title: miRNA expression of lung cancer cells A549 and cisplatin (DDP) resistant lung cancer cells A549/DDP

status: Public on Aug 16 2016

city: Nanjing

first: Jifeng

last: Feng

address: No.42, Baiziting

country: China

institute: Jiangsu Cancer Hospital

summary: To investigate the difference of miRNA expression between lung cancer cell A549 and its DDP-resistant cell strain A549/DDP, we have employed miRNA microarray expression to discover the difference expression of miRNAs of A549 cells and A549/DDP. We conducted RT-qPCR to examine the expression levels of top differential expressed miRNAs, namely, miR-197-5p, miR-4443, miR-642a-3p, miR-27b-3p and miR-100-5p, confirming low variability between two methods.

overall_design: The A549/DDP was established from A549 in our laboratory, by exposing A549 to gradually increasing DDP concentrations, until the final concentration at 1μg/ml. To avoid the influence of drug to the A549/DDP cells, they were cultured in a drug-free medium for at least two weeks before gene expression analysis. miRNA expression of A549 and A549/DDP was then analzyed.

first: Xiaobing

last: Qin


title: Gene expression profiling of longissimus dorsi muscle,subcutaneous and abdominal adipose tissues in Yan yellow cattle

status: Public on Aug 18 2016

city: Changchun

first: Shuang

last: Ji

state: Jilin

address: 5333,xi'an road

department: College of Animal Science

institute: Jilin University

summary: Microarray technologies,which can measure the expression of thousands of genes simultaneously are useful in understanding global gene networks and identifying novel genes and functional gene classes.The adipose depots may have various adipogenic state-specific genes and regulations of adipose accretion patterns in beef cattle.Therefore,the purpose of this study was to examine the molecular mechanisms of longissimus dorsi muscle,subcutaneous and abdominal adipose tissue depots in a native Chinese yellow breed by identifying differentially expressed genes using Bovine Genome Array.The GO and pathway analysis further validated differentially expressed genes identified in array analysis.

overall_design: A total of 9 bulls of the same breed (Yan yellow cattle) were included in the study.The sample collection procedure was approved by animal care committee of Husbandry Bureau of Yanji City.All cattle were reared under identical conditions and the samples were obtained according to standard procedures.The samples were immediately frozen in liquid nitrogen and stored at -80°C for microarray analysis.

first: Run-Jun

last: Yang

first: Ze-Zhong

last: Li

first: Jing

last: Tian

first: Wei-Ying

last: Liu

first: Bo-Xing

last: Sun

first: Zhi-Hui

last: Zhao


title: Impact of heat stress on  transcriptional adaptation of mammary epithelial cells in riverine buffalo (Bubalus bubalis)

status: Public on Aug 26 2016

city: Karnal

first: Manishi

last: Mukesh

state: Haryana

address: Po Box 129, GT Road By Pass

department: Animal Biotechnology

country: India

institute: ICAR-National Bureau of Animal Genetic Resources

summary:
The primary mammary epithelial cells of riverine buffalo were exposed to thermal stress condition at 42C for one hour. The cells were subsequently allowed to recover at 37C and harvested at different time intervals (30 min to 48 h) along with control samples (un-stressed).
The study has identified several genes from different functional classes and biological pathways which could be termed as heat responsive in buffalo MEC

overall_design: The study has utilized 4x44K Agilent chip using single color matrix  to generate transcriptome data of buffalo MEC at different time points (30 min, 2h, 4h, 8h, 12h, 16h and 24h) post heat stress and compared with unstressed cells

first: Neha

last: Kapila

first: Ankita

last: Sharma

first: Amit

last: Kishore

first: Ashok

middle: K

last: Mohanty

first: Pawan

last: Tripathi

first: Monika

last: Sodhi


title: Overexpression of sigC in the wild type

status: Public on Aug 22 2016

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

country: Japan

institute: Research institute of Innovative Technology for the Earth (RITE)

summary: Bacteria modify expression of different types of terminal oxidase in response to oxygen availability. Corynebacterium glutamicum, a facultative anaerobic bacterium in Actinobacteria, possesses aa3-type cytochrome c oxidase and cytochrome bd-type quinol oxidase, the latter of which is induced upon oxygen limitation. We report here that an extracytoplasmic function sigma factor, SigC, is unprecedentedly responsible for the regulation. Chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis detected eight SigC-binding regions in the genome, leading to identification of a consensus promoter sequence for SigC recognition. The promoter sequences were found upstream of genes for cytochrome bd, heme a synthesis enzymes, and uncharacterized membrane proteins, all of which were upregulated by sigC overexpression. In contrast, that found on the antisense strand upstream of an operon encoding the cytochrome bc1 complex conferred a SigC-dependent negative effect on the operon expression. The SigC regulon was induced by cytochrome aa3 deficiency without modification of expression of sigC itself, but not by deficiency of the bc1 complex. These findings suggest that SigC is activated in response to impairment of electron transfer via cytochrome aa3, not directly to shift in oxygen levels. Our results provide a novel paradigm for transcriptional regulation of the aerobic respiratory system in bacteria.

overall_design: Comparison of gene expression profiles of the wild type before and after sigC overexpression at the exponential phase. Three independent experiments were performed.

first: Koichi

last: Toyoda


title: Identifying Transcription Factors Expressed by V0v Spinal Cord Interneurons

city: Syracuse

first: Samantha

middle: Jane

last: England

state: NY

address: 107 College Place

department: Biology

country: USA

institute: Syracuse University

summary: We isolated and expression profiled V0v spinal interneurons, as well as all spinal neurons and all trunk cells using Fluorescence Activated Cell Sorting (FACS) of different transgenic zebrafish lines in which these cells express fluorescent proteins at 27 hours post fertilization (hpf). We used a custom-designed Agilent microarray to study the expression of transcription factors in these cell types.

overall_design: Twelve samples were analysed in total, all at 27 hours post fertilisation (hpf). Four biological replicates were performed for each of the three cell types under study - V0v spinal interneurons (isolated from Tg(evx1:EGFP)SU1), all spinal neurons (isolated from Tg(elavl3:EGFP)) and all trunk cells (FAC-sorted trunk cells).

middle: J

first: Sarah

middle: M

last: de Jager

first: Katharine

middle: E

last: Lewis


title: Gene expression profiles of 13 European maize (Zea mays L.) inbred lines: factorial 1999LP1

city: Hamburg

first: Stefan

last: Scholten

state: Hamburg

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

country: Germany

institute: University of Hamburg

summary: We applied a custom 2k micro-array with 2232 oligonucleotide sequences (50-70 nt) to a factorial with 13 parental inbred lines (4 Dent, 9 Flint) of European maize (Zea mays L.). The selection of oligonucleotides was based on 47k-array expression data from a 14x7 factorial with 98 hybrids (GSE17754). The main fraction of oligonucleotides (1639) represents genes that showed differential expression between the parental genotypes in the 14x7 factorial and consistent association with HP for GY in cross validation runs to estimate prediction accuracies for this trait. In addition the array contains partial overlapping fractions of genes that correlated with HP/GY (378), HP/GDMC (200), or MPH/GY (345) and 205 representatives of the 6 most overrepresented biological processes among genes correlated with HP/GY in the 14x7 factorial.

overall_design: Four seedlings of each maize inbred line (9 Flint lines: F005, F012, F013,  F023, F030, F034, L005, L007, L012; 4 Dent lines: P006, P033, S002, S028) as well as of two control lines (F043, S067) were grown for 7 days under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 per cent air humidity) with randomized plate positions. The whole 7-day-old-seedlings were sampled and frozen in liquid nitrogen. The biological replicates were pooled and homogenized prior to RNA extraction.


title: Gene expression profiles of GPR15 knock out macrophages

status: Public on Aug 25 2016

city: Xuzhou

first: Bin

last: Pan

state: Jiangsu

address: #99 West Huaihai Road

department: Hematology

institute: The Affiliated Hospital of Xuzhou Medical University

summary: To confirm the changed gene expression profiles in GPR15 knock out (KO) macrophages, we applied a SurePrint G3 Mouse Gene Expression service from Takara Bio Inc (Kusatsu, Shiga, Japan) to analyze gene expression profiles in lipopolysaccharide (LPS)-stimulated GPR15KO macrophages, comparing with wild type (WT) macrophages. Most significantly up-regulated genes in GPR15KO macropahges included Il6, Il17a, Il23, Tnfsf8, Il1b, Ifna2 and Ccnd2. On the contrary, several inflammation-related genes, including Ccl17, Itgax, Nrp1 and Rasgrf2, were down-regulated in WT macrophages, compared to GPR15 KO macrophages.

overall_design: Abdominal macrophages from WT and GPR15 KO mice were stimulated with PBS or LPS (100 ng/ml) for 4 hrs. Total RNA were extracted using a TRIzol-chloroform based method.

first: Takayuki

last: Ikezoe


title: MicroRNA miR-92a-2 targets TFPI2 to ameliorate oxidative stress of the hypoxia neuron [miRNA]

city: tianjin

first: hongsheng

last: gao

address: dongli

institute: university

summary: Comparison of the differential expression mRNA profiles from the brain cortex of hypoxia and normaixa rats by silica microarray chip.

overall_design: The array consists of 3 samples. Samples E（H001-0605002307） consist of total RNA from the brain cortex of hypoxia rats in simulation 7km altitude; Samples A（H002-0605002308）: total RNA from the brain cortex of hypoxia rats in simulation 3km altitude; samples Z（H001-0605002307) :total RNA from the brain cortex of normaixa rats in simulation sea level altitude

first: H

middle: S

last: Gao

first: Y

middle: Z

last: Wang


title: Gene expression profiles of 20 European maize inbred lines, factorial 2003LP1

summary: We applied a custom 2k micro-array with 2232 oligonucleotide sequences (50-70 nt) to a factorial with 20 parental inbred lines (14 Dent, 6 Flint) of European maize (Zea mays L.). The selection of oligonucleotides was based on 47k-array expression data from a 14x7 factorial with 98 hybrids (GSE17754). The main fraction of oligonucleotides (1639) represents genes that showed differential expression between the parental genotypes in the 14x7 factorial and consistent association with HP for GY in cross validation runs to estimate prediction accuracies for this trait. In addition the array contains partial overlapping fractions of genes that correlated with HP/GY (378), HP/GDMC (200), or MPH/GY (345) and 205 representatives of the 6 most overrepresented biological processes among genes correlated with HP/GY in the 14x7 factorial.

overall_design: Four seedlings of each maize inbred line (6 Flint lines: F030, F037, F039, F045, F047, L041; 14 Dent lines: P024, P033, P048, P066, P068, P070, P072, P074, P075, P080, P081, P083, P084, S046) as well as of two control lines (F043, S067) were grown for 7 days under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 per cent air humidity) with randomized plate positions. The whole 7-day-old-seedlings were sampled and frozen in liquid nitrogen. The biological replicates were pooled and homogenized prior to RNA extraction.


title: Gene expression profiles of 13 European maize inbred lines, factorial 2001LP2

summary: We applied a custom 2k micro-array with 2232 oligonucleotide sequences (50-70 nt) to a factorial with 13 parental inbred lines (9 Dent, 4 Flint) of European maize (Zea mays L.). The selection of oligonucleotides was based on 47k-array expression data from a 14x7 factorial with 98 hybrids (GSE17754). The main fraction of oligonucleotides (1639) represents genes that showed differential expression between the parental genotypes in the 14x7 factorial and consistent association with HP for GY in cross validation runs to estimate prediction accuracies for this trait. In addition the array contains partial overlapping fractions of genes that correlated with HP/GY (378), HP/GDMC (200), or MPH/GY (345) and 205 representatives of the 6 most overrepresented biological processes among genes correlated with HP/GY in the 14x7 factorial.

overall_design: Four seedlings of each maize inbred line (4 Flint lines: F012, F039, F040, L024; 9 Dent lines: P006, P024, P033, P040, P042, P048, P060, P064, P065) as well as of two control lines (F043, S067) were grown for 7 days under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 per cent air humidity) with randomized plate positions. The whole 7-day-old-seedlings were sampled and frozen in liquid nitrogen. The biological replicates were pooled and homogenized prior to RNA extraction.


title: Gene expression profiles of 29 European maize inbred lines, factorial 2012LP1

summary: We applied a custom 2k micro-array with 2232 oligonucleotide sequences (50-70 nt) to a factorial with 29 parental inbred lines (16 Dent,13 Flint) of European maize (Zea mays L.). The selection of oligonucleotides was based on 47k-array expression data from a 14x7 factorial with 98 hybrids (GSE17754). The main fraction of oligonucleotides (1639) represents genes that showed differential expression between the parental genotypes in the 14x7 factorial and consistent association with HP for GY in cross validation runs to estimate prediction accuracies for this trait. In addition the array contains partial overlapping fractions of genes that correlated with HP/GY (378), HP/GDMC (200), or MPH/GY (345) and 205 representatives of the 6 most overrepresented biological processes among genes correlated with HP/GY in the 14x7 factorial.

overall_design: Four seedlings of each maize inbred line (13 Flint lines: F047, F099, F101, F104, F145, F151, F154, F157, F159, F160, F161, F162, F169; 16 Dent lines: P135, P140, P159, P223, P235, P245, P261, P271, P272, P284, P290, P291, P299, P302, P312, P330) as well as of two control lines (F043, S067) were grown for 7 days under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 per cent air humidity) with randomized plate positions. The whole 7-day-old-seedlings were sampled and frozen in liquid nitrogen. The biological replicates were pooled and homogenized prior to RNA extraction.


title: Epigenetic clonality confers por prognosis in colorrectal cancer patients (SNP)

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

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

department: PEBC

country: Spain

institute: IDIBELL

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

summary:
In CRC, 1) to identify epigenetic changes at inter-tumor and intra-tumor level, and 2) to relate intra-tumor clonality to clinical, molecular and histopathologic parameters. From 79 FFPE tumors, 3 different regions were macrodissected: invasive front (IF), digestive tract surface (DTS) and central bulk (CB). Clinical, molecular, and histopathologic parameters were stablished. Epigenetic analysis was performed using Infinium 450K beadchip (Illumina) and R statistics. Intra-tumor regions clustered together by patient. The biggest epigenetic changes were in IF vs DTS/CB. By patient, the most often divergent region was IF (49.4%) comparing with DTS and CB (25.3% in both). It did not correlate with histopathologic, molecular and clinical parameters.Epigenetic clonality is higher at intra-tumor level. The highest changes are observed in IF vs DTS/CB. No association with histopathologic, molecular, and clinical characteristics was found.
SNP characterization of 9 patients of teh discovery cohort were hibridized on Infinium HumanOncoArray-500 v1 beadchip, to asses the genetic clonality of the samples among the three intratumoral regions studied.

overall_design: From 79 FFPE tumors, 3 different regions were macrodissected: invasive front (IF), digestive tract surface (DTS) and central bulk (CB). When available, metastasis and normal tissue were also collected.

first: Anna

last: Martinez-Cardus

first: Manel

last: Esteller


title: Genome-wide analyses of C. glutamicum SigC

type: Genome binding/occupancy profiling by array

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

platform_organism:
Corynebacterium glutamicum
Corynebacterium glutamicum R

overall_design: Refer to individual Series


title: Oligouridylate binding protein 1b functions in plant heat stress tolerance

status: Public on Aug 21 2016

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

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

department: Center for Sustainable Resource Science

institute: RIKEN

summary: To understand affected genes by overexpression of origouridylate binding protein 1b (UBP1b) under heat stress conditions, transcriptional profiling of UBP1box and control plants were analyzed under normal and heat stress (40°C) conditions using Arabidopsis custom microarrays.

overall_design: Microarray analysis was conducted using UBP1b-ox and Venus control plants subjected to non-stress and heat-stress condition for 1 h.

first: Cam

middle: C

last: Nguyen

first: Kentaro

last: Nakaminami

first: Shuhei

last: Kobayashi

first: Yukio

last: Kurihara

first: Maho

last: Tanaka

first: Motoaki

last: Seki


title: Gene expression profiles of 29 European maize inbred lines and 26 of their hybrids: factorial 2010LP1

summary: We applied a custom 2k micro-array with 2232 oligonucleotide sequences (50-70 nt) to a factorial with 29 parental inbred lines (14 Dent, 15 Flint, 26 hybrids selected for their heterosis levels so that the extreme values and also the average values were covered) of European maize (Zea mays L.). The selection of oligonucleotides was based on 47k-array expression data from a 14x7 factorial with 98 hybrids (GSE17754). The main fraction of oligonucleotides (1639) represents genes that showed differential expression between the parental genotypes in the 14x7 factorial and consistent association with HP for GY in cross validation runs to estimate prediction accuracies for this trait. In addition the array contains partial overlapping fractions of genes that correlated with HP/GY (378), HP/GDMC (200), or MPH/GY (345) and 205 representatives of the 6 most overrepresented biological processes among genes correlated with HP/GY in the 14x7 factorial.

overall_design: Four seedlings of each maize inbred line (15 Flint lines: F047, F055, F062, F072, F087, F090, F101, F103, F104, F117, F124, F134, F136, F137, F138; 14 Dent lines: P048, P092, P135, P140, P150, P154, P159, P165, P167, P204, P209, P210, P211, P214), of26 hybrids from those lines (P135.F047, P135.F072, P135.F087, P135.F103, P135.F117, P140.F047, P140.F072, P140.F087, P140.F103, P140.F117, P154.F047, P154.F072, P154.F087, P154.F103, P154.F117, P159.F047, P159.F072, P159.F087, P159.F103, P159.F117, P167.F047, P167.F072, P167.F087, P167.F103, P167.F117), and of two control lines (F043, S067) were grown for 7 days under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 per cent air humidity) with randomized plate positions. The whole 7-day-old-seedlings were sampled and frozen in liquid nitrogen. The biological replicates were pooled and homogenized prior to RNA extraction.


title: Human Renal Cancer Cells: Control vs STF-62247-treated cells

status: Public on Aug 23 2016

city: Moncton

first: Daniel

last: Leger

state: New Brunswick

address: 35 Providence Street

department: IARC

country: Canada

institute: Atlantic Cancer Research Institute

summary: Transcriptomic profiling of Renal Cancer Cells (RCC) in response to a small molecule, STF-62247. These microarrays have been used to compared with proteomic profiling data in the paper entitled Quantitative proteomics to study a small molecule targeting the loss of VHL in Renal Cell Carcinomas

overall_design:
Two condition experiments, one cell line (RCC4), untreated control and STF-62247-treated. Biological triplicates N=3, indendently grown and harvested. Cells were treated with 1.25uM STF-62247 or vehicle (DMSO) for 48h.
Oligo microarrays done in triplicate dye swaps for a total of 6 slides.

first: Nadia

last: Bouhamdani

last: Léger

first: Ian

last: Chute

first: Kevin

last: Cormier

first: Sandra

last: Turcotte


title: Leptin-Mediated Gene Expression Profiling Exhibits New Candidate Genes Associated with Osteoarthritis in Rat

status: Public on Aug 19 2016

city: Shanghai

first: Ziming

last: Zhang

address: 1665 Kongjiang Road

department: School of Medicine

institute: Shanghai Jiao Tong University

summary: Osteoarthritis (OA) is the most prevalent chronic joint disease and the precise genetic mechanisms are yet to be fully elucidated.   The aim of this study is to evaluate, for the first time, the differences in gene expression profiles of healthy and leptin-induced cartilage in rat.  To investigate the underlying pathogenic factors in OA, alterations in gene expression between leptin-induced articular cartilage rat models and healthy control rat models were investigated using the Whole Rat Genome Oligo Microarray.   In the present study, 1857 differentially expressed genes (DEGs; 1197 up-regulated and 660 down-regulated) were identified. Expression of some OA-related known genes is known to be associated with leptin induction, including matrix metalloproteinase (MMP), inflammatory factors, growth factors and genes involved in cell death, apoptosis and osteoclast differentiation. However, some new candidate genes that had never been reported to be related with OA, such as BCL2L11, were consistently observed to be up-regulated, suggesting they might be involved in OA progression.   Our findings indicate that leptin plays an important role in the progression of OA by mediating expression change in multiple genes, although the molecular mechanisms need to be further clarified. Further study of these leptin-induced genes may provide new insights into understanding the molecular mechanisms underlying OA.

overall_design: To identify genes with changed expression in response to leptin, genome wide expression profiles were generated for leptin-affected cartilage (L group) and healthy controls (H group) in rats. 24 rats were divided into two groups: control animals (H group, n = 12) and leptin-induced animals (L group, n = 12). H group included two replicates, sample1 and sample2. L group also included two replicates, sample3 and sample4.

first: Zhu

last: Liu

first: Qing

last: Fan

first: Chao

last: Shen

first: Hai

last: Li

first: Jing

last: Ding

first: Fangchun

last: Jin

first: Lin

last: Sha


title: Chip-chip analysis of C. glutamicum SigC

first: Masayuki

last: Inui

overall_design: ChIP-chip analyses using a strain expressing the FLAG-tagged SigC in the background of the wild type at two growth phases (exporenatial and stationary phases). Two independent experiments were performed.

first: Koichi

last: Toyoda


title: AginAging: a portrait from gene expression profile in blood cells: a portrait from gene expression profile in blood cells.

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: In almost every countries the proportion of people over 60 years is growing faster that any other age group. Increased life expectancy is leading to the characterization of specific aspects of aging for the various physiological systems. The study of healthy aging is important to design strategies capable to maximize the health and to prevent chronic diseases in older people. Immunosenscence reflects the age-related changes of the immune system  and the reduced capacity of  elderly people to cope with new infections. To elucidate changes in gene expression related to systemic aging and immunosenescence in an unbiased manner we performed comparative microarray analysis on whole blood cell from healthy middle-aged versus elderly men, and correlated results with functional measurements of aerobic capacity. Blood cells from elderly subjects showed age-related changes in the expression of several markers of immunosenescence, inflammation and oxidative stress, and showed impairments in metabolic and biosynthetic capacities.

overall_design: Whole blood samples from twenty healthy men between the ages of 45-55 (n=11) and 65-75 (n=9) years old were analyzed for this study. For each subject blood was sampled in two different occasions, which were separated by at least 7 days. To preseve RNA quality and integrity 3 ml of blood have been collected intoTEMPUS Blood RNA tubes (ABI, Foster City, CA, USA). Total RNA has been depleted of globin mRNA using the GLOBINclear™-Human kit (Ambion, Austin, TX). To reduce variations due to confounding events, such as spontaneous up- and down-regulation of genes, the two samples of clean RNA from each subject were pooled into one single sample (1ug+1ug RNA).

first: Elisa

last: Calabria

first: Emilia

last: Mazza

first: Kenneth

last: Dyar

first: Silvia

last: Pogliaghi

first: Carlo

last: Morandi

first: Gianluca

last: Salvagno

first: Giancesare

last: Guidi

first: Stefano

last: Schiaffino

first: Federico

last: Schena

last: Capelli


title: A germline mutation of CDKN2A and a novel RPLP1-C19MC fusion detected in a rare melanotic neuroectodermal tumor of infancy: a case report [aCGH]

status: Public on Aug 29 2016

city: Oxford

first: Bass

last: Hassan

state: Oxfordshire

address: South Parks Road

department: Sir William Dunn School of Pathology, Oxford Molecular Pathology Institute

country: United Kingdom

institute: University of Oxford

type: Genome variation profiling by genome tiling array

summary:
Purpose: Melanotic neuroectodermal tumor of infancy (MNTI) is exceptionally rare and occurs predominantly in the head and neck (92.8% cases). A 2-month-old female patient presented with a mass arising in the fibula which was excised at our surgical center. This is only the eighth case of MNTI affecting an extremity, and the first reported in the fibula. To understand better the etiology of this MNTI, we used high-throughput sequencing technology to carry out an exhaustive genomic, transcriptomic and epigenetic characterization on the excised primary tumor and a derived cell line.
Methods: RNA was extracted from the flash frozen tumor and paired-end RNA-Seq was performed to identify potential oncogenic fusion genes and to quantify gene expression in the MNTI transcriptome. Genomic DNA was extracted from the tumor and from a sample of the patient's blood and whole-exome sequencing was done to detect somatic and germline variants. Copy number variation in the MNTI was determined by comparative genomic hybridization (CGH) of DNA from the tumor and blood to a SNP array. A cell line was derived from the tumor and was tested for sensitivity to a panel of compounds targeting epigenetic regulators.
Results: Whole-exome analysis indicated no somatic, non-synonymous coding mutations within the tumor, but a heterozygous, unique germline, loss of function mutation in CDKN2A (p16INK4A, D74A).  SNP-array CGH revealed the tumor to be euploid, with no detectable gene copy number variants.  Multiple chromosomal translocations were identified by RNA-Seq, and fusion genes included RPLP1-C19MC, potentially deregulating the C19MC cluster, an imprinted locus containing microRNA genes reactivated by gene fusion in embryonal tumors with multilayered rosettes. Since the presumed cell of origin of MNTI is from the neural crest, we also compared gene expression with a dataset from human neural crest cells (GEO acession: GSE28875) and identified 185 genes with significantly different expression. Consistent with the melanotic phenotype of the tumor, elevated expression of tyrosinase was observed.  Other highly expressed genes encoded muscle proteins and modulators of the extracellular matrix. The derived MNTI cell line was sensitive to inhibitors of lysine demethylase, but not to compounds targeting other epigenetic regulators.
Conclusions: In the absence of somatic copy number variations or mutations, the fully transformed phenotype of the MNTI may have arisen in infancy because of the combined effects of a germline CDKN2A mutation, tumor promoting somatic fusion genes and epigenetic deregulation. Very little is known about the etiology of MNTI and this report advances knowledge of these rare tumors by providing the first comprehensive genomic, transcriptomic and epigenetic characterization of a case.

overall_design:
Genomic DNA was extracted from the tumor and whole-exome and copy number comparative analyses were performed relative to a reference sample of genomic DNA from the patient’s blood (germline DNA).
This dataset represents aCGH samples.

first: David

last: Barnes

first: Edward

last: Hookway

first: Nick

last: Athanasou

first: Takeshi

last: Kashima

first: Udo

last: Oppermann

first: Simon

last: Hughes

first: Daniel

last: Swan

first: Dietrich

last: Lueerssen

first: John

last: Anson

first: A

middle: B


title: Gene expression profiles of 13 European maize inbred lines, factorial 1999LP2

first: Stefan

last: Scholten

overall_design: Four seedlings of each maize inbred line (4 Flint lines: F012, F023, F030, L012; 9 Dent lines: P006, P024, P027, P033, S002, S015, S016, S018, S028) as well as of two control lines (F043, S067) were grown for 7 days under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 per cent air humidity) with randomized plate positions. The whole 7-day-old-seedlings were sampled and frozen in liquid nitrogen. The biological replicates were pooled and homogenized prior to RNA extraction.


title: MicroRNA miR-92a-2 targets TFPI2 to ameliorate oxidative stress of the hypoxia neuron [mRNA]

first: hongsheng

last: gao

summary: Comparison of the differential expression mRNA profiles from the brain cortex of hypoxia and normaixa rats by silica microarray chip

overall_design: The array consists of 9 samples. Samples 1-3 consist of total RNA from the brain cortex of hypoxia rats in simulation 7km altitude; Samples 4-6: total RNA from the brain cortex of hypoxia rats in simulation 3km altitude; samples7-9: total RNA from the brain cortex of normaixa rats in simulation sea level altitude

first: H

last: Gao

first: Y

last: Wang


title: Gene expression profiling to identify potential therapeutic targets and improve prognostication of advanced penile squamous cell carcinoma

city: Birmingham

first: Sunil

last: Sudarshan

state: Alabama

address: 510 20th Street South

department: Urology

institute: UAB

summary: Advanced penile squamous cell carcinoma (PSCC) receiving first-line chemotherapy, visceral metastases (VM) and ECOG performance status ≥ 1 are poor prognostic factors for overall survival (OS). We hypothesized that tumor gene expression profiling may enhance prognostic stratification and identify potential therapeutic targets.

overall_design: We performed tumor tissue NanoString analysis of 25 patients with locally advanced or metastatic PSCC receiving first-line cisplatin-based chemotherapy to identify a prognostic gene expression signature after controlling for VM and PS status.

first: G

last: Sonpavde

first: D

last: Chandrashekar

first: S

last: Varambally


title: miRNA expression of exosomes derived from lung cancer cells A549 and cisplatin (DDP) resistant lung cancer cells A549/DDP

first: Jifeng

last: Feng

summary: To investigate the difference of miRNA expression in exosomes derived from A549 cells and its DDP-resistant cell strain A549/DDP, we have employed miRNA microarray expression to discover the difference expression of miRNAs in exosomes derived from A549 and A549/DDP. We conducted RT-qPCR to examine the expression levels of top differential expressed miRNAs, namely, miR-197-5p, miR-4443, miR-642a-3p, miR-27b-3p and miR-100-5p, confirming low variability between two methods.

overall_design: The A549/DDP was established from A549 in our laboratory, by exposing A549 to gradually increasing DDP concentrations, until the final concentration at 1μg/ml. To avoid the influence of drug to the A549/DDP cells, they were cultured in a drug-free medium for at least two weeks before gene expression analysis. After being incubated for 48-72h, the culture medium of cells was harvested. Exosomes were isolated by ultracentrifugation. And miRNA expression of exosomes derived from A549 and A549/DDP was then analzyed.

first: Xiaobing

last: Qin


title: Transcriptome analysis of the sigC deletion mutant

first: Masayuki

last: Inui

summary: Bacteria modify expression of different types of terminal oxidase in response to oxygen availability. Corynebacterium glutamicum, a facultative anaerobic bacterium in Actinobacteria, possesses aa3-type cytochrome c oxidase and cytochrome bd-type quinol oxidase, the latter of which is induced upon oxygen limitation. We report here that an extracytoplasmic function sigma factor, SigC, is unprecedentedly responsible for the regulation. Chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis detected eight SigC-binding regions in the genome, leading to identification of a consensus promoter sequence for SigC recognition. The promoter sequences were found upstream of genes for cytochrome bd, heme a synthesis enzymes, and uncharacterized membrane proteins, all of which were upregulated by sigC overexpression. In contrast, that found on the antisense strand upstream of an operon encoding the cytochrome bc1 complex conferred a SigC-dependent negative effect on the operon expression. The SigC regulon was induced by cytochrome aa3 deficiency without modification of expression of sigC itself, but not by deficiency of the bc1 complex. These findings suggest that SigC is activated in response to impairment of electron transfer via cytochrome aa3, not directly to shift in oxygen levels. Our results provide a novel paradigm for transcriptional regulation of the aerobic respiratory system in bacteria.

overall_design: Gene expression profile of the wild type at the exponential phase was compared with that of the sigC deletion mutant. Two indepent experiments using two independent mutants were performed.

first: Koichi

last: Toyoda


title: East Eurasian ancestry in the middle of Europe: genetic footprints of Steppe nomads in the genomes of Belarusian Lipka Tatars

status: Public on Aug 15 2016

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

summary: Medieval era encounters of nomadic groups of the Eurasian Steppe and largely sedentary East Europeans had a variety of demographic and cultural consequences. Amongst these outcomes was the emergence of the Lipka Tatars - a Slavic-speaking Sunni-Muslim ethno-religious minority residing in modern Belarus, Lithuania and Poland, whose ancestors arrived in these territories via several migration waves, mainly from the Golden Horde. Our results show that Belarusian Lipka Tatars share a substantial part of their gene pool with Europeans as indicated by their Y-chromosomal, mitochondrial DNA and autosomal variation. Nevertheless, Belarusian Lipkas still retain a strong genetic signal of their nomadic ancestry, witnessed by the presence of common Y-chromosomal and mitochondrial DNA variants as well as autosomal segments identical by descent between Lipkas and East Eurasians from temperate and northern regions. Hence, we document Lipka Tatars as a unique example of former Medieval migrants into Central Europe, who became sedentary, changed language to Slavic, yet preserved their faith and retained, both uni- and bi-parentally, a clear genetic echo of a complex population interplay throughout the Eurasian Steppe Belt, extending from Central Europe to northern China.

overall_design:
6 samples were analysed with the Illumina platform HumanOmniExpress-24 v1.0 BeadChip and are described herein.

Please note that the submitted information does not compromise participant privacy and is in accord with the original consent in addition to all applicable laws, regulations, and institutional policies. The submitter verified that there are no privacy concerns and that our human data can be open access.

first: Vasili

last: Pankratov

first: Alena

last: Kushniarevich

first: Oleg

last: Davydenko

first: Richard

last: Villems


title: MicroRNA miR-92a-2 targets TFPI2 to ameliorate oxidative stress of the hypoxia neuron

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


title: The Effects of Regular Post-Exercise Cold Water Immersion on DNA methylation in Muscle Following 10-weeks of Strength Training

city: Collegeville

first: Johannes

last: Freudenberg

state: Pennsylvania

address: 1250 S Collegeville Rd

department: Human Genetics

institute: GlaxoSmithKline

summary:
In this study, the primary objective was to characterise the impact of regular post-exercise (20 strength training sessions across 10 weeks) cold-water immersion (CWI) on DNA methhylation.  Secondary to this, the effect of regular post-exercise CWI on strength gains and post-exercise soreness was investigated.
We used microarrays to detail the global effects of CWI on DNA methylation in vastus lateralis muscle tissue.

overall_design: Healthy, trained road cyclists (mean ± SD; age 30 ± 8 years; height 181.5 ± 7.8 cm; mass 79.6 ± 11.3 kg) were enrolled in the study.  Participants were randomly and equally divided into two groups, one that utilised CWI as a recovery strategy and another which received a sham placebo recovery drink.

first: Phillip

middle: G

last: Bell

first: Joshua

last: Jackman

first: Arthur

last: Groy


title: The Effects of Regular Post-Exercise Cold Water Immersion on Gene Expression in Muscle Following 10-weeks of Strength Training

summary:
In this study, the primary objective was to characterise the impact of regular post-exercise (20 strength training sessions across 10 weeks) cold-water immersion (CWI) on mRNA expression.  Secondary to this, the effect of regular post-exercise CWI on strength gains and post-exercise soreness was investigated.
We used microarrays to detail the global effects of CWI on gene expression in vastus lateralis muscle tissue.


title: The Effects of Regular Post-Exercise Cold Water Immersion in Muscle Following 10-weeks of Strength Training

type:
Expression profiling by array
Methylation profiling by array


title: Phospho-site mutants of the RNA Polymerase II C-terminal domain alter subtelomeric gene expression and chromatin modification state in fission yeast

status: Public on Aug 10 2016

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

summary: Eukaryotic gene expression requires that RNA Polymerase II (RNAP II) gain access to DNA in the context of chromatin. The C-terminal domain (CTD) of RNAP II recruits chromatin modifying enzymes to promoters, allowing for transcription initiation or repression. Specific CTD phosphorylation marks facilitate recruitment of chromatin modifiers, transcriptional regulators, and RNA processing factors during the transcription cycle. However, the readable code for recruiting such factors is still not fully defined and how CTD modifications affect related families of genes or regional gene expression is not well understood. Here we examine the effects of manipulating the Y1S2P3T4S5P6S7 heptapeptide repeat of the CTD of RNAP II in Schizosaccharomyces pombe by substituting non-phosphorylatable alanines for Ser2 and/or Ser7 and the phosphomimetic glutamic acid for Ser7. Global gene expression analyses were conducted using splicing-sensitive microarrays and validated via RT-qPCR. The CTD mutations did not affect pre-mRNA splicing or snRNA levels. Rather, the data revealed upregulation of subtelomeric genes and alteration of the repressive histone H3 lysine 9 methylation (HeK9me) landscape. The data further indicate that H3K9me and expression status are not fully correlated, suggestive of CTD-dependent subtelomeric repression mechansims that act independently of H3K9me levels.

overall_design: Splicing sensitive S. pombe microarrays (Agilent-027365) were used to compare the splicing and expression profile of four mutant strains relative to WT control with 3-5 biological replicates and dye flipped samples

first: Maki

last: Inada


title: Chromatin organization in NPP-13 knockdown C. elegans embryos [array]

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary: C. elegans nuclear pore protein NPP-13 associates with small RNA genes transcribed by RNA Polymerase III. To test if the nuclear pore-chromatin interactions play a role in large-scale chromatin organization, we determined nuclear membrane-genome interactions and RNA Polymerase II localization in C. elegans embryos depleted for NPP-13.

overall_design: Genome-wide ChIP-seq and ChIP-chip for nuclear membrane protein LEM-2, RNA Polymerase II (AMA-1) and H3K4me3 were performed in mixed-stage C. elegans embryos depleted for NPP-13. As a control, ChIP was also performed in wild-type embryos treated with empty vector.

first: Jason

middle: D

last: Lieb


title: A Basic Domain in the Histone H2B N-terminal Tail is Important for Nucleosome Assembly by FACT

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: Nucleosome assembly in vivo requires assembly factors, such as histone chaperones, to bind to histones and mediate their deposition onto DNA. In yeast, the essential histone chaperone FACT (FAcilitates Chromatin Transcription) functions in nucleosome assembly and H2A-H2B deposition during transcription elongation and DNA replication. Recent studies have identified candidate histone residues that mediate FACT binding to histones, but it is not known which histone residues are important for FACT to deposit histones onto DNA during nucleosome assembly. In this study, we report that the histone H2B repression (HBR) domain within the H2B N-terminal tail is important for histone deposition by FACT. Deletion of the HBR domain causes significant defects in histone occupancy in the yeast genome, particularly at HBR-repressed genes, and a pronounced increase in H2A-H2B dimers that remain bound to FACT in vivo. Moreover, the HBR domain is required for purified FACT to efficiently assemble recombinant nucleosomes in vitro. We propose that the interaction between the highly basic HBR domain and DNA plays an important role in stabilizing the nascent nucleosome during the process of histone H2A-H2B deposition by FACT.

overall_design: 6 samples, 2 inputs and 4 ChIP samples for histone H2B (2 for wild-type and 2 for an H2B ∆30-37 mutant)

first: McKenna

last: Kyriss


title: PML1: IMR32 vs empty vector IMR32

status: Public on Aug 09 2016

city: London

first: Paolo

last: Salomoni

address: 72 Huntley St

department: Cancer Institute

institute: University College London

summary: Transcriptional profiling of neuroblastoma cell line expressing the PML1 isoform.

overall_design: Two-condition experiment: PML1 IMR32 vs empty vector IMR32. Two biological replicates, dye-swapped.

first: Ana

middle: P

last: Leite

first: Arturo

last: Sala


title: Gene expression profiling in LSD1 depleted Huh-1 cell line under hypoxic condition.

city: Daejeon

first: Yang

last: Suk-Jin

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB (Korea Research Institute of Bioscience and Biotechnology)

summary: To investigate the role for LSD1 under hypoxia condition. we depleted LSD1 gene with siRNA in Huh-1 cell lines under 1% O2 hypoxia condtion, and than perforemed gene expression microarray analysis. Using Gene Set Enrichment Analysis (GSEA), determined to identify the biological pathway.

overall_design: Determined the gene expression profile of the LSD konckdown effect under hypoxia condition. Using Gene Set Enrichment Analysis (GSEA) decided to identify the biological pathways.

first: Suk-Jin

last: Yang

first: Kyung

last: Park

first: Jung-Ae

last: Kim

first: Young

middle: I

last: Yeom


title: Expression profiling of fibroblasts treated with miR-211 and miR-320c

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

summary:
mRNA profiles generated from primary fibroblast upon treatment with miR-211, miR-302 or melanoma melanosomes.
Abstract: Melanoma originates in the epidermis and enters the metastatic and lethal phase upon invasion into the dermis. However, the interactions between melanoma cells and the dermis prior to this invasion have been poorly studied. Here we uncover that melanoma cells directly affect the formation of the dermal tumor niche by microRNA (miRNA) trafficking prior to invading the dermis. Melanocytes, the cells of melanoma origin, are specialized in trafficking of pigment vesicles, termed melanosomes and, interestingly, melanoma cells retain this trafficking ability. In melanoma in-situ specimens, we found melanosome markers in distal fibroblasts prior to the invasion of melanoma cells into the dermis. Melanoma-derived melanosomes carry miRNAs into primary fibroblasts that trigger changes in the fibroblasts, including increased proliferation, migration, and expression of pro-inflammatory genes, all known features of cancer-associated fibroblasts (CAFs). Specifically, we found that melanosomal miRNA-211 directly targets IGF2R and leads to MAPK signaling activation in fibroblasts, which reciprocally encourages melanoma growth. Treatment of melanoma cells with a melanosome release-inhibitor prevented CAF formation. Since the first interaction of melanoma cells with blood vessels occurs in the dermis, our data suggest a promising opportunity to block melanoma cell invasion by preventing the formation of the dermal tumor niche.
In the paper we showed the 10% of most differentially expressed  mRNA upon miR-211, miR-320c  and melanosomes treatment and overlap of 2000 downregulated mRNA upon miR-211 and melanosomes treatment with predicted target gene miR-211 and CAFs related genes

overall_design: Expresssion profiling was performed for primary fibroblasts transfected with miRNA-211 mimic and miRNA-320c mimic.

first: Shani

last: Dror

first: Jörg

last: Hoheisel

first: Laureen

last: Sander


title: Analysis of melanosomal miRNAs

summary: miRNA microarray profiling was performed for MNT-1 cells, pre-mature and mature melanosomes extracted from MNT-1 cells. In order to reveal the miRNAs that are most abundant in mature melanosomes, the most highly expressed miRNAs from mature melanosomes were compared with expression levels in pre-mature melanosomes. The analysis revealed five miRNAs that were highly expressed in mature melanosomes and had been previously associated with melanoma.

overall_design:
Total RNA was extracted from MNT-1 cells (2 replicates), pre-mature and mature melanosomes. The melanosomes were either treated with RNase prior to RNA extraction (2 replicates each) or untreated (1 replicate each). Melanosomes were extracted from MNT-1 melanoma cells by sucrose-based density gradient ultracentrifugation. The treatment of melanosomes with RNase prior to RNA extraction was performed in order to remove any kind of RNA that may interact with or stick unspecifically to the outer side of the melanosome membrane. After 10 mins of RNAse treatment, RNase inhibitor was added. The samples of MNT-1 cells and untreated melanosomes were considered for the normalization, but not for further analyses.
Microarray Unit of the Core Facility Genomics and Proteomics DKFZ


title: Analysis of melanosomal, exosomal and cellular miRNAs of melanoma cells

summary: miRNA microarray profiling was performed for exosomes and secreted melanosomes of MNT-1 cells as well as WM3682 and WM3314 cells and melanosomes isolated from cell homogenates. The aim of this study is to compare the miRNA content of exosomes and secreted melanosomes and to assess differences in the miRNA profiles of different melanoma cell lines and their melanosomes.

overall_design: Total RNA was extracted from MNT-1 exosomes and secreted melanosomes (2 replicates each) that were isolated from the conditioned medium of MNT-1 melanoma cells by differential ultracentrifugation. In addition, total RNA was isolated from WM3682 and WM3314 melanoma cells and melanosomes (1 replicate each). These latter melanosomes  were isolated from cell homogenates by filtration through a 0.45 µm filter, followed by FACS sorting. Contributor: Microarray Unit of the Core Facility Genomics and Proteomics DKFZ

first: Apcher

last: Sébastien


title: MicroRNA expression profile between human colorectal cancer SW480 and SW620 cell line

status: Public on Aug 01 2016

city: Xiamen

first: Wei

last: Yan

address: Hubin South Road 201

institute: Xiamen University

summary:
Two isogenic human colorectal cancer cell lines (primary SW480 cell line and its lymph node metastatic variant SW620 cell line),as an in vitro metastatic model.
We have demonstrated that SW620 cell line possesses high metastasis potential  and  SW480 cell linepossesses low metastatic potential.

overall_design: We want to compare the whole cell microRNAs profiles of two isogenic colorectal cancer cell lines (SW480 and SW620 cell line),  to gain an insight into the molecular events of colon cancer metastasis.


title: Perturbation of epigenetic processes by doxorubicin in the mouse testes: mRNA analysis

status: Public on Aug 04 2016

city: Didcot

first: Emma

middle: Louise

last: Marczylo

address: Harwell Campus, Chilton

department: Toxicology

institute: Public Health England

summary: mRNA profiling of mouse testis comparing treatment with doxorubicin to vehicle only control (published in Toxicology Research, DOI: 10.1039/C6TX00078A)

overall_design: Two-condition experiment, doxorubicin vs control at 3 time points (1wk, 4wk and 7 wk following treatment). Biological replicates: 6 control, 6 doxorubicin (implementing a dye swap design of n=3 forward and n=3 reverse). One replicate per dual colour array, which consists of two slides (total of 18 arrays and 36 slides/raw data files).

middle: L


title: SPROUTY2 target genes in human colon carcinoma cells

city: Madrid

first: Antonio

last: Barbachano

state: Madrid

address: c/ Arturo Duperier 4

institute: Instituto de Investigaciones Biomédicas "Alberto Sols"

summary: The role of SPROUTY2 (SPRY2) in human colon cancer is controversial. Our data support a tumorigenic action of SPRY2. We use microarrays to identify SPRY2 target genes in human SW480 ADH colon carcinoma cell line.

overall_design: RNA was obtained from SW480 ADH cells, Mock transfected or transfected with WT or two differents SPRY2 genes mutants. Hybridization was performed on Affymetrix microarrays. We performed three independent experiments.  Each experiment was conducted in triplicate.

first: Alberto

last: Muñoz


title: Transcriptomic responses of Anguilla anguilla elvers fed dietary LPS

status: Public on Jul 31 2016

city: Leioa

first: Ibon

last: Cancio

address: B/sarriena s/n

institute: UPV/EHU

summary:
Dietary immunostimulants are considered as an effective tool for enhancing the immune status of cultured organisms and improving their general welfare. Immunostimulants are chemical substances which activate transiently elements of the immune response and may potentially render animals more resistant to infectious diseases. They also reduce the risk of disease outbreaks, if administrated prior to situations known to result in stress and impaired general performance (e.g. handling, change of temperature and environment, weaning to inert diets) or prior to expected increase in exposure to pathogenic microorganisms and parasites. In this study, we have evaluated the effect of dietary LPS derived from Pantoea agglomerans (LPSp, SOMACY SL100, MACROPHI Inc., Japan) in Anguilla anguilla elvers considering the general condition, growth and immune status of the animals.
Elvers (1.7 ± 0.2 g) obtained from local fishermen (Delta del Ebro, Spain) were fed at different doses of c (0, 20 and 40 μg LPSp kg BW-1 day-1) for a period of 70 days (4 replicates per dietary group). LPSp was added to the diet (52% protein, 24% fat, 9% ash) by top coating the pellets with the lyophilized powder of LPSp dissolved in 2% fish oil (diets manufactured by ALLERQUA, Denmark). The trial was conducted in 100 L tanks (40 L functional volume) connected to a recirculation unit (IRTAmar®) and water quality was as follows: temperature, 21 ± 0.5 ºC; pH, 7.5 ± 0.1; photoperiod, 12 L:12 D and oxygen at saturation levels. At the end of the trial, fish were measured for growth (BW), size dispersion, histological organization of the intestinal mucosa and the transcriptomic responses of the spleen were evaluated by means of a 60K (15000 gene signatures) custom oligonucleotide microarray (Agilent Technologies Inc.).
No significant differences in BW nor survival were observed among groups regardless of the dose of LPSp (BW: 3.9 ± 0.3 g, survival: 98-99%). Micorarray analysis (LIMMA F<0.05; adj. p value < 0.005) resulted in 81 significantly up-regulated genes and only 3 down-regulated genes, in the highest LPSp dose. The lowest dose of LPSp up-regulated 26 genes and down-regulated 50. Both doses resulted in regulation of immune related genes, such as, sensors for detection of viral and bacterial products, innate antiviral response genes, cytokines, adipocytokines, and their regulatory nuclear factors. The pathway enrichment analysis (FatiGO; p < 0.005) of up-regulated genes (40 μg LPSp kg BW-1 day-1) indicated among the most significantly regulated KEGG pathways: cytokine-cytokine receptor interaction, Jak-STAT signalling, natural killer cell mediated cytotoxicity, Toll-like, RIG-I-like and NOD-like receptor signalling and Wnt, Notch and mTOR signalling. In conclusion, LPSp diet highly regulates spleen transcription levels, mainly enhancing the immune response capacity of the immunostimulated elvers.
This study was funded by the CENIT-ACUISOST project (CDTI, Spain), IRTA, Basque Government (S-PC08UN03; IT810-13) And UPV/EHU (UFI 11/37). Technical and human support provided by SGIker (UPV/EHU) is acknowledged. Authors are also in debt to G. Macià (IRTA-SCR) for fish care and maintenance during the trial.

overall_design: 21 samples are analyzed, 7 pools of 3 spleens in each experimental group,Control group; Diet of 20ug/kg and 40ug/kg

first: Oihane

last: de Cerio

first: K

last: Andree

first: M

last: Castillo

first: Enric

last: Gisbert


title: OX40L protects against inflammation-driven fibrosis

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary:
Fibrosis is a leading cause of deaths in industrialized countries and has no effective therapy. We demonstrated that blockade of OX40L prevented inflammation-driven fibrosis affecting the skin and the lungs and promotes regression of established dermal fibrosis in different murine models.
To characterize the pathways involved in the protection of skin fibrosis and affected by OX40L blocking, we used microarrays and identified distinct genes differentially expressed between ox40l+/+ and ox40l-/- in the bleomycin-induced dermal fibrosis mouse model.

overall_design: Total RNA were extracted from lesional skin samples of 3 ox40l+/+ and 4 ox40l-/- male mice aged 9 weeks treated with bleomycin for 3 weeks, and were hybridized on Affymetrix microarrays.

first: Muriel

last: Elhai

first: Yannick

last: Allanore

first: Jérôme

last: Avouac


title: Regulation of miRNA expression by TGF-b in endothelial cells

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

institute: Nagoya University

summary: Effect of transforming growth factor-beta (TGF-b) on miRNA expression profile in MS1 endothelial cells.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: MS1 endothelial cells were treated with/without TGF-b (72 hours), and subjected to miRNA microarray analysis.

first: H


title: Expression analysis of Candida glabrata CBS138 delta-vph2 mutant

city: Nagasaki

last: Nishikawa

address: 1-7-1 Sakamoto

institute: Nagasaki University Graduate School of Biomedical Sciences

summary: Investigation of whole genome gene expression level changes in Candida glabrata CBS138 delta-vph2 mutant, compared to the wild-type strain in SC broth (pH5.0 and pH7.4).  VPH2 gene encodes a protein that is the assembly factor of a functional V-ATPase. Loss of Vph2p leads to loss of a functional V-ATPase enzyme complex.

overall_design: A eight chip study using total RNA recovered from two separate wild-type cultures of Candida glabrata CBS138 and two separate cultures of Candida glabrata CBS138 delta-vph2 mutant in SC broth (pH5.0 and pH7.4), in order to confirm whether alkalization of the media affects the gene expression level of vph2 mutant.  Each chip measures the expression level of 5,217 genes from Candida glabrata CBS138 with six 60-mer probe pairs per gene, with two-fold technical redundancy.

first: Taiga

last: Miyazaki

first: Hironobu

last: Nakayama


title: Transcriptome profiling of zebrafish brain under hypoxia

city: Adelaide

first: Esmaeil

last: Ebrahimie

address: School of Biological Sciences, North Tce

country: Australia

institute: The University of Adelaide

summary: Adult zebrafish (Tübingen strain, sex not specified) at approximately 1 year of age were analysed. For experiments conducted under low oxygen conditions, nitrogen gas was bubbled through water to deplete oxygen before exposure of individual fish to the medium. Oxygen concentrations were measured using a dissolved oxygen meter (DO 6+, EUTECH instruments, Singapore). The dissolved oxygen level for hypoxia treatment was measured to be 1.20 ± 0.6 mg/l, whereas normal ambient oxygen levels were 6.6 ± 0.45 mg/l. Zebrafish were exposed to the hypoxic medium for 3 hours. Briefly, after each hypoxia trial, the animals were euthanized by hypothermic shock and then decapitated to remove the brain. Total RNA was extracted from samples mentioned above using the QIAGEN RNeasy mini kit (QIAGEN, GmbH, Hilden, Germany) and stored at −80°C before further analysis. RNA concentration was determined with a NanoVue™ UV–vis spectrophotometer (GE Healthcare Life Sciences, Fairfield, USA). RNA integrity and quality were then estimated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and the RNA integrity number (RIN) index was calculated for each sample. Only RNAs with a RIN number >7.0 were processed further. Microarray analysis of gene expression was performed using the Zebrafish Gene 1.0 ST Array (Affymetrix Inc. Santa Clara, CA). Briefly, 300ng of total RNA derived from a single adult brain was converted to amplified sense strand cDNA using the Ambion WT Expression Kit (Life Technologies, Carlsbad, CA). The resulting sense cDNA was fragmented and Biotin end-labelled using the Affymetrix Genechip WT Terminal Labeling Kit prior to hybridisation to the array at 45 °C for 16 hours.

overall_design: Two treatments including hypoxia and normoxia were studied. Each treatment had three biological replicates (i.e. three fish exposed to hypoxia and three fish exposed to normoxia). Six samples were analysed. Microarray analysis of gene expression was performed using the Zebrafish Gene 1.0 ST Array. The signal intensity of the chip was scanned using a GeneChipR Scanner 3000TG and analysed using Expression Console software (www. Affymetrix.com). CEL files were imported and intensities adjusted by RMA background correction and quantile normalization.

first: Seyyed

last: Hani Moussavi Nik

first: Morgan

last: Newman

first: Michael

last: Lardelli


title: Impact of E2 ubiquitin conjugating activity of MUC1 on gene expression

city: Omaha

first: Ryan

last: Hanson

state: Nebraska

address: 42nd and Emile

department: Eppley

institute: University of Nebraska Medical Center

summary: We identified a novel E2 ubiquitin conjugating activity within the C-terminus domain of MUC1.  To determine if E2 ubiquitin conjugating activity of MUC1 is responsible for regulating expression of oncogenic genes we isolated RNA from vector control cells, MUC1 wildtype overexpression cells, and cells that express a serine mutant lacking E2 activity.

overall_design: RNA was isolated from each of the 3 cell lines, S2013.Neo, S2013.MUC1-WT, and S2013.MUC1-Ser. Gene expression was analyzed by spotted microarray and the differences in gene expression were calculated between the cell lines

first: Roger

last: Brown

first: James

last: Grunkemeyer

first: Darci

last: Fink

first: Prakash

last: Radhakrishnan

first: Ashley

last: Mohr

first: Paul

last: Grandgenett

first: Pankaj

middle: K

last: Singh

last: Hollingsworth


title: HEPATIC GENE EXPRESSION PATTERNS IN JUVENILE TURBOTS (Scophthalmus maximus) AFTER EXPOSURE TO NO2 FUEL OIL AND TO STYRENE (PRAGMA, a pragmatic and integrated approach for the evaluation of environmental impact of oil and chemical spills at sea)

first: Ibon

last: Cancio

summary: Accidental spills of chemical or oil tankers such as Levoli Sun or Prestige have recently impacted the European seas. The analysis of the genes regulated by exposure to spilled chemical substances could help elucidating adaptatory and compensatory pathways that may participate in pathogenesis in marine biota. Hepatic expression profiles of male juvenile S. maximus exposed to a nº2 fuel-oil (FO) and to styrene were studied employing a turbot custom microarray containing 2715 3’-UTR biassed single-sequences, many of them unannotated. Hybridisations identified 169 and 293 genes significantly regulated after 3 and 14 days of exposure to FO, respectively. Typical PAH responsive genes such as AhRR, ARNT2, CYP1A1 and GST were significantly upregulated. Exposure significantly affected genes involved in protein metabolism, synthesis being the most regulated pathway with ribosomal proteins and various translation factors overexpressed. Protein synthesis could participate in compensatory pathways after FO induced protein damage. Additionally, two weeks of exposure resulted in the upregulation of ras pathway genes. Regarding styrene, gene expression was very variable within experimental groups and only 2 genes were significantly regulated after 3 days of exposure. After 1 week of exposure styrene modified the expression levels of 44 genes. Most highly regulated genes, that may constitute new biomarkers of exposure to styrene, included those coding for estrogen-responsive finger protein, transmembrane 9 superfamily member 4 or selenoprotein-T, but the only pathway found to be significantly regulated was once again that of protein synthesis.  Funded EU project PRAGMA, Spanish MEC (CANCERMAR), Basque Government (Consolidated Research Groups GIC07/26-IT-393-07).

overall_design: Turbots were exposed to fuel-oil  and to seawater control: 7 turbots in Control tank and 8 in Oiled tank. After 3 days of exposure turbots were in situ dissected and liver was extracted, inmersed in RNAlater  and frozen in liquid N2

first: Eider

last: Bilbao

first: Oihane

last: de Cerio

first: Belén

last: Pardo

first: Paulino

last: Martínez

first: Miren

last: Cajaraville


title: Fluidigm Biomark 96.96 nanofluidic arrays for qRT-PCR of 93 miRNAs: salivary extracellular vesicles

city: Koto

first: Kiyotaka

last: Shiba

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation for Cancer Research

summary: Crude extracellular vesicles (EVs) from eight healthy volunteers were separated into 6 fractions based on their densities by using the iodixanol-based density gradient centrifugation method. To determine the distribution of miRNAs among these fractions, quantities of 93 miRNAs were quantified by the TaqMan real time PCR method using the BioMark HD system (Fluidigm) equipped with 96.96 dynamic array (Fluidigm).

overall_design: Six samples were fractionated from a crude EVs by density gradient centrifugation. Total of 48 samples were prepared from 8 healthy volunteers. Technical replicate of 4 gave 8 x 6 x 4 x 93 = 17,856 data. As control Tris-HCl EDTA buffer (TE) was used.

first: Kazuya

last: Iwai

first: Tamiko

last: Minamisawa

first: Kanako

last: Suga

first: Yasutomo

last: Yajima


title: HEPATIC GENE EXPRESSION PATTERNS IN JUVENILE TURBOTS (Scophthalmus maximus) AFTER EXPOSURE  TO STYRENE (PRAGMA, a pragmatic and integrated approach for the evaluation of environmental impact of oil and chemical spills at sea)

overall_design: Turbots were exposed to styrene  and to seawater control. After 3 and 7 days of exposure turbots were in situ dissected and liver was extracted, inmersed in RNAlater  and frozen in liquid N2


title: MicroRNA Expression Profile of serum exosomes from Bortezomib-resistant and Bortezomib-response patients in multiple myeloma

city: Chengdu

first: Li

last: Zhang

state: Sichuan

address: No. 37 Guo Xue Xiang

department: Department of Hematology

institute: West China Hospital, Sichuan University

summary: MicroRNA microarray profilling analysis was performed on exosomes derived from serum in patients with myeloma in two conditions of therapeutic efficacy, Bortezomib resistance and Bortezomib response. Bortezomib is approved and widely used treating myeloma.

overall_design: Two kinds of sample were analyzed. MicroRNA microarray profilling analysis (using miRCURY LNA microRNA Array, 7th generation REV - hsa, mmu & rno, mirBase release 18, ProductNumber=208520,208521,208522) was performed on exosomes derived from serum in patients with myeloma in two conditions of therapeutic efficacy, Bortezomib resistance and Bortezomib response.


title: Genomic landscape affected by allelic imbalance in the cancerization filed of normal appearing airway

city: Houston

first: Yasminka

middle: Aleksandra

last: Jakubek

state: TX

address: 1155 Pressler St

department: Epidemiology

institute: University of Texas MD Anderson Cancer Center

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

summary: Normal appearing airway samples from non-small cell lung (NSCLC) cancer patients were profiled using illumina sequencing arrays. Allelic imbalance was detected in normal-appearing large and small airway samples and affected known lung cancer driver genes.

overall_design: Multiple airway samples from 45 patients were analyzed using illumina sequencing arrays in order to comprehensively asses the genomic landscape of airway epithelia adjacent to NSCLC. For each patients there was at least one small airway sample, a tumor samples, as well as germline control sample (blood and/or normal uninvolved lung). In addition to these samples additional samples were analyzed for a subset of patients these included large airway, nasal, and multiple core needle biopsies from the tumor.

last: Scheet

first: Humam

last: Kadara


title: The study of the hepatic transcription profiles of eels caged in an area affected by paper industry

summary: Ecotoxicogenomic studies face the problem of the lack of gene sequence information available for toxicologically relevant non-model pollution sentinel species. In this sense, next generation sequencing technologies allow obtaining deep de novo sequence information cost-effectively. We have thus employed the platform GS-FLX of Roche technologies, in order to sequence the multitissue transcriptome of a fish species under severe population decline, the European eel (Anguilla anguilla), using normalized cDNA (Evrogen). The European eel could be successfully employed in pollution biomonitoring studies as it is a euryhaline teleost that is quite resistant to chemical exposure. We have completed a one whole plate sequencing-run using the Titanium kit of Roche from which a total of 7.8x105 reads were obtained with a length average of 303.53 bp.  Annotated genes, for instance, could be further assessed as biomarkers of exposure to specific chemical compounds in marine, estuarine and river waters. Designed tool will be thus useful, in the study of: a.- the mode of action of chemical compounds in active monitoring studies using caged eels, b.- the physiological processes that are specific to freshwater eels such as the one of sexual development and reproduction, c.- reasons that could explain the disappearance of the species from European waters. In the first context, a caging experiment was  performed to measure the putative effects of a paper industry effluent on eel hepatic transcription levels. For this purpose, eels were caged upstream and downstream to the SMURFFIT-KAPPA paper industry in Iurreta (Biscay, Basque Country). Thus, hepatic transcription profiles reflect the stress levels suffered by eels.

overall_design: The experiment contains a time serial sampling: T0 = before sampling; T1 = after 3 days of exposure; T2=after 15 days of exposure. In addition, caged eels were placed in 2 sites, Upstream (Up) and Downstream (Do) of the hotspot. 6 samples were dissected per sampling group (5 groups= ToUP; T1UP; T1Do; T2Up; T2Do), 30 samples in total


title: Biological function of antisense RNAs that are synthesized by RNA-dependent RNA polymerases under abiotic stress

city: Yokohama

first: Akihiro

last: Matsui

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

department: Center for Sustainable Resource Science

institute: RIKEN

summary: To identify RDR1/2/6-dependent antisense RNA loci under 2hr drought stress, expression profiles of Poly (A+) RNA and Poly (A-) RNA between rdr1/2/6 and wild-type using the custom microarray (GPL19830) were analyzed.

overall_design: rdr1/2/6 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium for 2 hours. Then, the plants were transferred to  plastic dish  and kept for 1 week. Poly (A+) RNA and Poly (A-) fractions were separated from 100μg total RNA by treating with Ambion Poly A purist twice. Poly (A-) RNA sample was prepared by depleting rRNA using Invitrogen RiboMinus Plant Kit. 5 ng of Poly (A+) RNA  and 1.4 μg of Poly (A-) RNA samples were used for the expression profiling using the custom array (GPL19830).

first: Kayoko

last: Mizunashi

first: Maho

last: Tanaka

first: Kei

last: Iida

first: Motoaki

last: Seki


title: Comparison of the gene expression profiles of different strains of A. baumannii by microarrays

city: A Coruña

first: Margarita

last: Poza

address: As Xubias

department: Microbiology

institute: Fundacion Prof Novoa Santos-Insituto de Investigacion Biomedica

summary: In the present work we compare the gene expression profile of A. baumannii and a mutant knock-out strain of A. baumannii lacking a small RNA gene 13573 and the corresponding small RNA 13573 over-producing strain. The main objective is to recognize the main pathways in which the small RNA 13573 is involved. Moreover, the same wild type strain was used to infect mice and was further analyzed after the infection with the aim of finding genes differentially expressed in vivo.

overall_design: Three biological replicates have been performed for each comparison. The RNA collection from Acinetobacter baumannii strain over-expresing the small RNA (sample 13573) was compared with this isolated from A. baumannii harboring the empty vector (PETRA sample) while gene expression in the knock-out strain (KO sample) was compared with the wild type strain Acinetobacter baumannii ATCC 17978 (ATCC sample). The RNA from A.baumannii recovered from the infected animals (INF sample) was compared with the wild type (ATCC).

first: Soraya

last: Rumbo-Feal

first: Laura

last: Alvarez-Fraga

first: Alejandro

last: Beceiro


title: Immortalization capacity of HPV types is inversely related to chromosomal instability in immortal descendants.

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

summary: Human papillomavirus (HPV) induced immortalization of human foreskin keratinocytes (HFK) is a two-step process, including 1) the bypass of replicative senescence and acquisition of an extended lifespan, and 2) the outgrowth of immortal cells. Our previous study showed that the immortalization capacity of HPV is type dependent, as reflected by the presence or absence of a crisis period before reaching immortality. In the present study we determined how the HPV-type specific immortalization capacity relates to DNA damage induction and overall genomic instability. Early passage HFKs transduced with HPV types 16, 18, 31, 33, 35, 45, 51, 59, 66 and 70 showed an increased number of double strand DNA breaks compared to controls, without significant differences between the various HPV-types. However, immortal descendants of HPV-transduced HFKs that underwent a crisis period (HPV45-, 51-, 59-, 66- and 70-transduced HFKs) showed significantly more chromosomal aberrations compared to those without a crisis period (HPV16-, 18-, 31-, and 35-transduced HFKs) (p<0.01). In particular, regions on chromosome 5p, 8, and 9q were significantly more frequently altered in cells with crisis. Interestingly, the hTERT locus at 5p was exclusively gained in cell lines with crisis. Chromothripsis was detected in one of the HPV16-immortalized cell lines in which multiple rearrangements within chromosome 8 resulted in a gain of c-MYC. In conclusion, the present study shows that upon HPV-induced immortalization, the number of chromosomal aberrations is inversely related to the immortalization capacity of the virus type. This suggests that hrHPV types with reduced immortalization capacity in vitro, as reflected by a crisis period, require more genetic host cell aberrations to trigger immortalization.

overall_design: DNA copy number analysis of human keratinocytes transformed by high-risk HPV

first: Denise

middle: M

last: Schütze

first: Oscar

last: Krijgsman

first: Renske

last: Steenbergen


title: Identification of the PhoB regulon and role of PhoU in the phosphate-starvation response of Caulobacter crescentus (expression)

status: Public on Aug 06 2016

city: Cambridge

first: Michael

last: Laub

state: MA

address: 31 Ames St

institute: MIT

summary: An ability to sense and respond to changes in extracellular phosphate is critical to the survival of most bacteria. For Caulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria, Caulobacter responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here, we use ChIP-Seq to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB in both phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes in phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help Caulobacter scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in Caulobacter as depleting PhoU has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit a striking accumulation of large polyphosphate granules suggesting that PhoU participates in controlling intracellular phosphate metabolism.

overall_design: RNA was collected from cultures grown to mid-exponential phase in rich medium (PYE) at 30 degrees C.  The strain grown in the presence of 50 mM vanillate was compared to the same strain grown in the absence of vanillate.

middle: T

first: Emma

last: Lubin


title: Hepatic transcription profile study on European eels (Anguilla anguilla) exposed to Hg and b-sitosterol

first: Ibon

last: Cancio

summary:
Many enigmas surround different aspects of freshwater eel biology and life cycle. In the same way different hypothesis about why eels are disappearing from European continental waters have been proposed. One such proposal defends that poor fat accumulation of eels, due to pollution in continental waters, might be stopping eels from reproductive migration to the Sargasso Sea. Thus, habitat deterioration could be blamed for the decline in the catchment potential of the European rivers. In this context, and with the aim to study the mode of action of environmentally relevant chemicals in eels, the multi tissue transcriptome was sequenced (454 Titanium Roche) in order to design a high density custom oligonucleotide microarray (eArray, Agilent). To validate this tool a laboratory experiment was carried to analyze the gene trasncrition profiles related to chemical compounds released from pulp and paper mills; 100 μg/L mercury and 150 μg/L β-sitosterol (only Hg data is presented here). 20 yellow European eel (Anguilla anguilla) elvers (11.7±5.35 g) obtained from a local farm (Acuivas SL, Usurbil, Gipuzkoa) were exposed for 3, 6 and 9 days.   Pyrosequencing allowed the design and construction of a 60K microarray platform containing 3923 gene signatures identified through BlastN analysis and 7212 sequences annotated through BlastX coupled to Blast2Go analysis. Additional 226 sequences were incorporated from NCBI databases and 3551 from the information available in EeelBase in 2011. Two probes were generated per sequence and they were spotted twice in the array.
Hepatic gene expression profiling of the exposed eels indicated that Hg significantly down-regulated (LIMMA, adj. p<0.005) only gene signatures related to selenoprotein W-1 (SeW), something typically described in mammals exposed to methyl-mercury. Increasing the adj. p value to <0.05, 116 genes were significantly regulated (38 down-regulated and 79 up-regulated). Among them, we found additional selenoproteins such as ROS metabolism related genes; glutathione peroxidases (gpx1 & gpx4b) and thioredoxine which were up-regulated. In addition, complement system genes (C3 & C4b) were also up-regulated. Studying enriched Go pathways (p<0.005) and in relation with lipid homeostasis we observed that the following pathways were enriched after exposure to Hg: fatty acids degradation and metabolism of arachidonic acid, linoleic acid, ether lipids, alpha linolenic acid, and glycerophospholipids. In addition, among the top 10 significantly enriched KEGG pathways, p53 signalling, apoptosis, and MAPK signalling were present, suggesting possible effects on cell cycle regulation.
In summary, transcriptome pyrosequencing and subsequently designed microarray provided the molecular tools to successfully study the gene transcription profiles of toxic chemical compounds such as Hg in European eel tissues. In addition to study the molecular modes of action of specific chemical compounds, the developed gene expression microarray will be useful in active monitoring of the quality of freshwater environments using caged sentinel eels.
This study was funded by Basque Government (SAIOTEK S-PE09UN32; Consolidated Research Groups IT810-13) and UPV/EHU (UFI 11/37). Technical and human support provided by SGIker (UPV/EHU) is acknowledged.

overall_design:
An exposure laboratory experiment was performed in the “Ur Biologia eta Experimentazio Zerbitzua” (UBEZ) of the University of the Basque Country (UPV/EHU) A total of 84 eels, 20.23 ± 2.84 cm in length, were acclimatized to laboratory conditions for 2 weeks in a 10 L water glass tanks under controlled conditions: 12 h light/dark cycle at 18oC, conductivity 600 μS. During this period animals were fed with commercial flakes. Ammonium, nitrites and nitrates kits (Sera GmbH) were used to systematically asses the levels of nitrogenous compounds which were maintained at 0-0.5mg/l; 0-0.5 mg/l, and 5-10 mg/l, respectively. When highest concentrations within those ranges were achieved seawater was partially replaced.
A day before exposure experiment, animals were placed in 4 aquaria with 8 L of water at 600 μS. In each aquarium 21 eels were randomly distributed and exposed to: metal-mercury (Hg) (Fluka-Sigma-Aldrich) at a concentration of 100μg/L; and to a phitosterol, β-sitosterol (Sigma) at a concentration of 150 μg/ L. The last compound needed ethanol (0.01%) as vehicle. In addition to an ethanol control group, a water control (600μS) without contaminant was also prepared. Water used during the experiment was filtered at 0.5mm and treated with UV light. Toxic metabolites were measured everyday during experiment using ammonium, nitrites and nitrates test (Sera GmbH), and water was partially replaced every day. Eels were fed everyday with 10mg of commercial food per eel.
After 3, 6 and 9 days exposure (T1, T2 and T3 respectively) 7 eels were anaesthetized with 3-aminobenzoate methylsulfonate salt (Sigma-Aldrich). Size and weight were measured for Fulton´s conditioning index assessments, and liver was dissected and frozen with RNA later® in liquid nitrogen for molecular studies.

first: Oihane

last: de Cerio


title: HEPATIC GENE EXPRESSION PATTERNS IN JUVENILE TURBOTS (Scophthalmus maximus) AFTER EXPOSURE TO NO2 FUEL OIL (PRAGMA, a pragmatic and integrated approach for the evaluation of environmental impact of oil and chemical spills at sea)

overall_design: Turbots were exposed to fuel-oil  and to seawater control: 7 turbots in Control tank and 8 in Oiled tank. After 14 days of exposure turbots were in situ dissected and liver was extracted, inmersed in RNAlater  and frozen in liquid N2

first: Eider

last: Bilbao

first: Belén

last: Pardo

first: Paulino

last: Martínez

first: Miren

last: Cajaraville


title: Expression data from human HMGN4- and HMGN2-expressing mouse embryionic fibroblasts

city: Bethesda

first: Yuri

last: Postnikov

state: MD

address: 37 Convent Dr

institute: NIH

summary:
HMGN proteins, a family of non-histone nucleosome-binding proteins, maintain a dynamic balance between more and less compacted fibers via interactions with other architectural elements of chromatin.
This balance affects the ability of regulatory factors to access their target sites, which eventually modifies the expression profile of the cell.
We used microarrays to detail  gene expression change in mouse fibroblasts overexpressing human HMGN4  to identify outlier genes and distinct classes of up- and down-regulated genes during this process.

overall_design: Mouse embryonic fibroblasts (MEFs), MEFs, expressing hHMGN4 (MEF-N4)  or hHMGN2 (MEF-N2) or vector alone (MEF-V, served as a control) were harvested from exponentially grown cell culture  for RNA extraction and hybridization on Affymetrix microarrays.

first: Jamie

last: Kugler


title: MRF4 negatively regulates adult skeletal muscle growth by repressing MEF2 activity

status: Public on Jul 15 2016

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary: The myogenic regulatory factor MRF4 is expressed at high levels in myofibers of adult skeletal muscle, but its function is unknown. Here we show that knockdown of MRF4 in adult muscle causes hypertrophy and prevents denervation-induced atrophy. This effect is accompanied by increased protein synthesis and the widespread activation of genes involved in muscle contraction, excitation-contraction coupling and energy metabolism, many of which are known targets of MEF2 transcription factors. Genes regulated by MEF2 represent the top-ranking gene set enriched after Mrf4 RNAi, and a MEF2 reporter is inhibited by co-transfected MRF4 and activated by Mrf4 RNAi. The role of MEF2 in mediating the effect of MRF4 knockdown is supported by the finding that Mrf4 RNAi-dependent increase in fiber size is prevented by dominant negative MEF2, while constitutively active MEF2 is able to induce myofiber hypertrophy. The nuclear localization of the MEF2 co-repressor HDAC4 is impaired by Mrf4 knockdown, suggesting that MRF4 acts by stabilizing a repressor complex that controls MEF2 activity. The demonstration that fiber size in adult skeletal muscle is controlled by the MRF4-MEF2 axis opens new perspectives in the search for therapeutic targets to prevent muscle wasting, in particular sarcopenia and cachexia.

overall_design: Adult innervated and denervated rat soleus muscles were transfected with shRNA to Mrf4 (M1) or to LacZ as a control. Muscles were dissected and examined after 7 days. For each group/condition we selected three different muscles (biological replicas).

first: Irene

last: Moretti

first: Stefano

last: Ciciliot

first: Kenneth

last: Dyar

first: Reimar

last: Abraham

first: Marta

last: Murgia

first: Lisa

last: Agatea

first: Takayuki

last: Akimoto

first: Mattia

last: Forcato

first: Philippe

last: Pierre

first: N. Henriette

last: Uhlenhaut

first: Peter

middle: W

last: Rigby

first: Jaime

middle: J

last: Carvajal

first: Bert

last: Blaauw

first: Elisa

last: Calabria

last: Schiaffino


title: GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes. [gene expression]

status: Public on Jul 19 2016

city: Nankang, Taipei

first: Der-Hwa

last: Huang

state: Taiwan

address: 128, Sec2, Academia Rd.

department: Insititute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary:
GAF mutant larvae compare control WT larvae.
To determine the effects of GAF mutation on global larval gene expression.

overall_design: Two-genotype experiment, WT vs. GAF mutant. 3 biological replicates

first: Shih-Ying

last: Tsai


title: Meiotic behavior analysis of a balanced reciprocal translocation in the pig

status: Public on Jun 30 2016

city: Castanet-Tolosan

first: Herve

last: Acloque

address: 24 chemin de Borde Rouge

department: Animal Genetics

institute: INRA

summary:
Balanced constitutional reciprocal translocations are the most common structural chromosomal rearrangements identiﬁed in man and pigs. Carriers are generally phenotypically normal, but such rearrangements frequently lead to reproductive disorders.
In reciprocal translocation heterozygotes, the homologous regions of the normal and derivative chromosomes involved in the rearrangement pair during the prophase of the first meiotic division, thanks to the synaptonemal complex (SC), and form a particular structure called quadrivalent. In some cases, chromosomal regions (within the quadrivalent) remain unsynapsed, especially around the breakpoints, which may trigger meiosis checkpoints leading to spermatogenesis arrest at the pachytene stage. Several hypotheses have been proposed to explain such effects of pairing failure on gametogenesis. The first one is an altered transcription of the genes located on the unpaired segments. Indeed, studies conducted in mice revealed a transcriptional repression of unpaired regions by a specific mechanism called “Meiotic Silencing of Unsynapsed Chromatin” (MSUC) in individuals with a partial or total spermatogenesis arrest (Turner et al., 2005). If some genes necessary for the proper course of meiosis are located in such unsynapsed genomic regions, MSUC may result in an arrest of the meiotic division. Secondly, associations between the “quadrivalent” and the XY bivalent which is transcriptionally silenced by a phenomenon known as meiotic sex chromosome inactivation (MSCI, (Turner, 2007) were also observed in individuals with altered semen parameters (azoospermic or oligospemic) (Oliver-Bonet et al., 2005; Sciurano et al., 2007a, 2012). Such an association could result in a partial reactivation of the XY body (XYB) leading to the expression of some genes located on the X chromosome (Lifschytz and Lindsley, 1972), or result in the spreading of the XYB inactivation towards the autosomal segments attached to the XYB, without reactivation of the latter (Jaafar et al., 1993).
Beyond the potential spermatogenesis failure mentioned above, reciprocal translocations are systematically responsible for the production of genetically unbalanced gametes. Here we report the detailed analysis of the whole meiotic process (from spermatocytes to spermatozoa) in the case of a constitutional balanced reciprocal translocation responsible for severe oligoasthenoteratospermia.

overall_design: Total RNA was extracted in 3 replicates from testicular biopsies control animals, from testicular biopsy of an oligospermic boar and from testicular biopsy of a severe oligo-astheno-teratospermic boar carrier of the trcp(1;14) reciprocal translocation.

first: Alain

last: Pinton

first: Hervé

first: Harmonie

last: Barasc

first: Annabelle

last: Congras

first: Valentine

last: Marquet

first: Stéphane

last: Ferchaud

first: Nicolas

last: Mary

first: Isabelle

last: Raymond Letron

first: Anne

last: Calgaro

first: Anne-Marie

last: Loustau-Dudez

first: Nathalie

last: Mouney-Bonnet

first: Martine

last: Yerle

last: Ducos


title: An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene [array]

status: Public on Jul 07 2016

city: Majadahonda

first: Antonio

last: Martin-Galiano

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Bacterial genetics

institute: Instituto de Salud Carlos III

summary: We studied the response to increased DNA-supercoiling in Streptococcus pneumoniae by using seconeolitsine (SCN), a DNA topoisomerase I inhibitor. A homeostatic transcriptional response allowing recovering of supercoiling density was observed in cells treated with subinhibitory SCN concentrations. Supercoiling increases up to 40.7% (6 µM SCN) and 72.9% (8 µM SCN) were reverted to 8.5% and 44.1%, respectively. Likewise, recovery of viability and DNA-supercoiling were observed when cells were treated with those SCN concentrations and the drug was removed. The main DNA topoisomerase gene affected was topA, whose transcription depended on the supercoiling level. A two stage global transcriptomic response with 8 µM seconeolitsine was detected. The early stage (5 and 15 min, 10% of the genome) represented a response induced by increased supercoiling. The second stage represented supercoiling recovery (30 min, 2.0% of the genome). Almost 25% of the early responsive genes formed clusters with coordinated transcriptional regulation. Twelve clusters were evident, with sizes of 6.7 to 31.4 Kb (9 to 22 responsive genes). Strikingly, clusters did not contradict those observed under DNA relaxation, suggesting that bacteria manage supercoiling stress using overlapping responses. This is the first study describing a global transcriptomic response triggered by an increase in DNA supercoiling in bacteria.

overall_design: RNA was extracted from S. pneumoniae R6 cultures during exponential growth, amplified and used for microarray hibridization. Two independent replicates were performed.

first: María

last: Ferrándiz

first: Adela

last: de la Campa


title: Nucleic Acid Programmable Protein Arrays (NAPPA) Somatic p53 Mutations

status: Public on Jun 01 2016

city: Tempe

first: Benjamin

last: Katchman

state: AZ

address: 727 E. Tyler St.

institute: Arizona State University

summary:
Purpose: Mutations in TP53 induce autoantibody immune responses in a subset of cancer patients, which have been proposed as biomarkers for early detection. Here, we investigate the association of p53 specific autoantibodies with multiple tumor subtypes and determine the association with p53 mutation status and epitope specificity.
Experimental Design: IgG p53 autoantibodies (p53-AAb), were quantified in 412 serum saples using a programmable ELISA assay from patients with serous ovarian, pancreatic adenocarcinoma, and breast cancer. To determine if patients generated mutation specific autoantibodies we designed a panel of the most relevant 51 p53 point mutant proteins, to be displayed on custom programmable protein microarrays. To determine the epitope specificity we displayed 12 overlapping tiling fragments and 38 N- and C-terminal deletions spanning the length of the wild-type p53 proteins.
Results: We detected p53-AAb with sensitivities of 58.8% (ovarian), 22% (pancreatic), 32% (triple negative breast cancer), and 10.2% (HER2+ breast cancer) at 94% specificity. Sera with p53-AAb contained broadly-reactive autoantibodies to 51 displayed p53 mutant proteins, demonstrating a polyclonal response to common epitopes. All p53-AAb displayed broad polyclonal immune response to both continuous and discontinuous epitopes at the N- and C-terminus as well as the DNA binding domain.
Conclusion and clinical relevance: In this comprehensive analysis, mutations in tumor p53 induce strong, polyclonal autoantibodies with broadly reactive epitope specificity.

overall_design:
The immunoreactivity was compared between 60 pancreactic ductal adenocarcinoma cases and 63 benign pancreatic disease controls against 52 unique mutant p53 and 379 human proteins that were printed on microscope slides.
[Contributor] Arizona State University


title: Molecular Characterization of Acute Cellular Rejection Occurring during Intentional Immunosuppression Withdrawal in Liver Transplantation

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Acute cellular rejection occurs frequently during the first few weeks following liver transplantation. During this period its molecular phenotype is confounded by pro-inflammatory events elicited by surgery, ischemia-reperfusion injury and early post-transplant complications. To unambiguously define the molecular profile associated with rejection we collected sequential biological specimens from liver transplant patients at least 3 years after transplantation who developed rejection while enrolled in trials of intentional immunosuppression withdrawal

overall_design: Transcriptomic RISET 2.0 chips were employed using portal blood vein from 37 liver trasplant patients.Two timepoints were selected: before immunosupressive weaning and rejection time point.

first: A

last: Pennycuick

first: J

last: Sanchez-Fueyo


title: microRNA Expression Profiling of MIF-high and MIF-low Pancreatic Ductal Adenocarcinoma using Nanostring nCounter Platform

first: Perwez

middle: S

last: Hussain

address: 37 Convent Drive, Building 37, Room3044B

institute: National Cancer Institute

summary:
We identified differentially expressed microRNAs between MIF-high and MIF-low tumor groups. These microRNAs were then investigated for their potential downstream targets using an integrative strategy, which combines miR-Walk target prediction module and mRNA expression array data to identify key MIF-induced signalling pathways driving tumor progresion and disease aggressiveness.
Genes that associated with prognostic significance was then subjected to mechanistic study.

overall_design: miRNA expression profiling of 69 pancreatic ductual adenocarcinoma was performed in two sets. The batch effect between the two sets of data was removed using Partek Genomic Suite

first: S

first: Shouhui

last: Yang

first: Aaron

last: Schetter

first: Wei

last: Tang


title: A comprehensive 30K microarray platform to test transcriptomic responses in Biomphalaria glabrata

status: Public on Jul 30 2016

city: Albuquerque

first: Coen

last: Adema

state: NM

address: 1 University of New Mexico

department: CETI Biology MSC03 2020

institute: University of New Mexico

summary: Transcriptional profiling of Biomphalaria snail (whole body tissues) comparing BS90 strain untreated with sterile wounding and septic injury using a new comprehensive microarray platform design. Goal was to compare responses to differen immune challenges within one strain.

platform_organism:
Schistosoma mansoni
Biomphalaria glabrata
Echinostoma paraensei

overall_design: Three-condition experiment one strain untreated vs. injury vs. septic injury, Biological replicates: 2 control replicates, 3 injured replicates, 2 septic injury replicates.

first: Si-Ming

last: Zhang

first: Journey

middle: R

last: Nolan

first: George

middle: H

last: Rosenberg

first: Coenraad


title: Peripheral Blood Methylation Profiling of Female Crohn’s Disease Patients

status: Public on May 28 2016

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

institute: Academic Medical Center Amsterdam

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of female Crohn's disease patients versus healthy female controls. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,000 CpGs in peripheral blood samples. Samples included 25 healthy controls and 18 female patients with histologically confirmed CD.

overall_design:
Bisulfite converted DNA from the 43 samples (25 healthy controls and 18 female patients with histologically confirmed CD) were hybridized to the Illumina Infinium 450k Human Methylation Beadchip
Please note that three patient samples (Crohn100, Crohn32, and Crohn75) did not pass QC test and were removed from data processing. Therefore, only 15 patient samples are included in the records.

first: Andrew

middle: Y

last: Li Yim

first: Nicolette

last: Duijvis

first: Jing

last: Zhao

first: Wouter

last: de Jonge

first: Geert

last: D'Haens

first: Marcel

last: Mannens

first: Adri

middle: N

last: Mul

first: Anje

middle: A

last: te Velde