei

last: Nagata


title: Prognostic and predictive value of a microRNA signature in adults with T-cell lymphoblastic lymphoma

status: Public on Apr 30 2018

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: microRNA profiling of  T-cell lymphoblastic lymphoma vs fetal thymus

overall_design: MicroRNA profiles of 75 tissue samples from 75 adults with T-cell lymphoblastic lymphoma in CR1 compared with 20 fetal thymus samples from 20 fetuses autopsied

first: Q

last: Cai

first: D

last: Xie

first: H

last: Wang


title: Comparison of ectopic gene expression in Cdx1+/+ and Cdx1-/- thymic medullary epithelial cells

summary: We have found that Cdx1 can promote ectopic gene expression in thymic epithelial cells. We isolated MHCIIhi CD80hi medullary thymic epithelial cells from Cdx1-/- and Cdx1+/+ and compare gene expression between the two subsets, also in the context of Cdx1-mediated changes in intestinal epithelial cells.

overall_design: Three independent replicates were analysed per group. For thymic epithelial cells: thymi were minced, digested with collagenase, dispase and DNAse. Supernatants were stained  with anti-Epcam, anti-CD45, UEA1, CD80 and MHCII for FACSsort; Fluorogold was used to exclude dead cells. Replicates were pooled from material from 4-6 thymi. For small intestine, cells from 3 mice were pooled per replicate.

first: Philipp

last: Rauf


title: Microarray data of Spred1 WT and KO hematopoietic stem/progenitor cells

status: Public on Apr 26 2018

city: Kanazawa

first: Yuko

last: Tadokoro

address: Kakuma

department: Cancer Research Institute

institute: Kanazawa University

summary: To comprehensively investigate differences of gene expression patterns between Spred1 WT and KO HSCs/progenitors, we isolated HSCs/progenitor cells and performed the microarray analysis.

overall_design: Spred1 WT and KO CD48-KSL (CD48-/c-Kit+/Sca-1+/Lineage marker-) cells were sorted using cell sorter. Total RNA of the sorted cells was isolated and we performed the microarray analysis.

first: Atsushi

last: Hirao


title: The dynamics of gene expression in vertebrate embryogenesis at single cell resolution

status: Public on Apr 28 2018

city: Boston

first: James

middle: Alexander

last: Briggs

state: Massachusetts

address: 200 Longwood Avenue, Harvard Medical School

department: Department of Systems Biology

institute: Harvard Medical School

summary: Time series of single cell transcriptome measurements can reveal dynamic features of cell differentiation pathways. From measurements of whole frog embryos spanning zygotic genome activation through early organogenesis we derived a detailed catalog of cell states in vertebrate development and a map of differentiation across all lineages over time. The inferred map recapitulates most if not all developmental relationships, and associates new regulators and marker genes with each cell state. We find that many embryonic cell states appear earlier than previously appreciated. We also assess conflicting models of neural crest development. Incorporating a matched time series of zebrafish development from a companion paper, we reveal conserved and divergent features of vertebrate early developmental gene expression programs.

overall_design: 136,966 single cell transcriptomes were profiled from whole Xenopus tropicalis embryos at ten timepoints during the first 24 hours of its embryonic development. The data includes 75 total single cell RNA sequencing libraries, collected in 2 replicate timeseries. 4 of the 75 libraries focussed on dissected neural plate border tissue. The counts data for all pass filter cells are available in a single matrix (see "Corrected_combined.annotated_counts.tsv.gz" and "Raw_combined.annotated_counts.tsv.gz"). Alternatively, raw FASTQ or unfiltered counts files are also available for each individual library.

first: Caleb

last: Weinreb

first: Daniel

last: Wagner

first: Sean

last: Megason

first: Leonid

last: Peshkin

first: Marc

middle: W

last: Kirschner

first: Allon

last: Klein


title: Gene expression analysis of SHH-activated immortalized cranial neural crest cells (O9-1)

city: Madison

first: Joshua

last: Everson

state: WI

address: 2015 Linden Drive, Rm 3217

department: Comparative Biosciences

institute: UW-Madison

summary: We sought to identify Hedgehog-regulated genes in mouse cranial neural crest cells (O9-1)

overall_design: Mouse cranial neural crest cells (O9-1) were allowed to attach for 24 hrs and media were replaced with DMEM containing 1% FBS ± SHH-N peptide at 0.4 μg/mL.  48 hrs after treatment, cells were lysed and RNA was collected per the GE Illustra RNAspin kits (GE Healthcare) general protocol for a cell monolayer.

first: Robert

last: Lipinski


title: Gene expression profiling of miR-183/96 knock out mouse cochlea

city: Downers Grove

first: Michael

last: Ebeid

state: IL

address: 555 31st St, Anatomy

department: Anatomy

institute: Midwestern University

summary:
Transcriptome analysis of P16 cochlea from wild type and miR-183/96 Knock out mice
Gene expression analysis of miR-183/96 KO cochlea revealed a set of hair cell-relevant differentially expressed genes that could adversely impact hair cell physiology and contribute to the observed phenotype.

overall_design: We analyzed cochleae from 4 wild type and 4 miR-183/96 KO mice using the Affymetrix mouse gene 2.0 ST platform. Array data was processed by Affymetrix Expression Console software.

first: Marsha

last: Pierce

first: Garrett

last: Soukup


title: Gene expression data from kidney of systemic Iah1-knockout mouse

first: Misato

last: Kobayashi

state: Aichi

summary:
SMXA-5 mouse shows a high-fat induced fatty liver. The QTL for fatty liver was mapped on mouse chromosome 12, designated as Fl1sa.
Iah1 gene is a candidate gene for Fl1sa. Kidney is the highest tissue of Iah1 gene expression in mouse.  We compared the kidney's gene expressions between Iah1-WT mouse and Iah1-KO mouse.

overall_design: Total RNA of male Iah1-WT mice and Iah1-KO mice fed a high-fat diet for 12 weeks were extracted from kidney of three mice. The RNAs form three mice were pooled and hybridized on one Affymetrix microarry.

first: Miyako

last: Suzuki

first: Junko

last: Tsujimura

first: Shinsaku

last: Kanamori

first: Atsuhi

last: Murai

first: Fumihiko

last: Horio


title: Antagonistic interactive effects of CO2 and nitrogen on microbial community enhance the persistence of soil C storage

first: Qun

last: Gao

state: Beijing

address: Shuang Qing Road

department: Environmental sicence and engineering

institute: Tsinghua University

summary: To study long-term elevated CO2 and enriched N deposition interactive effects on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. There exist antagonistic CO2×N interactions on microbial functional genes associated with C, N, P S cycling processes. More strong antagonistic CO2×N interactions are observed on C degradation genes than other genes. Remarkably antagonistic CO2×N interactions on soil microbial communities could enhance soil C accumulation.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Samples were collected under four different carbon dioxide and nitrogen treatment (aCaN,eCaN,aCeN and eCeN) in each of the four plant species richness levels:1, 4, 9, 16 ; In plots with 1 plant species, each treatment has 32 replicates ; In plots with 4 and 9 plant speices, each treatment has 15 replicates ; In plots with 16 plant species, each treatment has 12 replicates.

first: Yunfeng

last: Yang

first: Jizhong

last: Zhou


title: Gene expression data from liver of systemic Iah1-knockout mouse

summary:
SMXA-5 mouse shows a high-fat induced fatty liver. The QTL for fatty liver was mapped on mouse chromosome 12, designated as Fl1sa.
Iah1 gene is a candidate gene for Fl1sa. We compared the liver's gene expressions between Iah1-WT mouse and Iah1-KO mouse.

overall_design: Total RNA of male Iah1-WT mice and Iah1-KO mice fed a high-fat diet for 12 weeks were extracted from liver of three mice. The RNAs form three mice were pooled and hybridized on one Affymetrix microarry.


title: Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in Cryptosporidium baileyi infection

city: Yangling

first: Guan-jing

last: Ren

state: Shaanxi

address: NO.22 Xinong Road

department: College of Veterinary Medicine

institute: Northwest A&F University

summary: Background: Cryptosporidium baileyi is the most common Cryptosporidium species in birds. However, effective prevention measures and treatment for C. baileyi infection were less understood. Long non-coding RNA (lncRNA) and circular RNA (circRNA) were discovered to play an important role in regulating occurrence and progression of many diseases and identified as effective biomarkers for diagnosis and prognosis of several diseases. In the present study, the expression profiles of mRNA, lncRNA and circRNA associated with C. baileyi infection were investigated for the first time.  Results: The tracheal tissues of experimental (C. baileyi infection) and control chickens were collected for deep RNA sequencing, and 545,479,934 clean reads were obtained. Of them, 1376 novel lncRNAs were identified, including 1161 long intergenic non-coding RNAs (lincRNAs) and 215 anti-sense lncRNAs. 124 lncRNAs were found to be significantly differentially expressed between experimental and control groups. Additionally, 14,698 mRNAs and 9085 circRNAs were identified, and significantly different expressions were observed for 1317 mRNAs and 104 circRNAs between two groups. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of their targets and background genes suggested that these dysregulated genes would be involved in the interaction between host and C. baileyi.  Conclusions: The present study firstly provides the expression profiles of mRNAs, lncRNAs and circRNAs during C. baileyi infection, and describes a novel perspective on the potential roles of lncRNAs and circRNAs underlying the pathogenesis mechanism of Cryptosporidium infection.

overall_design: 3 control and 3 experimental chickens were analyzed

first: Guan

middle: j

first: Guang

middle: h

last: Zhao


title: Early-life exposure to genistein alters glucocorticoid signaling in the adult mouse uterus.

status: Public on Apr 10 2018

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Female mice treated on post-natal day 1-5 with corn-oil control or 50 mg/kg genistein were evaluated as adults for the uterine response to 1 mg/kg nM dexamethasone (or saline vehicle). Adult mice were adrenalectomized and ovariectomized 2 weeks prior to dexamethasone (or vehicle) treatment.

overall_design: Mice treated post-natal day 1-5 with 20ul corn-oil or 50 mg/kg genistein dissolved in corn-oil. Adults underwent adrenalectomy and ovariectomy at 6 weeks of age. At 8 weeks of age, mice received 100ul saline (vehicle) or 1 mg/kg dexamethasone dissolved in saline and tissues were harvested after 4hr.

first: Shannon

last: Whirledge

first: John

last: Cidlowski


title: Transcriptome of mouse epithelial cells

first: Ana

last: Izcue

summary: We have compared the transcriptional profiles from three epithelial cell types to find common and differentially expressed genes. Epithelial cells from small intestine and kidney from C57BL/6 mice were sorted and their transcriptional profiles compared. Cells were gated as viable, Epcam+ CD45- for kidney, and viable, Epcam+ CD45- MHCIIhigh for small intestine MHCIIhi and viable, Epcam int CD45- MHCII low for small intestine MHCIIlo.

overall_design: Three independent replicates were analysed per group. Kidney epithelial cells: kidneys were minced, digested with collagenase, dispase and DNAse. Supernatants were stained with Epcam and CD45 for FACSsort; Fluorogold was used to exclude dead cells. Small intestinal epithelial cells: small intestines were cut open, contents removed and minced. Fragments were washed and incubated with EDTA, and supernatants were stained with Epcam, CD45 and MHCII; Fluorogold was used to exclude dead cells. For small intestine, cells from 3 mice were pooled per replicate. For Kidney, cells from 4 mice were pooled per replicate.

first: Philipp

last: Rauf


title: Micro RNA Analysis of the Ossification of Posterior Longitudinal Ligament (OPLL).

first: Michiyo

last: Tsuru

summary: Proteomics analysis was conducted using sera from 31 OPLL patients and 17 healthy individuals, detecting a significantly defective protein in the former as compared with the latter. The continuous and mixed types of OPLL were compared, demonstrating a lower level of the protein in the former than the latter. Clinically, the continuous type, i.e., the ossification of the entire longitudinal ligament, was frequently detected in severe cases.

overall_design: The micro-RNA analysis of a healthy and a patient of OPLL of tissue and blood.

first: Kensei

last: Nagata


title: Prediction of Peripheral neuropathy in multiple myeloma patients receiving Bortezomib and Thalidomide: A Genetic Study based on Single Nucleotide Polymorphism Array

city: Salamanca

first: Maria

middle: Eugenia

last: Alonso

state: Salamanca

address: Paseo San Vicente, 88-182

department: Hematology

institute: Complejo Asistencial Universitario de Salamanca

summary: Bortezomib and thalidomide-based therapies have significantly contributed to improved survival of multiple myeloma (MM) patients. However, treatment-induced peripheral neuropathy (TiPN) is a common adverse event associated with them. Risk factors for TiPN in MM patients include advanced age, prior neuropathy, and other drugs, but there are conflicting results about the role of genetics in predicting the risk of TiPN. Thus, we carried out a genome-wide association study (GWAS) based on more than 300,000 exome single nucleotide polymorphisms (SNPs) in 172 MM patients receiving therapy involving bortezomib and thalidomide. We compared patients developing and not developing TiPN under similar treatment conditions (GEM05>65, NCT00443235). The highest-ranking SNP was rs45443101, located in the PLCG2 gene, but no significant differences were found after multiple comparison correction (adjusted p=0.1708).  Prediction analyses, cytoband enrichment and pathway analyses were also performed, but none yielded any significant findings. A copy number approach was also explored, but this gave no significant results either. In summary, our study did not find a consistent genetic component associated with TiPN under bortezomib and thalidomide therapy that could be used for prediction, which makes clinical judgment essential in the practical management of MM treatment

overall_design: Peripheral blood (PB) DNA samples were obtained from 172 MM patients recruited at the GEM05MAS65 clinical trial (NCT00443235). Samples were stored at two institutions: University Hospital of Salamanca (n=122) and Hospital 12 de Octubre of Madrid (n=50). Induction treatment was given according to the GEM2005MAS65 which compared Bortezomib/Melphalan/Prednisone (VMP) vs. Bortezomib/Thalidomide/Prednisone (VTP).

first: R

last: Garcia-Sanz

first: L

last: Corchete

first: M

last: Alcoceba

middle: C

last: Chillon

first: C

last: Jimenez

first: I

last: Prieto

last: Garcia-Alvarez

first: N

last: Puig

last: Rapado

first: S

last: Barrio

first: A

last: Oriol

last: Blanchard

first: J

last: De la Rubia

last: Martínez

last: Lahuerta

last: Gonzalez

middle: V

last: Mateos

middle: F

last: San Miguel

last: Martínez-López

last: Sarasquete


title: Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (GXE) on the berry transcriptome [array]

status: Public on Apr 09 2018

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

summary: Changes in the performance of genotypes in different environments are defined as genotype 3 environment (G3E) interactions. In grapevine (Vitis vinifera), complex interactions between different genotypes and climate, soil and farming practices yield unique berry qualities. However, the molecular basis of this phenomenon remains unclear. To dissect the basis of grapevine G3E interactions we characterized berry transcriptome plasticity, the genome methylation landscape and within-genotype allelic diversity in two genotypes cultivated in three different environments over two vintages. We identified, through a novel data-mining pipeline, genes with expression profiles that were: unaffected by genotype or environment, genotype-dependent but unaffected by the environment, environmentally-dependent regardless of genotype, and G3E-related. The G3E-related genes showed different degrees of within-cultivar allelic diversity in the two genotypes and were enriched for stress responses, signal transduction and secondary metabolism categories. Our study unraveled the mutual relationships between genotypic and environmental variables during G3E interaction in a woody perennial species, providing a reference model to explore how cultivated fruit crops respond to diverse environments. Also, the pivotal role of vineyard location in determining the performance of different varieties, by enhancing berry quality traits, was unraveled.

overall_design: Vitis vinifera berries from Sangiovese and Cabernet Sauvignon cultivars were harvested at four different developmental stages (i.e., pea size (PS), pre-veraison (PV), mid-ripening (MR) and fully ripe (FR)), in three central Italian locations (i.e., Bolgheri in the Tuscany coast, Montalcino in the Tuscany Appennines and Riccione in the Adriatic coast) (Fig. 1a, Supplementary Tables 1-2) during two consecutive growing seasons (2011 and 2012) in biological triplicates for a total of 144 samples.

first: Sara

last: Zenoni

first: Marco

last: Sandri

first: Gabriella

last: De Lorenzis

first: Gabriele

last: Magris

first: Emanuele

last: DePaoli

last: Di Gaspero

first: Cristian

last: Del Fabbro

first: Michele

last: Morgante

first: Lucio

last: Brancadoro

first: Mara

last: Rossoni

first: Marianna

last: Fasoli

first: Paola

last: Zuccolotto

first: Mario

last: Pezzotti


title: Single-cell RNA-seq of ASPM mutant ferret embryonic forebrain

status: Public on Apr 18 2018

city: New Haven

first: Byoung-Il

last: Bae

state: CT

address: Department of Neurosurgery, School of Medicine, Yale University

institute: Yale University

summary: As described in our paper "Aspm knockout ferret reveals an evolutionary mechanism governing cerebral cortical size" (Johnson et al., Nature 2018), we used the standard Drop-seq method and analysis of Macosko et al. (2015) to capture, sequence, and analyze mRNA from single cells from Aspm wild-type, heterozygous, and knock-out littermate ferrets at embryonic day 35. Bulk reference samples were processed using standard Illumina mRNA-seq library prep and sequencing protocols, and the samples were described previously (Johnson, Wang et al., Nature Neurosci 2015)

overall_design: Embryonic forebrain tissue was harvested and cryopreserved, then processed into single-cell suspension for Drop-seq after genotyping. An equal number of KO and WT/Het littermates from two litters were sequenced in three runs, with genotypes and litters balanced across runs to minimize batch effects.

first: Matthew

last: Johnson


title: Gene Amplification Associated Overexpression of the RNA Editing Enzyme ADAR1 Enhances Human Lung Tumorigenesis

status: Public on Apr 08 2018

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

institute: IDIBELL

summary: The introduction of new therapies against particular genetic mutations in non-small cell lung cancer is a promising avenue for improving the survival of these patients, but the target population is small. There is a need to uncover new potential actionable genetic lesions and non-conventional cancer pathways, such as RNA editing, are worthy to explore. Herein we show that the adenosine-to-inosine editing enzyme ADAR1 undergoes gene amplification in non-small cancer cell lines and primary tumors in association with higher levels of the corresponding mRNA and protein. From a growth and invasion standpoint, the depletion of ADAR1 expression in amplified cells reduces their tumorigenic potential in cell culture and mice models, whereas its overexpression causes the opposite effects. From a functional perspective, ADAR1 overexpression enhances the editing frequencies of target transcripts such as NEIL1 and miR-381. In the clinical setting, patients with early stage lung cancer, but harboring ADAR1 gene amplification, show poor outcome.  Overall, our results indicate a role for ADAR1 as a lung cancer oncogene undergoing gene amplification-associated activation that affect downstream RNA editing patterns and patient prognosis.

overall_design: 5 Cell lines were hybridized on the Infinium Human Omni5 Beadarray.

first: Carmen

last: Anadón

first: Manel

last: Esteller


status: Public on Apr 04 2018

city: Istanbul

first: Esra

last: Yucel

state: Topkapı

address: Davutpasa Cd. No:4

department: Diagnosis Centre For Genetic Disorders

country: Turkey

institute: Koc University Hospital

summary: Clinical findings of this case has been reported previously by Sergio de Sousa (American Journal of Medical Genetics Part A 146A:2799–2803 (2008)).  RSPO2 gene has been identified by our group (İstanbul, Turkey, 2014) as responsible gene for Tetra-Amelia with lung aplasia phenotype.  To find causative pathogenic variations,  sanger sequencing of fetal DNA was performed and did not reveal any variations.  300K SNP array was performed to analyse possible CNVs.  A homozygous 154kb deletion on chr8 (deletion break points:108,809,266-108,963,256) covering intron 5 (partial), exon 6 and 3'UTR (partial) of RSPO2 gene was identified as the causative deletion.

overall_design: Genomic DNA extracted from AF culture cells was scanned according to the array barcodes and  Infinium HumanCytoSNP-12 v2.1 BeadChips datasheets (Illumina).  Data was analysed with GenomeStudio  Software (Illumina)

first: Umut

last: Altunoglu

first: Hulya

last: Kayserili


title: Expression data from differentiating equine satellite cells (ESC) culture incubated with HMB and exposed to hydrogen peroxide

status: Public on Apr 03 2018

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

summary: Transcriptional profiling of HMB-treated (24h) differentiating equine satellite cells (3rd day of differentiation) exposed to hydrogen peroxide (1h; last hour of pre-incubation with HMB) compared to control HMB-untreated cells. Goal was to determine the effects of HMB pre-incubation on gene expression in equine satellite cells exposed to hydrogen peroxide.

overall_design: Two-condition experiment, HMB-treated (24h) differentiating equine satellite cells and exposed to hydrogen peroxide (1h during 24h pre-incubation with HMB) (3rd day of differentiation) vs. differentiating equine satellite cells without HMB treatment (control). Biological replicates: 4 reps of examined condition , 4 control replicates

first: Anna

last: Ciecierska

first: Karolina

last: Chodkowska


title: Wound healing process after ventricular resection in zebrafish: time course (zebrafish)

status: Public on Apr 02 2018

city: Hsinchu

first: Yung-Jen

last: Chuang

state: Taiwan

address: No. 101, Sec. 2, Kuang Fu Road

department: Department of Medical Science

country: Taiwan

institute: National Tsing Hua University

summary: The mechanism of cardiomyocyte prliferation and migration after ventricular resection is a complex and dynamic process. To resolve this, we chose the zebrafish model organism for studying post-injury heart regeneration and wound healing progress via systems biology approach. Transcriptome microarray data and histological analysis of injured fish were sampled at different time points during recovery process. Time-course microarray data following wound healing of zebrafish were obatined. From this set of data, we constructed two intracellular protein–protein interaction (PPI) networks to provide insights into the ventricular resection wound healing mechanism.

overall_design: Each fish in each group was injured by ventricular resection from day 0 to 28, respectively. These injured fish were collected at 0, 0.25, 1, 3, 6, 10, 15, 21, 28 dpi (day post injury).  0.625μg of Cy3 cRNA for C. albicans array and 1.65 μg of Cy3 cRNA for zebrafish array was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Each time points contain two biological repeats.

first: Che

last: Lin

first: Bor-Sen

last: Chen

first: Wen-Ping

last: Hsieh

first: David

middle: H

last: Wong


title: Expression data from healthy murine bronchial epithelial cells and syngeneic murine lung squamous carcinoma (LUSC) from DBA2 mice.

city: Chapel Hill

first: Alessandro

last: Porrello

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary:
The process of lung squamous carcinoma tumorigenesis and metastasis is poorly characterized. Additionally, few models of this process exist in an immune-competent context. In order to address this problem, we utilized the KLN-205 lung squamous carcinoma cell lines that is derived from carcinogen exposure in DBA2 mice.
We used healthy bronchial epithelial cells from adult DBA2 mice as a healthy control. Following an in vivo selection strategy to enrich for metastatic subclones (LN2-2, LN4-2, LN4K1), we used Affymetrix murine microarrays to study differentially expressed genes as the cells go from heathy, to tumorigenic but poorly metastatic to tumorigenic and highly metastatic (LN4K1).

overall_design: Murine bronchial epithelial cells, KLN-205 and its metastatic subclones were grown to 60-80% confluence for RNA extraction and hybridization on Affymetrix microarrays. Then, differentially expressed genes were assessed as cells progressed from healthy, to tumorigenic to both tumorigenic and strongly metastatic (LN4K1).

first: Chad

last: Pecot


title: Medicago truncatula roots infected (or not) with the oomycete Aphanomyces euteiches

status: Public on Mar 15 2018

city: Castanet Tolosan

first: Elodie

last: Gaulin

address: Pole de Biotechnologie Végétale, BP42617 Auzeville

department: Plant Pathology

country: France

institute: UMR5546 CNRS-Univ Paul Sabatier

summary: The objective of this study was to evaluate the effect of the oomycete Aphanomyces euteiches (strain ATCC201684) on the legume model Medicago truncatula (F83005-5 line) transcritpome.

overall_design: A total of 15 samples were analysed comprising 3 biological replicates for each of the 3 timepoints of the kinetic (1 day, 3 days, 9 days) on M truncatula roots, 3 biological replicates of a pool of A. euteiches mycelium grown 1, 3 or 9 days on CMA medium (8,5g/L Corn Meal Agar), and 3 biological replicates from zoospores samples.

first: Chiel

last: Pel

first: Helene

last: San Clemente

first: Marine

last: Veyssiere

first: Olivier

last: Bouchez


title: Belimumab for the Treatment of Early Diffuse Systemic Sclerosis: Results of a Randomized, Placebo Controlled Pilot Trial

status: Public on Mar 01 2018

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

summary: Changes in gene expression were consistent with mechanism of action and show that clinical response to treatment with belimumab is associated with significant decrease in profibrotic genes and pathways.  Additional study is needed to determine the role of belimumab in the treatment of dcSSc

overall_design: To assess the safety and efficacy of treatment with belimumab in patients with early diffuse cutaneous systemic sclerosis (dcSSc) treated with background mycophenolate mofetil (MMF).

first: Jessica

middle: K

last: Gordon

first: Viktor

last: Martyanov

first: Jennifer

last: Franks

first: Elana

middle: J

last: Bernstein

first: Jackie

last: Szymonifka

first: Cynthia

last: Magro

first: Horatio

last: Wildman

middle: A

first: Michael

last: Whitfield

first: Robert

last: Spiera


title: MicroRNA expression data from β-hydroxy-β-methylbutyrate (HMB) pre-incubated differentiating equine satellite cells (ESC) exposed to hydrogen peroxide

first: Tomasz

last: Sadkowski

summary: Transcriptional profiling of HMB-treated (24h) differentiating equine satellite cells (3rd day of differentiation) exposed to hydrogen peroxide (1h; last hour of pre-incubation with HMB) compared to control HMB-untreated cells. Goal was to determine the effects of HMB pre-incubation on miRNA expression in equine satellite cells exposed to hydrogen peroxide.

overall_design: Two-condition experiment, HMB-treated (24h) differentiating equine satellite cells  and exposed to hydrogen peroxide (1h during 24h pre-incubation with HMB) (3rd day of differentiation) vs. differentiating equine satellite cells without HMB treatment (control). Biological replicates: 4 reps of examined condition , 4 control replicates

first: Anna

last: Ciecierska

first: Karolina

last: Chodkowska


title: Functional and genomic characterization of a xenograft model system for the study of metastasis in triple-negative breast cancer

status: Public on Mar 13 2018

city: Melbourne

first: Andrew

last: Pattison

state: Vic

address: Wellington Rd

country: Australia

institute: Monash University

summary: To define the molecular regulators of metastasis of triple-negative breast cancer, we conducted a rigorous characterization of four populations of MDA-MB-231 human triple-negative breast cancer cells that display a range of intrinsic spontaneous metastatic capacities in immuno-deficient mice, from non-metastatic to highly metastatic to lung, liver, spleen and spine. PAT-Seq gene expression profiling of primary tumor cells identified the fibroblast growth factor homologous factor, FGF13, as a candidate metastatic virulence gene highly upregulated in aggressively metastatic MDA-MB-231HM tumors.

overall_design: SNP  analysis from of 4 increasingly metastatic breast cancer tumour cell lines

first: Cameron

middle: N

last: Johnstone

middle: D

first: Paul

last: Harrison

first: David

middle: R

last: Powell

first: Peter

last: Lock

first: Robin

last: Anderson

first: Traude

last: Beilharz


title: Circular RNAs are super abundant in cervical tumor and plasma detected by high throughput microarray [standard_RNA_circRNA]

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

summary: Circular RNAs (circRNAs) are a new class of endogenous and regulatory non-coding RNAs, but their expressions in tumor and plasma are largely unknown. Here, our study firstly suggested that microarray should be more efficient than RNA sequencing for circRNA profiling. Then, we detected ~80,000 circRNAs expressed in cervical tumors and matched normal tissues by microarray, and ~23,000 of them are differently expressed. The numbers of up- and down-regulated circRNAs during tumorigenesis are almost equal. In addition, we discovered that the expression of different circRNA isoforms from the same linear RNA also different. Strikingly, as much as ~18,000 circRNAs could be robustly detected in plasmas, and ~8,000 circRNAs show different expression after surgery of tumor removal. Altogether, taking advantage of the huge number of circRNAs detected in tumor and plasma, we provide strong evidence for circRNA expression, regulation and potential clinical application as non-invasive biomarkers.

overall_design: The circRNA expression in Universal Human Reference RNA (UHRR, 2 replicated samples) was compared to circRNA expression in Ambion’s Human Brain Reference total RNA (HBRR, 2 replicated samples) from the Microarray Quality Control (MAQC) project; The circRNA expression in cervical tumor (10 samples) was compared to circRNA expression in adjacent normal tissue (control, 10 samples) of 10 patients; The mRNA expression in cervical tumor (10 samples) was compared to mRNA expression in adjacent normal tissue(control, 10 samples) of 10 patients; The circRNA expression in preoperative plasma samples (control,7 samples) was compared to circRNA expression in postoperative plasma samples (14 samples) of 8 out of 10 cervical cancer patients. Microarray based circRNA expression profiles were acquired using CapitalBio circRNA Human Gene Expression Microarray V1.0 screening for 87,935 distinct human circRNA candidates.

first: Shuaishuai

last: Teng

first: Junquan

last: Xu

first: Guannan

last: Su

first: Jianqing

last: Zhao

first: Wenyan

last: Qin

first: Qianyong

last: Zhu

first: Dong

last: Wang


title: Circular RNAs are super abundant in cervical tumor and plasma detected by high throughput microarray [Plasma_circRNA]


title: Circular RNAs are super abundant in cervical tumor and plasma detected by high throughput microarray [cervical_cancer_mRNA]


title: Circular RNAs are super abundant in cervical tumor and plasma detected by high throughput microarray [cervical_cancer_circRNA]


title: Genome-wide epigenetic maps in the liver from male and female Wistar and Sprague-Daley rats

status: Public on Mar 07 2018

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

summary: We carry out methyl DNA immunoprecipitation (meDIP) and hydroxymethyl DNA immunoprecipitaion (hmeDIP)  prior to sequencing on the Ion Proton semiconductor sequencing platform to report on the genome-wide epigenetic patterns in rat livers

overall_design: Genome-wide patterns were generate on the Ion Proton P1 sequencer.

middle: P

first: Raffaele

last: Ottaviano

first: Angie

last: Fawkes

first: Richard

last: Clark

first: Lee

last: Murphy

last: Meehan


title: The Caenorhabditis elegans Female-Like State: Decoupling the Transcriptomic Effects of Aging and Sperm Status

city: Medford

first: David

last: Angeles-Albores

state: MA

address: 61 Locust St

institute: Northwestern University

summary: Understanding genome and gene function in a whole organism requires us to fully comprehend the life cycle and the physiology of the organism in question. Caenorhabditis elegans XX animals are hermaphrodites that exhaust their sperm after 3 d of egg-laying. Even though C. elegans can live for many days after cessation of egg-laying, the molecular physiology of this state has not been as intensely studied as other parts of the life cycle, despite documented changes in behavior and metabolism. To study the effects of sperm depletion and aging of C. elegans during the first 6 d of adulthood, we measured the transcriptomes of first-day adult hermaphrodites and sixth-day sperm-depleted adults, and, at the same time points, mutant fog-2(lf) worms that have a feminized germline phenotype. We found that we could separate the effects of biological aging from sperm depletion. For a large subset of genes, young adult fog-2(lf) animals had the same gene expression changes as sperm-depleted sixth-day wild-type hermaphrodites, and these genes did not change expression when fog-2(lf) females reached the sixth day of adulthood. Taken together, this indicates that changing sperm status causes a change in the internal state of the worm, which we call the female-like state. Our data provide a high-quality picture of the changes that happen in global gene expression throughout the period of early aging in the worm.

overall_design: 4 conditions; 3 samples per condition. Young adults are 1d old adults without visible eggs. Aged adults are 6th day adults, post-egg-laying. The fog-2 mutant strain used was JK574

first: Daniel

last: Leighton

first: Tiffany

last: Tsou

last: Khaw

first: Igor

last: Antoshechkin

first: Paul

last: Sternberg


title: Whole genome QTL study identifies candidate loci associated to syringomyelia

city: Montreal

first: Philippe

last: Lemay

state: Quebec

address: 3175 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: Université de Montréal

summary: Background: Syringomyelia (SM) is a common condition affecting brachycephalic toy breed dogs and is characterized by the development of fluid-filled cavities within the spinal cord. It is often concurrent with a complex developmental malformation of the skull and craniocervical vertebrae called Chiari-like malformation (CM) characterized by a conformational change and overcrowding of the brain and cervical spinal cord particularly at the craniocervical junction. CM and SM have a polygenic mode of inheritance with variable penetrance.

overall_design: To identify the presence of causative haplotype for Syringomyelia 96 Cavalier King Charles Spaniels dogs were genotyped using Illumina CanineHD Beadchip. This cohort consisted of 41 cases and 55 controls. Linear and mixed regression model were used to define association between morphologic traits and genetic data

first: Frédéric

last: Ancot

first: Susan

last: Knowler

first: Karen

last: Kennedy

first: Sandra

last: Griffiths

first: Giunio

middle: B

last: Cherubini

first: Jane

last: Sykes

last: Mandigers

first: Guy

last: Rouleau

first: Clare

last: Rusbridge

first: Zoha

last: Kibar


title: miRNA expression in lung tissue

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

summary: Sex differences in the incidence and prognosis of respiratory diseases have been reported.  Studies have shown that women are at increased risk of adverse health outcomes from air pollution than men, but sex-specific immune gene expression patterns and regulatory networks have not been well studied in the lung. MicroRNAs (miRNAs) are environmentally sensitive posttranscriptional regulators of gene expression that may mediate the damaging effects of inhaled pollutants in the lung, by altering the expression of innate immunity molecules. Here, male and female mice of the C57/Bl6 background were exposed to 2ppm of ozone or filtered air (control) for 3 hours. Female mice were also exposed at different stages of the estrous cycle. Following exposure, lungs were harvested and total RNA was extracted.  We used PCR arrays to study sex-differences in the expression of 84 miRNAs predicted to target inflammatory and immune genes. Our results identified differentially expressed miRNA signatures in the lungs of male vs. female exposed to ozone. In silico pathway analyses identified sex-specific biological networks affected by exposure to ozone that ranged from direct predicted gene targeting to complex interactions with multiple intermediates.  We also identified differences in miRNA expression and predicted regulatory networks in females exposed to ozone at different estrous cycle stages. These results indicate that both sex and hormonal status can influence lung miRNA expression in response to ozone exposure, indicating that sex-specific miRNA regulation of inflammatory gene expression could mediate differential pollution-induced health outcomes in men and women.

overall_design: Male and female C57BL/6 mice of 8 weeks of age were exposed to 2ppm ozone (O3) or filtered air (FA) for 3 hours. Females were exposed at different stages of the estrous cycle: diestrus 1 (D1), diestrus 2 (D2), proestrus (P), estrus (E). Total RNA was extracted from whole lung homogenates and PCR arrays were used to determine the expression of 84 miRNAs associated with inflammation and immunity (3-9 animals per condition).

first: Nathalie

last: Fuentes


title: Effect of GMG-43-AC on hair follicles

city: Jerusalem

first: Yuval

last: Ramot

address: Kiryat Hadassah, POB 12000

country: Israel

institute: Hadassah - Hebrew University Medical Center

summary: In recent years, there is a growing interest in the role of PPARγ agonists in skin biology. Specifically, we have previously shown that agonistic PPARγ modulators affect hair follicle growth and function. PPARγ-mediated signalling has also been implicated in the regulation of mitochondrial energy metabolism in several tissues (adipose and brain), but how PPARγ-stimulation affects mitochondrial biology in the skin is still unknown. In this study, we aimed to explore the effects of PPARγ-stimulation in organ cultured human hair follicles.

overall_design: 25 freshly isolated HFs from two females were treated with 0.01 mM GMG-43AC (provided by Giuliani SpA, Milan, Italy) or vehicle for 6h.


title: Rostrocaudal Areal Patterning of Human PSC-Derived Cortical Neurons by FGF8 Signaling

status: Public on Feb 27 2018

city: Stanford

first: Kent

last: Imaizumi

state: CA

address: 318 Campus Drive

institute: Stanford University

summary: The cerebral cortex is subdivided into distinct areas that have particular functions. The rostrocaudal (R-C) gradient of fibroblast growth factor 8 (FGF8) signaling defines this areal identity during neural development. In this study, we recapitulated cortical R-C patterning in human pluripotent stem cell (PSC) cultures. Modulation of FGF8 signaling appropriately regulated the R-C markers, and the patterns of global gene expression resembled those of the corresponding areas of in vivo human fetal brains. Furthermore, we demonstrated the utility of this culture system in modeling the area-specific forebrain phenotypes (presumptive upper motor neuron (UMN) phenotypes) of amyotrophic lateral sclerosis (ALS). We anticipate that our culture system will contribute to studies of human neurodevelopment and neurological disease modeling.

overall_design: Total RNA from human ES cell-derived control neurospheres (n=3) and FGF8-treated neurospheres (n=3) was analyzed.

first: Wado

last: Akamatsu

first: Hideyuki

last: Okano


title: Murine Kidney Tissue: Unilateral ureteral obstructed (UUO) mice vs. Sham control

status: Public on Feb 23 2018

first: Bo

last: Wu

state: Ca

address: 300 Pasteur Dr. Grant/S259

department: Urology

summary: Gene expression changes induced by  unilateral ureteral obstruction in mice.

overall_design: Two-condition experiment, Kidney tissue from UUO mice vs. Sham mice. Biological replicates: 60 UUO replicates, 60 sham replicates.

first: James

last: Brooks


title: Murine Kidney Tissue: Reversible unilateral ureteral obstructed mice (RUUO) vs. Sham control

summary: Gene expression changes induced by reversible unilateral ureteral obstruction in mice.

overall_design: Two-condition experiment, Kidney tissue from RUUO mice vs. Sham mice. Biological replicates: 36 UUO replicates, 39 sham replicates.


title: A Linc1405/Eomes Complex Promotes Cardiac Mesoderm Specification and Cardiogenesis

city: Shanghai

first: Xudong

last: Guo

address: No.1239, Siping Road

institute: Tongji University

summary: Large intergenic non-coding RNAs (lincRNAs) play widespread roles in epigenetic regulation during multiple differentiation processes, but little is known about their mode of action in cardiac differentiation. Here, we identified the key roles of a lincRNA, termed linc1405, in modulating the core network of cardiac differentiation by functionally interacting with Eomes. Chromatin- and RNA- immunoprecipitation assays showed that exon2 of linc1405 physically mediates a complex consisting of Eomes, Trithorax group (TrxG) subunit WDR5, and histone acetyltransferase GCN5 binding at the enhancer region of Mesp1 gene and activates its expression during cardiac mesoderm specification of embryonic stem cells. Importantly, linc1405 co-localizes with Eomes, WDR5, and GCN5 at the primitive streak and linc1405 depletion impairs heart development and function in vivo. In summary, linc1405 mediates a Eomes/WDR5/GCN5 complex that contributes to cardiogenesis, highlighting the critical roles of lincRNA-based complexes in the epigenetic regulation of cardiogenesis in vitro and in vivo.

overall_design: The microarray analysis for Linc1405 knockdown in the indicated days of cardiomyocyte differentiation

first: Yanxin

last: Xu


title: The SCN9A channel and plasma membrane depolarization promote cellular senescence through Rb pathway

status: Public on Feb 21 2018

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

institute: Inserm 1052

summary: Oncogenic signals can induce premature senescence (OIS) in normal human cells causing a proliferation arrest and the elimination of these defective cells by immune cells. In order to identify new regulators of OIS, we performed a loss-of-function genetic screen and identified that the loss of SCN9A sodium channel allowed cells to escape from OIS. Here we studied the transcriptome profiles  of an OIS model based on human mammary epithelial cells stably expressing hTert to be immortalized and MEK:ER, a 4-hydroxytamoxifen (4-OHT) inducible oncogene MEK:ER (HEC-TM cells), to induce the oncogenic signal. We used an shRNA in order to knockdown SCN9A expression during OIS, and KCL treatment to study the impact of membrane depolarization on senescence induction. We showed that SCN9A and plama membrane depolarization mediated the repression of mitotic genes through a calcium/Rb/E2F pathway to promote senescence. Taken together, our work delineates a new pathway, which involves the NFkB transcription factor, SCN9A expression, plasma membrane depolarization.

overall_design: For each condition three independent biological replicates were analysed. Untreated HEC-TM cells condition have been used as control and the data have been normalized on this control.

first: Jean-Michel

last: Flaman

first: David

last: Bernard


title: Murine Kidney Tissue: Calcineurin beta 1 knockout mice vs wild type control

summary: Gene expression changes between knockout mice vs wild type control

overall_design: Two-condition experiment, Kidney tissue from KO mice vs. WT mice. Biological replicates: 18 KO replicates, 18 WT replicates.


title: Morphological and transcriptomic analyses reveal three discrete primary stages of postembryonic development in the common fire salamander, Salamandra salamandra

city: Braunschweig

first: Eugenia

last: Sanchez

address: Mendelssonhstrasse 4

department: Zoological Institute

institute: Technische Universität Braunschweig

summary: The postembryonic development of amphibians has been characterized as divided into three predominant periods, hereafter named primary developmental stages: premetamorphosis (PreM), prometamorphosis (ProM), metamorphic climax (Meta), and completion of metamorphosis (PostM), largely based on examination of anuran development. Here, we categorized the postembryonic development of larvae of a poisonous fire salamander (Salamandra salamandra) by integrating morphology and gene expression (transcriptomic) data. Morphological analysis revealed three distinct clusters suggestive of PreM, ProM, and Meta, which were confirmed in parallel by microarray-derived gene expression analysis. In total, 3,510 probes targeted transcripts differentially expressed between the clusters we identified. Genes upregulated in PreM related to organogenesis, and those upregulated in Meta underlie structural proteins and relate to development of anatomical structures and pigmentation. Biosynthesis pathways of pigments (pteridines and melanin) were upregulated during late ProM and Meta. Gas chromatographic analysis of alkaloids indicated the onset of steroidal alkaloid biosynthesis at ProM. When comparing gene expression in the fire salamander to that in other amphibians—three anurans, Xenopus laevis, X. tropicalis, and Michrohyla fissipes, and one caudate, Ambystoma mexicanum—, we identified genes with conserved expression patterns involved in basic metamorphic processes such as skin restructuring and tail fin resorption. Our results support that primary stages of postembryonic development in caudates are homologous to those of anurans, and offer a baseline for the study of the evolution of developmental modes.

overall_design: We collected tail-clip tissue of Salamandra salamandra larvae reared under standard conditions at different developmental stages. Total RNA was extracted from this tissue, and its expression was analyzed with an Agilent microarray.

first: Eliane

last: Küpfer

first: Daniel

last: Goedbloed

first: Arne

middle: W

last: Nolte

first: Tim

last: Lüddecke

first: Stefan

last: Schulz

first: Miguel

last: Vences

first: Sebastian

last: Steinfartz


title: miRNA expression of gefitinib-resistant cell lines

first: Lu

address: 280 South Chongqing Rd

department: Pharmacology

institute: Shanghai Jiao Tong University, School of Medicine

summary: To identify novel miRNAs involved in acquired EGFR TKI resistance in NSCLC, genome-wide miRNA expression analysis was performed in gefitinib-resistant sub-cell lines and gefitinib-sensitive parental cell lines.

overall_design: Gefitinib-resistant sub-cell lines were generated by growing gefitinib-sensitive EGFR-mutant NSCLC cell lines (PC9 and HCC827) in increasing concentrations of gefitinib to a final concentration of 10 uM up to 6 months.

first: Xu

last: Lu

first: Chen

last: Hongzhuan


title: RNA-Seq study of gene expression in feather branching

status: Public on Feb 20 2018

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary: Feather branching morphogenesis is a complex process which is likely to be regulated by many genes. Also, feathers from different body regions are drastically different in their morphology, thus suggesting differential gene expression. To understand the feather epithelial branching process, we profiled gene expression in the ramogenic feather epithelium in adult chicken where branching begins. Feathers from the neck, wing, and tail regions in their actively growing phase were each profiled.

overall_design: Feathers from the neck, wing, leg regions in adult chicken in their actively growing phase were plucked. Feathers were dissected under a stereo dissection microscope. The mesenchymal pulp were discarded. The ramogenic feather epithelium was pooled from five feathers. Total RNAs were extracted from the feather epithelium, and processed for RNA-seq.

first: Zhicao

last: Yue


title: Prognostic liver signature profiles (114-gene signature) in liver biopsy tissues from severe alcoholic hepatitis patients (NanoString)

status: Public on Feb 18 2018

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Importance: Severe alcoholic hepatitis (AH) is a highly lethal disease with a 3-month mortality up to 50%. Corticosteroids are the current standard of care although nearly 40% of the patients do not respond and accurate pre-treatment predictors of survival are lacking.   Objective: To develop a prognostic score based on molecular and clinical variables before initiation of corticosteroids.  Design, Setting, and Participants: Gene expression profiling of fixed liver biopsy obtained for diagnosis of severe AH assessed in 3 independent cohorts (1 prospective cohort for prognostic gene signature and integrative score derivation, and 2 retrospective cohorts for validation). Samples were obtained from 4 European and 1 US medical centers between July 2006 and February 2015.   Exposures: Biopsy proven severe AH patients treated with corticosteroids.   Main Outcome Measures: Identification of a gene signature combined with a validated clinical index to develop an integrative prognostic score of survival without death or liver transplantation in a derivation cohort (n=71). Prognostic performance of the score was validated in an independent multi-center validation cohort 1 (n=48). Finally, the score was implemented in an FDA-approved clinical diagnostic platform (NanoString) and tested in another independent validation cohort 2 (n=20).  Results: A prognostic score, integrating a 123-gene signature and the model for end-stage liver disease (gs-MELD score), was defined in the derivation cohort, in which poor- and good-prognosis patients were discriminated with a cut-off value of 2.66 at 3 months (event-free survival rates of 32% vs. 76%, respectively, p<.001) and 6 months (26% vs. 65%, respectively, p<.001). In the validation cohort 1, the score similarly discriminated poor- and good-prognosis patients at 3 months (43%, [95% CI, 26%-70%] vs. 96% [95% CI, 89%-100%], respectively, p<.001, c-index of 0.83 [95% CI, 0.66-0.99]) and 6 months (34% [95% CI, 18%-61%] vs 84% [95% CI, 72%-100%], respectively, p<.001, c-index of 0.80 [95% CI, 0.66-0.94]), and outperformed other existing clinical indices. The NanoString-based gs-MELD score remained predictive of 3- (p=.03) and 6-month (p=.009) even-free survival in the validation cohort 2.  Conclusion and Relevance: The gs-MELD score, incorporating clinically applicable gene signature test and the MELD score, enables pre-treatment survival prediction in severe AH patients.

overall_design: Gene expression profiling of formalin-fixed paraffin-embedded liver biopsy tissues obtained at the time of enrollment.

first: Eric

last: Trépo

first: Nicolas

last: Goossens

first: Naoto

last: Fujiwara

first: Gene

last: Im

first: Denis

last: Franchimont