title: Expression Profiling of Arabidopsis Long Noncoding RNAs Under Continuous Light Condition

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

summary: Long intergenic noncoding RNAs (lincRNAs), Natural Antisense Transcripts (NATs), and microRNAs (miRNAs) play important roles in many biological processes. To profile circadian regulated long noncoding RNAs (lncRNAs), we grow Arabidopsis plants (Col-0) under short day SD (8h light/16h dark) condition and used the ATH lincRNA v1 array to profile lincRNA, NAT and miRNA gene expression under continuous light condition. Using JTK_CYCLE to search for cycling expression pattern of genes, we found ~900 genes encoding lincRNAs, NATs and miRNAs showed significant cycling expression patterns (Adjusted P-value < 0.05).

overall_design: 6 time points x 2 replicates.

first: Rossana

last: Henriques

first: Huan

last: Wang

first: Nam-Hai

last: Chua


title: Expression data from early stage CRC patients' tumors [NanoString-Design]

status: Public on Aug 02 2017

city: Singapore

first: Steve

last: Rozen

address: 8 College Road

country: Singapore

institute: Duke-NUS

summary: This study was conducted in order to identify biomarkers for a prognostic gene expression signature for metastases in early stage CRC.

overall_design: Expression profiles from 97 metastasis negative and 47 metastasis positive early stage CRC tumors were obtained.

first: Yee-Syuen

last: Low

first: Christopher

last: Blöcker

first: Iain

middle: B

last: Tan

first: Steven

middle: G

first: Peh-Yean

last: Cheah


title: Transcriptome analysis of adenine-treated murine microglial cells

status: Public on Aug 01 2017

city: Taipei

first: Guang-Huar

last: Young

state: Taiwan (TWN)

address: 6F.-3, No.21, Ln. 583, Ruiguang Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.C.)

department: Scientific Research

country: Taiwan

summary: In previous study, we demonstrated adenine-induced cell signaling on anti-inflammation in BV2 cells. To investigate the changes of transcriptome mediated by adenine, we used microarrays to compare the difference in expression levels.

overall_design: A chip study using total RNA recovered from two separate wild-type cultures of murine microglial cells and separate cultures of adenine-treated cells.

first: Han-Min

last: Chen


title: Identification of miR-210 as a new myo-miR in trout

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

summary: In fish, few miRNAs have been shown to muscle specific and data on miRNA involved in myogenesis are scarce. In order to identify new miRNA involved in satellite cells differentiation, we used a methionin depletion/replenishment protocol to synchronize myogenic cell differentiation. Our results clearly validated that methionine removal (72H) from the culture medium strongly decreased myoD1 and myogenin expression indicating a differentiation arrest. In contrast, methionine replenishment rescued the expression of myoD1 and myogenin showing a resumption of the differentiation. Then, we performed a miRNA array analysis of myogenic cells from three conditions: in presence of methionine (CTRL), absence of methionine during 72h (Meth-) and absence of methionine during 48H following 24H of methionine replenishment (Meth -/+). A clustering analysis identified three clusters : the cluster I corresponds to miRNA upregulated only in Meth -/+ conditions; the cluster II corresponds to miRNA downregulated only in Meth -/+ conditions; the cluster III corresponds to miRNAs with high expression in control, low expression in absence of methionine (Meth -) and middle expression after methionine replenishment (Meth -/+). The cluster III was very interesting because it followed (?) the resumption and differentiation and contained 7 miRNAs with muscle-related function (e.g. miR-133a) and one (miR-210) with unknown function. Based on our already published miRNAs repertoire (Juanchich et al 2016), we confirmed that miR-133a had an expression only in white muscle and we showed that miR-210 had the highest expression in white muscle. We also showed that miR-210 expression was upregulated during differentiation of satellite cells suggesting that miR-210 was potentially involved in the differentiation of satellite cells in trout.

overall_design: Trout cells in methionine depleted DMEM, in methionine supplemented DMEM, and supplemented DMEM during 24h after a 48h methionine restriction period

first: M

last: Latimer

last: Sabin

first: A

last: Le Cam

first: I

last: Seiliez

first: P

last: Biga

first: J

middle: C

last: Gabillard


title: Gene expression profiles from livers of ethinylestradiol- and chlorpromazine-treated C57BL6/mice after 25 days

status: Public on Aug 10 2017

city: Bilthoven

first: Alexa

last: Vitins

address: P.O. Box 1

country: Netherlands

institute: RIVM

summary: Toxicogenomics is used as a tool to identify mechanisms and markers of cholestasis in C57BL/6 mice treated by oral gavage using ethinylestradiol(EE2) and chlorpromazine (CPZ). A 25 day dose range finding study was performed, which resulted in no changes in clinical chemistry (serum cholesterol, total bile acids, and total bilirubin) or histopathology (hepatocyte vacuolization). Whole genome expression profiling of the liver was assessed after 25 days of repeated exposure with 10 mg/kg bw for CPZ and 3.70 mg/kg bw for EE2.

overall_design: 10 samples were analyzed per compound; 5 for the time-matched vehicle and 5 for the treatment. There are 20 samples in total. EE2 and CPZ were dissolved in sunflower oil and PBS, respectively.

first: Anne

middle: S

last: Kienhuis

middle: P

first: Jeroen

middle: L

last: Pennings

first: Tessa

middle: E

last: Pronk

first: Ewoud

middle: N

last: Speksnijder

first: Marianne

last: Roodbergen

first: Leo

middle: T

last: van der Ven


title: Expression data of the seedlings of Arabidopsis wild type and css1 mutant

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: NAIST

summary:
We used microarrays to compare global gene expression patterns between Arabidopsis wild type and css1, a mitochondria-related mutant (Nakagawa and Sakurai, Plant and Cell Physiol. 47(6): 772-783).
The result identified several classes of upregulated genes by the mutation including JA biosynthesis and signaling.

overall_design: The total RNA was prepared from 9-day-old Arabidopsis seedlings grown on agar plates containing 2% sucrose and used for microarray hybridization. Two replicative hybridization experiments per genotype (wild-type and css1) were carried out using the independent biological RNA samples.

first: Naoki

last: Nakagawa

first: Takashi

last: Hirayama


title: Expression data from nucleus accumbens of rats infused  with lentivirus LV-GFP and LV-miR-495 overexpression  constructs

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

country: USA

institute: University of New Mexico

summary:
The goal of the study was to determine the effect of lentiviral- mediated overexpression of miR-495 (LV-miR-495) on the levels of gene expression in the nuclues accumbens of rats relative to control rats injected with the empty vector (LV-GFP).
We used Rat Gene 2.0 ST Affymetrix expression arrays ( to identify genes whose expression levels were downregulated by overexpression of miR-495.

overall_design: Rats were infused with replication deficient lentiviral contructs LV-miR-495 or control LV-GFP (System Biosciences, Inc)  using sterotaxic injections. One week post-infusion the animals were sacrificed and the nucleus accumbens  microdissection and processed for RNA extraction using Trizol and RNA was used for hybridization on Affymetrix Rat Gene 2.0 ST arrays. We used 3 biological replicates: rats 1, 3 and 9 were infused with control LV-GFP and rats

first: Janet

last: Neisewander


title: Comprehensive gene expression analysis identifies a unique molecular profile and macrophage infiltration in undifferentiated uterine sarcomas [expression]

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

summary:
Sarcomas originating from the endometrial stroma include low- and high-grade endometrial stromal sarcomas (ESS) that are associated with specific translocations, and highly malignant undifferentiated uterine sarcomas (UUS). UUS is considered a poorly defined group of tumors and is often seen as a “diagnosis of exclusion” after ESS and leiomyosarcoma (LMS) have been ruled out.
Through gene expression profiling, we show that UUS form a well-defined group of tumors with a unique genetic profile distinct from LMS and both subtypes of ESS.

overall_design: Total RNA was extracted from 25 frozen tumor samples from 9 low-grade ESS cases, 8 UUS cases and 4 high-grade ESS cases and 4 uterine LMS cases; Agilent One-Color technology.

first: Maria

last: Debiec-Rychter

first: Matt

last: van de Rijn


title: Comprehensive gene expression analysis identifies a unique molecular profile and macrophage infiltration in undifferentiated uterine sarcomas [aCGH]

type: Genome variation profiling by genome tiling array

summary:
Sarcomas originating from the endometrial stroma include low- and high-grade endometrial stromal sarcomas (ESS) that are associated with specific translocations, and highly malignant undifferentiated uterine sarcomas (UUS). UUS is considered a poorly defined group of tumors and is often seen as a “diagnosis of exclusion” after ESS and leiomyosarcoma (LMS) have been ruled out.
Using aCGH, we showed that UUS more complex genomic aberrations that low- and high-grade ESS.

overall_design: aCGH was performed using genomic DNA was extracted from 19 frozen tumor specimens (9 low-, 3 high-grade ESS and 7 UUS).


title: The function of OsbHLH068 is partially redundant with its homolog, AtbHLH112, in the regulation of the salt stress response but has opposite functions to control flowering in Arabidopsis

status: Public on Aug 07 2017

first: Vicki

last: Hsieh-Feng

address: No. 1, Sec. 4, Roosevelt Rd.

institute: NTU

summary: The transcription factor (TF) basic/Helix-Loop- Helix (bHLH) is important for plant growth, development, and stress responses. OsbHLH068, which is a homologous gene of AtbHLH112 that is up-regulated under drought and salt stresses, as indicated by previous microarray data analysis. However, the intrinsic function of OsbHLH068 remains unknown. In the present study, we characterized the function and compared the role of OsbHLH068 with that of its homolog, AtbHLH112. Histochemical GUS staining indicated that OsbHLH068 and AtbHLH112 share a similar expression pattern in transgenic Arabidopsis during the juvenile-to-adult phase transition. Heterologous overexpression of OsbHLH068 in Arabidopsis delays seed germination, decreases salt-induced H2O2 accumulation,and promotes root elongation, whereas AtbHLH112 knock-out mutant displays an opposite phenotype. Both OsbHLH068-overexpressing transgenic Arabidopsis seedlings and the Atbhlh112 mutant display a late-fowering phenotype. Moreover, the expression of OsbHLH068-GFP driven by an AtbHLH112 promoter can compensate for the germination deficiency in the Atbhlh112 mutant, but the delayed-flowering phenotype tends to be more severe. Further analysis by microarray and qPCR indicated that the expression of FT is down-regulated in both OsbHLH068-overexpressing Arabidopsis plants and Atbhlh112 mutant plants, whereas SOC1 but not FT is highly expressed in AtbHLH112-overexpressing Arabidopsis plants. A comparative transcriptomic analysis also showed that several stress-responsive genes, such as AtERF15 and AtPUB23, were affected in both OsbHLH068- and AtbHLH112-over-expressing transgenic Arabidopsis plants. Thus, we propose that OsbHLH068 and AtbHLH112 share partially redundant functions in the regulation of abiotic stress responses but have opposite functions to control  flowering in Arabidopsis, presumably due to the evolutionary functional divergence of homolog-encoded proteins.

overall_design: Gene expression of 17-day-old Col-0 and heterologous overexpressed OsbHLH068 in Arabidopsis was measured.  Three biological repeats were collcted for the experiment.

first: Hung-Chi

last: Chen

first: Pei-Chun

last: Liao

first: Wan-Hsing

last: Cheng

first: Li-Yu

last: Liu

first: Yun-Wei

last: Yang

first: Ming-Hsin

last: Lai

first: Men-Chi

last: Chang


title: KB001b:Gene expression profiling of the growth plate of large and small breed dogs provides new insights in endochondral bone formation

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: The regeneration of bone in large bone defects remains a challenge in orthopaedics. It may be possible that  the difference in the adult height of mammals, and hence in endochondral bone formation, can serve to identify targets for bone regeneration. In line with this hypothesis, the intra-species disparity in adult height of Great Danes and Miniature Poodles was investigated at a transcriptional level. Microarray analysis of the growth plate of 5 Great Danes and 5 Miniature Poodles revealed 2981 unique genes that were differentially expressed in the two breeds, including many genes with an unknown role in skeletal development. A signalling pathway impact analysis indicated activation of the cell cycle, extracellular matrix receptor interaction, the tight junction pathway, and inhibition of pathways associated with inflammation and the complement cascade. In addition, the BMP pathway was examined, including BMP-2, which is currently used clinically, and BMP-6. As these proteins registered dissimilar mRNA expression the differential effects of BMP-2 and BMP-6 on in vitro osteogenic and chondrogenic differentiation were studied. BMP-6 was at least as potent as BMP-2 in inducing osteogenesis in canine MSCs. However, BMP-2 was a more potent inducer of chondrogenesis than BMP-6. In conclusion, investigating the differential expression of genes involved in endochondral bone formation in small and large breed dogs, could be a promising strategy to identify new targets for bone regenerative medicine.

overall_design: Microarray expression dataset including growth plate samples from 5 miniature poodles and 6 great danish dogs. Comparisons were analyzed in dyeswap on a 2-color platform against a common reference sample, consisting of a multitude of canine organs, including liver, spleen, kidney, lung, heart, intestine and bone.

first: Michelle

last: Teunissen

first: Frank

last: Riemers

first: Jacqueline

last: Alblas

first: Marianna

last: Tryfonidou

first: Dik

last: van Leenen

first: Louis

last: Penning

first: Bjorn

last: Meij

first: A.

last: Vlijn

last: Miranda-Bedate


title: The biphasic Fusarium graminearum transcriptome during symptomless and symptomatic wheat infection

city: Ribeirao Preto

first: Neil

last: Brown

address: Av. do Cafe

country: Brazil

institute: USP

summary: The analysis of the Fusarium graminearum transcriptome during symptomless and symptomatic infections of wheat floral tissue at 7 days post infection, to identify the correct spatio-temperol regulation of multiple virulence strategies.

overall_design: Fusarium graminearum PH-1 was inoculated into the floral cavity of the two florets, of the two spikelets, in the middle of the wheat head. At 7 days post infection the inoculated spikelets and the 7 sequential rachis internodes below the inoculated spikelet were collected. The individual wheat tissues were pooled for ten wheat heads to form a single biological replicate. Non-infected wheat spikelets and rachis was collected as a negative control. Three biological replicate were collected per treatment.

first: Kim

last: Hammond-kosack


title: Transcriptome analysis of phosphonate-pretreated tomato in response to inoculation with Phytophthora parasitica

first: Ruey-Fen

last: Liou

address: 1, Sec. 4, Roosevelt Road

department: Plant Pathology and Microbiology

institute: National Taiwan University

summary:
Phosphonate related fungicides such as neutralized phosphorous acid (NPA) are effective for the control of plant diseases caused by Oomycetes including Phytophthora parasitica. It has been proposed that phosphonate may induce plant resistance. However, the mechanism underlying phosphonate-induced resistance remains unclear.
The purpose of this study is to identify genes that are differentially expressed in phosphonate-pretreated tomato plants in response to inoculation with Phytophthora parasitica.

overall_design: We treated the tomato plants with NPA or water (ddH2O, as a control) for three days, and then inoculated the plants with zoospores of P. parasitica. For microarray analysis by the use of Affymetrix Tomato Genome Array, total RNAs were isolated from plant leaves at: (1) 3 days post treatment (dpt) with NPA or water, (2) 6 hours post inoculation (hpi) of the NPA- or water-pretreated plants, (3) 12 hpi of the NPA- or water-pretreated plants. To reduce the biological variability, each hybridization experiment was performed with RNA prepared from pools of five plants. The total set of experiments was repeated three times.

first: Chu

last: Lin

first: Pao

middle: J

last: Ann

first: Ruey

middle: F


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

status: Public on Jul 31 2017

city: beijing

first: lei

last: yan

state: beijing

address: Block 88 Kechuang 6th Street

department: sales

country: China

institute: capitalbiotech

summary: P21-activated kinase 1 (Pak1) is a key oncogenic kinase and a lot of work about the mechanism of Pak1 action in cancer have been reported, while it remains unknown whether Pak1 could potentially regulate the biology of regulatory miRNAs by new interacting substrate. Here, we identified that Pak1 modulated the miR-132 expression in gastric cancer cells. Pak1 interacted with and phosphorylated activating transcription factor-2 (ATF2) on Serine 62 (Ser62), which blocked ATF2 translocation into cell nucleus. We further demonstrated that ATF2 induced miR-132 transcription via binding to the miR-132 promoter in the -30 to -39 region. Moreover, overexpression of miR-132 in gastric cancer cells significantly reduced cell adhesion, migration and invasion in vitro and hematogenous metastasis in vivo. MiR-132 targeted CD44 and fibronectin (FN) and promoted lymphocytes to gather around gastric cancer cells and kill them. More importantly, downregulation of miR-132 in gastric cancer was specifically associated with hematogenous metastasis, instead of lymph node or implantation metastasis. Taken together, miR-132 is a key negative regulator in the hematogenous metastasis of gastric cancer. A novel cell signaling pathway Pak1-ATF2-miR-132-CD44/FN is established and may be a new therapeutic target for hematogenous metastasis of gastric caner.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

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

first: Funan

last: Liu

first: Zhenguo

last: Cheng


title: Characterization of Whole Genome DNA Methylation Profile Associated with Post-Traumatic Stress Disorder in OIF/OEF Veterans

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

type: Methylation profiling by genome tiling array

summary: Emerging knowledge suggests that post-traumatic stress disorder (PTSD) is causally associated with epigenetic changes although its molecular underpinnings are still largely elusive. We postulate that differentially methylated probes mined from peripheral whole blood could be candidates for potential PTSD diagnostic signatures. Working within the Systems Biology PTSD Biomarker Consortium (SBPBC), we investigated a training set comprising of 48 PTSD male veterans (CAPS > 40) and 51 age/ethnicity matched controls (CAPS < 20). Agilent whole genome array detected ~5,600 differentially methylated CpG islands (CpGI) annotated to ~2,800 differentially methylated genes (DMG). The majority (84.5%) of these DMGs was hypermethylated in PTSD veterans. Thereof ~30% promoter-bound DMGs were used for functional analysis. Taking cues from the clinical information, the curated networks were enlisted into four major clusters, namely PTSD-associated complications, PTSD-relevant endocrine signaling, nervous system development and nervous system functions. Enduring impacts of PTSD was manifested by differentially methylated genes enriching networks associated with LTP, fear memory architecture and complications linked to insulin resistance and innate immunity.  These networks were further validated by an independent test set comprising of 31/29 PTSD+/- veteran selected using aforementioned screening protocol. Two independent assay platforms presented technical validations. Probing the combined 83/83 PTSD+/- cohort, whole genome array from Illumina, Inc. validated most of the networks of interest. Methylation statuses of eight DMGs relevant to PTSD and comorbidities were confirmed by targeted bisulfite sequencing. This list presents a potential set of PTSD biomarkers of translational potential.

overall_design:
Working within the Systems Biology PTSD Biomarker Consortium (SBPBC), we investigated a training set comprising of 48 PTSD male veterans (CAPS > 40) and 51 age/ethnicity matched controls (CAPS < 20). Agilent whole genome array detected ~5,600 differentially methylated CpG islands (CpGI) annotated to ~2,800 differentially methylated genes (DMG). In this study, further validation was conducted by an independent test set comprising of 31/29 PTSD+/- veteran.
Clinician-Administered PTSD Scale (CAPS); The IP (sample of interest) samples labeled with Cy5 and the WCE (whole cell extract; reference)  labeled with Cy3.

first: Rasha

last: Hammamieh

first: Nabarun

last: Chakraborty

first: Seid

last: Muhie

first: Ruoting

last: Yang

first: Raina

last: Kumar

first: Bernie

last: Daigle

first: Yuanyang

last: Zhang

first: Duna

middle: A

last: Amara

first: Stacy-Ann

last: Miller

first: Seshamalini

last: Srinivasan

first: Rachel

last: Yehuda

first: Linda

last: Petzold

last: Doyle

first: Owen

last: Wolkowitz

first: Sindy

last: Mellon

first: Charles

last: Marmar

first: Marti

last: Jett


title: Contribution of Poly-unsaturated Fatty Acids on Cerebral Neurobiology: An Integrated Omics Approach with Epigenomic Focus [expression]

first: Aarti

last: Gautam

summary: The epigenetic landscape is vulnerable to variations in diet. Here, we investigated the influence of different PUFA dietary supplements on rodents’ nervous system development and functions and potential consequences for neurodegenerative disorders. We have previously studied the genomic plasticity of these biofunctions in mice fed on high n-3 PUFA enriched diet (ERD). In conjunction, in the present study, we introduced a second equicaloric diet with n-3 PUFA optimally balanced by n-6 PUFA (BLD). The typical lab diet with high n-6 PUFA was the baseline.  Randomly grouped C57BL/6j mice were fed on any of these three diets from their neonatal age to late adolescent. Post-euthanasia, the transcriptomic landscape of hemibrains was investigated in parallel for two epigenetic mechanisms, namely the miRNA profile and DNA methylation. Integrating data we focused on those genes which had both hypermethylated CpG islands and silenced transcripts. Of these, 308 and 131 genes were perturbed by ERD and BLD, respectively, in comparison to the baseline. Also, miRNA:mRNA pairs were screened to identify those overexpressed miRNAs that silenced gene transcription. There were 18 and 39 miRNAs that met the cutoff in ERD- and BLD-fed mice, respectively. The majority of miRNAs overexpressed by BLD are associated with Alzheimer’s and schizophrenia. BLD allowed hypermethylation of those genes that enriched the networks associated with calcium-releasing neurotransmitters. Downstream networks leading to LTP, memory, cognition and learning were perturbed in sync. ERD permitted hypermethylation of genes that enrich the cytoskeletal development network and promote the formation of neuronal precursors. We present the conclusions taking into full account the limited knowledge regarding the epigenetic influence on biofunctions.  Since this study has single time point, we could not verify if these functional attributes are the cause or the consequences of epigenetic plasticity. Hence, a more comprehensive study in this regard is essential.

overall_design: A N-3 PUFA-enriched diet (ERD, n3:n6= 7:1) and a balanced diet (BLD, n3:n6= 1:1) were customized to contain equivalent caloric content as that of the standard lab diet (STD, n3:n6= 1:6). These diets were administered to three groups of C57BL/6j male mice from their weaning age until late adolescence. Left hemibrains were analyzed for differential transcripts, DNA methylation and microRNAs.

first: Seshmalini

first: Bintu

last: Sowe

first: George

last: Dimitrov

last: Hammamieh


title: Expression profiling of mRNAs and long noncoding RNAs in mouse Abdominal Aortic Aneurysm (AAA)

city: Beijing

first: Qinghua

last: Cui

address: 38 Xueyuan Road

institute: Peking University

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

summary: mRNA and Long noncoding RNA profiles in the mouse abdominal aorta with AAA and without AAA.

overall_design: In the study presented here, we mixed the five mouse abdominal aorta samples,five mouse abdominal aorta samples for mourse with AAA, and five mouse abdominal aorta samples for mouse with AAA treated by naringenin (NGN). We identified the genome-wide expression level of mRNAs and lncRNAs.

first: Q

first: W

last: Kong


title: Genotype specific phenotypic behaviour of auxotrophic and prototrophic gene deletion collections

status: Public on Aug 11 2017

city: Vancouver

first: Erica

last: Acton

state: British Columbia

address: Pharmaceutical Sciences Building, Wesbrook Mall

department: Genome Science and Technology

country: Canada

institute: University of British Columbia

summary: To systematically characterize the phenotypic behavior of two 'prototrophic' version of the Yeast Knockout (YKO) gene deletion collection, we compared genome-wide finess assays across a diverse set of drug and environmental conditions. This analysis uncovered experimental liabilities in the the prototrophic collections distinct from the YKO auxotrophies that shows that auxotrophic repair (regardless of methodology) does not restore wildtype behaviour.

overall_design: We compared the YKO auxotrophic deletion collection to 2 prototrophic collections in 15 media conditions and 4 drug conditions, in triplicate, resulting in 236 total Affymetrix Chips, as well as 37 Bar-seq samples for comparison to the microarray data. We compared both the deletion strain content of these collections as well as their quantitative fitness profiles.

first: Amy

last: Lee

first: Bill

last: Zhao

first: Stephane

last: Filbotte

first: Sunita

last: Sinha

first: Jennifer

last: Chiang

first: Pat

last: Flaherty

first: Corey

last: Nislow

first: Guri

last: Giaever


title: Kidney Hypothermic Perfusion with Mesenchymal Stromal Cells or Microvesicles Protects Rat Kidney from Ischemia By Upregulation of Cell Energy Metabolism and Ion Membrane Transport Key Genes

status: Public on Jul 21 2017

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: We evaluated in a rat model of Donor after Circulatory Death (DCD) the effects of pretransplant kidney conditioning with Mesenchymal Stromal Cells (MSC) or MSC derived microvescicles (MV) on ischemic injury. Fisher rats (F) were used as kidney donors, Transgenic Sprague-Dawley rats expressing Enhanced Green Fluorescence Protein (EGFP) as MSC donors. After 20 min of warm ischemia nephrectomy was performed and kidneys were perfused with Belzer solution (BS), BS supplemented with MSC (MSC) or with MV (MV) for 4 h, at 4°C. Renal damage was evaluated by histology, renal gene expression by microarray analysis and RT-PCR. Malondialdehyde, lactate, LDH, glucose and pyruvate were measured in effluent fluid. MSC/MV kidneys showed a significant minor global ischemic damage and up-regulation of three genes encoding proteins that improve cell energy metabolism (Isocitrate dehydrogenase 2, NADH dehydrogenase Fe-S protein 8, Pyruvate dehydrogenase beta) and three genes encoding proteins involved in ion membrane transport (Calbindin 1, Monocarboxylate transporter 1, Vacuolar H+-ATPase d2 subunit). Lactate, LDH and malondialdehyde in effluent fluid were significantly lower in MSC/MV kidneys than BS. Glucose was lower while pyruvate higher in MSC/MV effluent than BS, suggesting a larger use of energy substrates by MSC/MV kidneys. MSC/MV perfusion of kidneys in addition to BS through HMP protects from ischemia injury by preserving the enzymatic machinery essential for cell viability and prepares kidney to reperfusion damage.

overall_design: A rat model of DCD was reproduced. Rats were anesthetized using Isoflurane 2-5%. After 20 min of warm ischemia obtained by abdominal aorta clamping, nephrectomy was performed. Kidneys were then perfused with Belzer solution (BS), or BS supplemented with 3 millions of MSC (MSC), or BS supplemented with MV derived from 3 millions of MSC (MV). We studied 5 kidneys per group. Continuous perfusion was performed for 4 h at 4°C, than the effluent fluid was collected and stored at -20°C. Kidneys were fixed in 10% formalin for morphological studies, frozen in liquid nitrogen for RT-PCR. We studied also another group of non perfused kidneys (n 5) (NP) obtained after 20 min of warm ischemia and preserved in RNAlater to microarray studies. Malondialdehyde, lactate, LDH, glucose and pyruvate were measured in effluent fluid. All experiments were quadruplicated.

first: Marilena

last: Gregorini

first: Valeria

last: Corradetti

first: Eleonora

last: Pattonieri

first: Chiara

last: Rocca

first: Samantha

last: Milanesi

first: Andrea

last: Peloso

first: Silvana

last: Canevari

first: Loris

last: De Cecco

first: Maria

last: Avanzini

first: Melissa

last: Mantelli

first: Marcello

last: Maestri

first: Pasquale

last: Esposito

first: Antonio

last: Dal Canton

first: Teresa

last: Rampino


title: Transcriptome analysis of neutralized phosphorous acid (NPA)-induced resistance in tomato against Phytophthora parasitica

first: Ruey-Fen

last: Liou

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

overall_design: Refer to individual Series


title: Cell interactions, signals and transcriptional hierarchy governing placode progenitor induction

status: Public on Jul 12 2017

city: London

last: Streit

address: Centre for Craniofacial & Regenerative Biology, King's College London

country: United Kingdom

institute: Kings College London

summary:
Cranial placodes contribute to all sense organs and sensory ganglia in the vertebrate head. Despite their diversity they originate from a common pool of Six1/Eya2+ progenitors. In a molecular screen we identify new factors upstream of the Six1/Eya2 cassette and use these to dissect the transcriptional hierarchy that controls progenitor specification. We find that although two different tissues, the lateral head mesoderm and the prechordal mesendoderm, induce placode progenitors, both initiate a common transcriptional state, but over time gradually impart regional character.
Thus, as cells acquire placode progenitor identify they pass through successive transcriptional states each identified by a distinct set of factors and controlled by different signalling pathways. Thus, we propose a new model for placode progenitor induction reminiscent of Waddington’s evocation-individuation model for neural induction.

overall_design: Sensory placode progenitors of the pre-placodal region are induced by signals from the lateral head mesoderm. To identify transcripts up- and downregulated during this process, the lateral head mesoderm was dissected from HH6 chick embryos and grafted into the extraembryonic area opaca of HH4- chick hosts. After 12 hours, the mesoderm was removed and the underlying epiblast was collected as was the contralateral non-induced area opaca (control). RNA was prepared and processed for hybridization to Affymetrix arrays

first: A

first: M

last: Hintze

last: Tambalo

first: N

last: Christophorou

last: Anwar

first: T

last: Grocott

first: R

last: Prajapati


title: Cocoa polyphenols and fiber modify colonic gene expression in rats

status: Public on Jul 09 2017

city: Barcelona

first: Francisco Jose

last: Pérez-Cano

state: Catalunya

address: Edifici B, 3a planta,  Av. Joan XXIII s/n

department: Departament de Fisiologia-Farmàcia

country: Spain

institute: Universitat de Barcelona

summary: Cocoa intake has been associated with health benefits, improving cardiovascular function and metabolism, as well as modulating intestinal immune function. The aim of this study was to take an in-depth look into the mechanisms affected by the cocoa intake by evaluating the colonic gene expression after nutritional intervention, and to ascertain the role of the fiber of cocoa in these effects. To achieve this, Wistar rats were fed for 3-weeks with either a reference diet, a diet containing 10% cocoa (C10), a diet based on cocoa fiber (CF) or a diet containing inulin (I). At the end of the study, colon was excised to obtain the RNA to evaluate the differential gene expression by microarray. Results were validated by RT-PCR. The C10 group was the group with most changes in colonic gene expression, most of them down-regulated but a few in common with the CF diet. The C10 diet significantly up-regulated the expression of Scgb1a1 and Scnn1g and down-regulated Tac4, Mcpt2, Fcer1a and Fabp1 by twofold, most of them related to lipid metabolism and immune function. The CF and I diets down-regulated the expression of Serpina10 and Apoa4 by twofold. Similar patterns of expression were found by PCR. Cocoa consumption down-regulated genes related to the immune system (B cell and mast cell functionality), lipid metabolism in the colon tissue. Most of the beneficial effects attributed to cocoa were due not only to its fiber content, but also to the possible contribution of polyphenols and other compounds.

overall_design: Four experimental groups (REF, Cocoa, Cocoa Fiber and Inulin diets (n=4 per group)

first: Malen

last: Massot-Cladera

first: Àngels

last: Franch

first: Margarida

last: Castell

first: Francisco


title: Contribution of Poly-unsaturated Fatty Acids on Cerebral Neurobiology: An Integrated Omics Approach with Epigenomic Focus [methylation]

first: Aarti

last: Gautam

first: Nabarun

last: Chakraborty

first: Seid

last: Muhie

first: Raina

last: Kumar

first: Seshmalini

last: Srinivasan

first: Bintu

last: Sowe

first: George

last: Dimitrov

first: Stacy-Ann

last: Miller

first: Marti

last: Jett

first: Rasha

last: Hammamieh


title: Ncb2 ChIP-chip on Gu4 (azole susceptible, AS) and Gu5 (azole resistant, AR) cells of Candida albicans using polyclonal antibody

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

type: Genome binding/occupancy profiling by array

summary: Comparative analysis of genome wide binding profile of Ncb2 in azole sensitive (AS, Gu4) and azole resistant (AR, Gu5) clinical isolates of Candida albicans. The goal was to study the role of Ncb2 in acquisition of drug resistance by comparing the binding profiles of Ncb2 in both the isolates.

overall_design: Agilent two-color ChIP on chip  experiment, Organism: Candida Albicans , Agilent Candida Albicans COC_4X180K chip on ChIP AMADID: 038045 designed by Genotypic Technology Private Limited.

first: M

last: Shariq

first: S

last: Dhamgaye

last: Nair

first: A

middle: K

last: Mondal

first: G

last: Mukhopadhyay

last: Prasad


title: Contribution of Poly-unsaturated Fatty Acids on Cerebral Neurobiology: An Integrated Omics Approach with Epigenomic Focus

last: Gautam

type:
Expression profiling by array
Methylation profiling by array


title: Arabidopsis ila3 mutant seedlings versus wild-type seedlings.

status: Public on Jul 30 2017

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

institute: IBMCP

summary: Transcriptional profiling of wild-type Col seedlings compared to ila3 mutant seedlings

overall_design: Two-condition experiment, Wild-type vs. ila3 seedlings. 3 biological replicates.


title: Silencing of ASCL1 in U87MG glioma cells

status: Public on May 22 2017

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

country: Germany

institute: TUM

summary:
ASCL1 is known to act as transcriptional activator of notch signaling pathway. We have found that ASCL1 is over expressed in secondary glioblastoma.
In order to delineate its functional role in gliomagensis we have used gene silencing approach to identify genes differentially regulated upon ASCL1 down regulation in U87MG glioma cell line.

overall_design: U87MG cells either mock silenced using scrambled si RNA or silenced using siRNA targetted against ASCL1 were harvested at 48hrs post transfection. Gene expression was profiled after microarray for control and ASCL1 silenced cells.

first: Shrinivas

last: Dighe

first: Sainitin

last: Donakonda

first: Swati

last: Sinha

middle: R

last: Rao


title: Differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24 - Impact of polymorphic probes on the detection of differentially expressed genes

status: Public on May 21 2017

city: Stadt Seeland

first: Renate

middle: Hanna

last: Schmidt

state: Sachsen-Anhalt

address: Corrensstrasse 3

department: Breeding Research

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

overall_design:
Refer to individual Series

Please note that the biological material for the two studies is identical but the data (both raw and normalized data) were processed in two different ways (as detailed in the sample data processing field)


title: DKK3 overexpression increases malignant property in  head and neck squamous cell carcinoma-derived HSC-3 cells.

status: Public on Jul 22 2017

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary:
We hypothesized that DKK3 may exert oncogenic function supecifically in head and neck squamous cell carcinoma (HNSCC). DKK3 overexpression in HNSCC cell resulted in elevated cellular proliferation, migration, invasion and in vivo tumor growth.
This elevated malignant properties was not driven by Wnt/beta-catenin pathway.

overall_design: Single analysis for each condition (HSC-3 no transfection, HSC-3 GFP transfection and HSC-3 DKK3 transfection)

first: Naoki

last: Katase


title: Transcriptome analysis of tomato in response to treatment with neutralized phosphorous acid (NPA)

city: Taipei

first: Ruey-Fen

last: Liou

summary:
Phosphonate related fungicides such as neutralized phosphorous acid (NPA) are effective for the control of plant diseases, especially those caused by Phytophthora and other oomycetes. It has been suggested that phosphonate may induce plant resistance, however, the mechanism is not clear thus far.
We performed microarray analysis using Affymetrix Tomato Genome Array to identify tomato genes that are differentially expressed in response to NPA treatment.

overall_design: At 6 and 12 hours post treatment (hpt) of the tomato plants with NPA or water (ddH2O, as the control), total RNAs were isolated from leaves and subjected to microarray analysis by the use of Affymetrix Tomato Genome Array. To reduce the biological variability, each hybridization experiment was performed with RNA prepared from pools of five plants. The total set of experiments was repeated twice.

first: Chu

last: Lin

first: Pao

last: Ann

first: Ruey


title: Three TF Gene Co-expression Modules are involved in Pressure-Overload Cardiac Hypertrophy in Male Mice

status: Public on May 31 2017

city: Taipei city

first: Yao-Ming

last: CHANG

address: No.128, Academia Rd. Nangang Dist.

institute: Academia Sinica


title: The Increased Toxicity of UV-Degraded Nitroguanidine and IMX-101 Exposures in Zebrafish Larvae: Evidence Implicating Oxidative Stress [1]

status: Public on Aug 25 2017

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary: Abstract —  Insensitive munitions (IMs) improve soldier safety by decreasing sympathetic detonation during training and use in theatre.  The environmental effects of IM constituents such as nitroguanidine (NQ) and IM mixture formulations such as IMX-101 remain largely unknown.  In the present study, we investigated the acute (96h) toxicity of NQ and IMX-101 to zebrafish larvae, both in the parent IMs and in IMs irradiated with environmentally-relevant levels of ultraviolet (UV) energy.  Zebrafish were exposed to control and ten concentrations of NQ ranging from 1 to 732 mg/L (measured concentrations) or seven concentrations of IMX-101 ranging from 2 to 122 mg/L (measured concentrations) of the parent material or material that had been UV-irradiated (UV-treated) at the equivalent of 24 hours of sunlight.  The UV-treatment increased the toxicity of NQ by 17-fold, indicated by a decreased LC50 from 1323 mg/L (parent compound) to 77.2 mg/L.  Similarly, UV-treatment increased the toxicity of IMX-101 by nearly two fold (LC50 decreased from 131.3 to 67.6 mg/L).  Molecular responses to parent and UV-treated IMs were assessed using global transcript expression assays.  Both gene set enrichment analysis (GSEA) and differential transcript expression analysis coupled with pathway and annotation cluster enrichment were conducted to provide functional interpretations of expression results and hypothetical modes of toxicity.  The parent NQ exposure caused significant enrichment of functions related to immune responses and proteasome-mediated protein metabolism occurring primarily at low, sublethal exposure levels (5.5 and 45.6 mg/L).  Enriched functions in the IMX-101 exposure were indicative of increased xenobiotic metabolism, oxidative stress mitigation, protein degradation, and anti-inflammatory responses, each of which displayed predominantly positive concentration-response relationships.  UV-treated NQ had a fundamentally different transcriptomic expression profile relative to parent NQ where positive concentration-response relationships were observed for genes involved in oxidative-stress mitigation pathways whereby we hypothesize that the increased toxicity of UV-treated NQ resulted from increased oxidative stress.  This hypothesis was supported by transcriptomic responses indicative of oxidative-stress responses involved in zebrafish development, especially neurological development of visual systems and the brain.  Transcriptomic profiles were similar between UV-treated versus parent IMX-101 exposures, however, more significant and diverse enrichment as well as greater magnitudes of differential expression for oxidative stress responses were observed in UV-treated IMX-101 exposures.  Further, transcriptomics indicated potential for cytokine signaling suppression providing potential connections between oxidative stress and anti-inflammatory responses.  Given these result, we hypothesize that the increased toxicity of UV-irradiated NQ and the IMX-101 mixture result from breakdown products with increased potential to elicit oxidative stress.

overall_design: Six separate microarray analyses were conducted within this study.  The 6 designs were conduced as follows:  1. NQ parent compound, 2. UV-Treated NQ, 3. Two-way design, NQ Parent x UV-Treated NQ, 4. IMX-101 parent material, 5. UV-treated IMX-101, 6. Two way design, IMX-101 parent x UV-Treated IMX-101.  This GEO entry represents analysis number 1. - NQ parent compound:   Zebrafish larvae were exposed to NQ at 0 (control), 1.4, 2.8, 5.5, 11.0, 22.7, 45.6, 90.4, 181, 348, and 732 mg/L (measured concentrations).  Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Danio rerio larvae were exposed in static nonrenewal acute 96-h bioassays.  Exposure chambers were 300-ml high-form lipless beakers with a test solution volume of 250 ml.  Eight larval fish per beaker were exposed in the parent or UV-treated NQ treatments each including 4 exposure replicates and 6 control replicates.  Larval zebrafish were fed newly hatched Artemia nauplii two hours before the initiation of exposures and at the 48-h timepoint.  Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.

first: Jacob

last: Stanley

first: Mitchell

last: Wilbanks

first: Michael

last: Mayo

first: Pornsawan

last: Chappell

first: Shinita

last: Jordan

first: Lee

last: Moores

first: Alan

last: Kennedy

first: Natalie

last: Barker


title: Grape seed extracts-mediated lipid mobility in C. elegans

status: Public on May 24 2017

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

summary: Oligomeric proanthocyanidins (OPCs) reduce triglycerides in the nematode C. elegans. Lipase was strongly inhibited in vitro accompanied by the reduction of total triglyceride storage capacity in vivo; Lipophilic staining was also attenuated in wild type worms and high-fat mutants exposed to OPCs. Apart from biochemical analyses, lipid metabolism was also genetically regulated, emphasizing the necessity to study underlying regulation mechanisms in intact animals. To gain a deeper insight into the potential gene targets of purified oligomeric proanthocyanidin trimer gallate (pOPC7), a binary microarray assay was carried out with wild type N2 populations continuously exposed to a bacterial diet with or without pOPC7.

overall_design: The global transcriptome was compared in wild type N2 raised in the presence or absence of oligomeric proanthocyanidin trimer gallate (pOPC7) extracted from Vitis vinifera grape seeds at the concentration of 2 µg/mL for 48 hours (L1 to L4 stage).

first: Yu

last: Nie

first: Eugene

last: Schuster

first: Matt

last: Arno


title: Differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24 - Impact of the exclusion of polymorphic probes via a sequence-based approach

first: Renate

last: Schmidt

summary: In order to identify differentially expressed genes in developing seeds of Arabidopsis thaliana three different stages of seed development were analysed (9-10, 10-11 and 12-13 days after flower opening) for two Arabidopsis thaliana accessions, Col-0 and C24. For each stage and accession three biological replicates were analysed.

overall_design:
In order to compare transcriptomes of developing seeds of accessions Col-0 and C24 it was analysed which features of the ATH1-121501 array showed nucleotide exchanges and/or frame shifts when aligned to the genome sequence of C24. This information was used to generate a restricted data set exclusively consisting of probes that were identical to the genome sequences of both Col-0 and C24. Moreover, probes had to reveal perfect sequence alignments with TAIR10 representative gene models. Probe sets had to consist of three or more probes. Expression data for the two accessions were compared for developing seeds of the same stage. For each of the accessions gene expression at the different developmental stages was also compared.

Please note that the biological material is identical to GSE94762 samples, but the data (both raw and normalized data) were corrected/processed in two different ways (as detailed in the sample data processing field)

first: Anastassia

last: Boudichevskaia


title: Zinc-dependent regulation of zinc import and export genes by Zur

status: Public on May 18 2017

city: Seoul

first: Kanglok

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

type: Genome binding/occupancy profiling by genome tiling array

summary: We determined the genomic locations of the Zur binding sites by chromatin immuno-precipitation of cross-linked DNA and hybridization on a tilling oligonucleotide array on exponentially grown cultures of M145 and zur mutant.

overall_design: Three independent biological samples were prepared separately from the wild-type cells and pooled before hybridization on a single array. Three more independent biological samples were prepared from zur deletion mutant cells, pooled, and hybridized on another single array. After normalization, the signal from the mutant cells was subtracted from the signal from the wild-type cells to recover Zur specific signal.

first: Seung-Hwan

last: Choi

first: Kang-Lok

first: Jung-Ho

last: Shin

first: Yoo-Bok

last: Cho

first: Sun-Shin

last: Cha

first: Jung-Hye

last: Roe


title: Identification of A Novel bZIP Transcription Factor in Camellia sinensis as A Negative Regulator of Freezing Tolerance in Transgenic Arabidopsis

status: Public on Jul 01 2017

city: Hangzhou

first: Lu

last: Wang

state: Zhejiang

address: 9th, South Meiling Road

institute: Tea Research Institute, Chinese Academy of Agricultural Sciences

summary:
Basic region/leucine zipper (bZIP) transcription factors play vital roles in the abiotic stress response of plants. However, little is known about the function of bZIP genes in Camellia sinensis. Here, we show that CsbZIP6 is induced during cold acclimation in tea plant. Constitutive overexpression of CsbZIP6 in Arabidopsis lowered the plants’ tolerance to freezing stress and ABA exposure during seedling growth. Compared to wildtype (WT) plants, CsbZIP6 overexpression (OE) lines exhibited increased levels of electrolyte leakage (EL) and malondialdehyde (MDA) contents and reduced levels of total soluble sugars (TSS) under cold stress conditions. Microarray analysis of transgenic Arabidopsis revealed that many differentially expressed genes (DEGs) between OE lines and WT plants could be mapped to ‘response to cold’ and ‘response to water deprivation’ terms based on GO analysis. Interestingly, CsbZIP6 overexpression repressed most of the cold- and drought-responsive genes as well as the starch metabolism under cold stress conditions. Taken together, our data suggests that CsbZIP6 functions as a negative regulator of the cold stress response in Arabidopsis thaliana, potentially by down-regulating cold-responsive genes.
To obtain insights into the molecular mechanisms by which CsbZIP6 mediates senstivity to cold stress in Arabidopsis plants, gene expression profiles in leaves of two CsbZIP6 OE lines and WT plants under normal (22ºC) and cold (4ºC) conditions were compared. The Agilent Arabidopsis Gene Expression (4×44K, Design ID: 021169) was used in this experiment.

overall_design: Arabidopsis seedlings were germinated, grown on 1/2 MS for 2 weeks and then transferred to soil. Thirty-day-old plants (WT, OE-1, OE-2) were grown at 4 oC (‘cold’) or normal conditions (‘normal’) for 4 days before the leaves were sampled, snap frozen in liquid nitrogen and stored at -80ºC until RNA isolation. Each replicate was collected from one seedling. Three biological replicates were used for the analysis except for the ‘normal’ OE-2 samples which lack a replicate because of substandard RNA quality. In total, 17 arrays were used in the study.

first: Hongli

last: Cao

first: Wenjun

last: Qian

first: Nana

last: Li

first: Hao

last: Xinyuan

first: Yajun

last: Yang

first: Xinchao


title: “Like Sugar in Milk”: Reconstructing the genetic history of the Parsi population

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

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

summary: Genomewide SNP data of Parsi population of India has been used to study their origin and migration.

overall_design: 19 samples were analysed with the Illumina platform Human660W-Quad v1.0 Genotyping BeadChip and are described herein.

first: Richard

last: Villems

first: Mait

last: Metspalu

first: Gyaneshwer

last: Chaubey


title: The transcriptional response to the olive fruit fly (Bactrocera oleae) reveals extended differences between tolerant and susceptible olive (Olea europaea L.) varieties

status: Public on May 06 2017

city: Rende

first: Fabrizio

last: Carbone

state: CS

address: C.da Li Rocchi Vermicelli

department: Research Centre for Olive, Citrus and Tree Fruit

institute: Council for Agricultural Research and Economics (CREA)

summary: Comparative profiling of damaged (pool of different stages of fly attack) and control undamaged fruits of cv Ortice and cv Ruveia (Olea europaea L.), characterized by a different tolerance to Bactrocera oleae, generated a comprehensive repertory of transcripts useful to study the genes modulated by Bactrocera oleae attack.

overall_design: To profile the variation in gene expression of olives during B. oleae feeding and to characterize the differences between the two varieties with contrasting susceptibility to olive-fly we used a CombiMatrix CustomArray™ 90K arrays (CombiMatrix Corporation) based on 61,825 olive probes (60,706 non-redundant) out of the 87,720 sequences of the pooled library (454 pyrosequencing results of four cDNA libraries obtained from damaged and undamaged drupes of the ‘Ortice’ and ‘Ruveia’ varieties). For each biological condition, three independent samples (i.e. from different trees) were obtained as pools of three to five independently extracted technical replicates.

first: Filomena

last: Grasso

first: Gaetano

last: Perrotta

first: Rosa

last: Rao


title: Impact of cytosine methylation on DNA binding specificities of human transcription factors.

status: Public on May 05 2017

city: BETHESDA

first: Syed

middle: Khund

last: Sayeed

state: maryland

address: Building 37, NIH

department: Center for Cancer Research

institute: National Cancer Institute

summary:
The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. The methylation is heritable across cell divisions, and contributes to the epigenetic memory that maintains the differentiated state of distinct cell types. Active gene regulatory elements are generally undermethylated relative to their flanking regions, and the undermethylation is thought to be important for their activity. Consistently with this model, the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By systematic analysis of 542 human TFs using methylation sensitive SELEX, we find here that a large number of TFs also prefer to bind to CpG methylated sequences. Most of these represent the extended homeodomain family. Structural analysis of HOXB13, CDX1, CDX2 and LHX4 revealed that the specificity of homeodomain proteins towards methylcytosine depends on amino-acids that form direct hydrophobic interactions with the 5-methyl group of methylcytosine. Our results provide a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity, and reveal that many developmentally important homeodomain proteins display strong preference for binding to mCpG containing sequences.
Genome-scale analysis reveals that binding of most transcription factors is affected by CpG methylation, and that many developmentally important homeodomain TFs directly recognize the 5-methyl group of methylcytosine.

overall_design: Protein binding microarray (PBM) experiments were performed for a set of 8 Human transcription factors: LHX9, NKX2.5, DLX3, POU5F1, MAX, NFATC2, CUX1 and CUX2, for their ability to bind 5-methylcytosine in CG sequence context. Briefly, the PBMs involved binding GST-tagged DNA-binding domains of the human TFs to double-stranded methylated or unmethylated 44K Agilent microarrays.  These microarrays are based on DeBruijn sequence design.  Details of the PBM protocol are described in Mann et al., Genome Res. 2013 Jun;23(6):988-97.

first: Yimeng

last: Yin

first: Ekaterina

last: Morgunova

first: Arttu

last: Jolma

first: Eevi

last: Kaasinen

first: Biswajyoti

last: Sahu

last: Khund-Sayeed

first: Pratyush

last: Das

first: Teemu

last: Kivioja

first: Kashyap

last: Dave

first: Fan

last: Zhong

first: Kazuhiro

last: Nitta

first: Minna

last: Taipale

first: Alexander

last: Popov

first: Paul

last: Ginno

first: Silvia

last: Domcke

first: Jian

last: Yan

first: Dirk

last: Schübeler

first: Charles

last: Vinson

first: Jussi


title: LASSIM -a network inference toolbox for genome-wide mechanistic modeling [USF2, KLF6/COPEB, CBL and HIS1 siRNA]]

status: Public on Jun 12 2017

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

summary: We present LASSIM, which is a toolbox built to build and infer parameters within mechanistic models on a genomic scale. This is made possible due to a property shared across biological systems, namely the existence of a subset of master regulators, here denoted the core system. The introduction of a core system of genes simplifies the inference into small solvable sub-problems, and implies that all main regulatory actions on peripheral genes come from a small set of regulator genes. This separation allows substantial parts of computations to be solved in parallel, i.e. permitting the use of a computer cluster, which substantially reduces the time for the computation to finish.

overall_design: Data contains 31 samples: 8 controls, 6 CBL knockdowns, 6 USF2 knockdowns, 6 COPEB(KLF6) knockdowns and 5 HIS1 knockdowns.

first: Rasmus

last: Magnusson

first: Guido

last: Mariotti

first: Mattias

last: Köpsén

first: William

last: Lövfors

first: Rebecka

last: Jörnsten

first: Jörg

last: Linde

first: Torbjörn

last: Nordling

first: Elin

last: Nyman

first: Sylvie

last: Schulze

first: Colm

last: Nestor

first: Huan

last: Zhang

first: Gunnar

last: Cedersund

first: Mikael

last: Benson

first: Andreas

last: Tjärnberg

first: Mika

last: Gustafsson


title: Temperature-mediated changes in hepatic gene expression of a mammalian herbivore (Neotoma lepida)

status: Public on May 02 2017

city: Salt Lake City

first: Patrice

middle: Kurnath

last: Connors

state: UT

address: 257 south 1400 east

department: Biology

institute: University of Utah

summary: The effects of ambient temperature and dietary plant toxins on differential gene expression in the liver were compared in herbivorous rodents (woodrats, genus Neotoma) using microarrays custom-designed for woodrats.  Expression profiles revealed a greater number of up-egulated genes at 22C comapred to a thermoneutral temperature (27C).  Genes and pathways up-regulated at 22C were related to growth and biosynthesis, suggesting the liver could be in a building state at this temperature.  Conversely, genes associated with gluconeogenesis, apoptosis and protein misfolding, which likely reflected a more stressed state for the liver.  Taken together, these results highlighted the important role of temperature on gene expression profiles in the desert woodrat.  As crucial players in many ecosystems, understanding how herbivorous mammals will respond to climate change is imperative to accurately predict repercussions and aid in conservation efforts.

overall_design: Gene expression in woodrats was compared across 4 treatment groups (N= individuals 4 per group) based upon temperature (22C or 27C) and dietary plant toxins (control or creosote diets).  Animals were temperature acclimated for at least 14 days, and then fed experimental diets for 8 days.  RNA was extracted from liver tissue and one-color arrays were performed at the University of Utah Microarray Core facility.

first: M Denise

last: Dearing

first: Jael

last: Malenke


title: Comparing the intestinal transcriptome of Meishan and Large White piglets during late fetal development reveals genes involved in glucose and lipid metabolism and immunity as valuable clues of intestinal maturity

status: Public on Jun 01 2017

city: Castanet tolosan

first: Laurence

last: Liaubet

address: chemin de borde rouge

department: Animal Genetic

institute: INRA

summary: To further knowledge of piglet maturity, we have developed a microarray analysis to describe biological processes and to find candidate genes for key roles in piglet maturity. The objective was to identify which genes and biological processes are specifically involved in the difference between two extreme breeds: Large White (LW) and Meishan (MS). The LW breed is a selected breed known to show an increased rate of mortality at birth, while the MS breed presents more robust piglets at birth. MS and LW sows were inseminated with mixed semen (LW and MS) hence each litter was composed of pure fetuses (LW or MS) and crossed fetuses (LWMS from MS sows and MSLW from LW sows).

overall_design: To assay for changes in gene expression during piglet maturity, mRNA was isolated from 64 fetal jejunum (intestinal)  samples with 8 different conditions: two fetal gestational ages (90 or 110 days of gestation), associated with four genotypes (two extreme breeds for mortality at birth (MS and LW) and two crossed breeds (MSLW and LWMS)). MS fetuses are known to have a better survival at birth than LW fetuses. An understanding of maturity is possible with the comparison between the fetal gestational ages and between the two extreme breeds. The impact of parental genotypes is studied with the presence of crossed fetuses. After quality control and normalization, only 63 samples were conserved (represented here).

first: Y

last: Yao

first: V

last: Voillet

first: M

last: Jegou

last: San Cristobal

first: S

last: Dou

last: Romé

last: Lippi

last: Billon

last: Père

first: G

last: Boudry

first: L

last: Gress

first: N

last: Iannuccelli

first: P

last: Mormède

first: H

last: Quesnel

last: Canario

first: I

last: Le Huërou-Luron


title: Hallmarks of the dynamic responses to silica in Thalassiosira pseudonana - Identification, characterization and classification of signature genes and their corresponding motifs

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom Thalassiosira pseudonana was subjected to silicon (Si) shift-up and shift-down situations. Cellular and molecular signatures, dynamic changes and co-regulated clusters representing the hallmarks of cellular and molecular responses to changing Si availabilities were characterised. 62 silaffin-like proteins (SFLPs), two kinases and a novel family of putatively frustule-associated transmembrane proteins induced by Si shift-up and a possible role in frustule biosynthesis were identified. A separate cluster analysis performed on all significantly regulated SFLPs, as well as fourteen new proteins with silaffin-like motifs, resulted in the classification of silaffins, cingulins and SFLPs into distinct clusters. The genes in the Si-responsive clusters are in general highly divergent, but positive selection does not seem to be the driver behind this variability. This study provides a high-resolution map over transcriptional responses to changes in Si availability in T. pseudonana. Hallmark Si-responsive genes are identified, characteristic motifs and domains are classified, and taxonomic and evolutionary implications outlined and discussed.

overall_design: Thalassiosira pseudonana (CCAP 1085/2) was grown in axenic cultures at 20°C, illuminated with 130 µmol photons m-2 s-1 in light:dark cycles of 16:8 hours. Both experiments (shift-up and shift-down) were initiated at least 4 hours after beginning of the light phase, and all consecutive samplings were performed within the same light period. The Si-depleted medium contained 0.7 µM Si, and was used to prepare the experimental medium for the shift-down experiment following the modified f/2 recipe, but with no Si added. For the shift-up experiment, 1000 mL pre-cultures were cultivated as batch cultures in medium with f/4-levels of Si (approximately 55-60 uM Si, including a seawater background of 4 uM) for three weeks prior to the experiment; the cultures were diluted with fresh medium when the Si was depleted. The silicon shift-down experiment was sampled before centrifugation (-2 h), and thereafter, samples were taken every hour or half hour for 7.5 hours after resuspension in silicate-free medium. Samples from time point 72 h were also included. The time points -2, 0.33, 1, 2, 4, 7.5, and 72 hours were selected for further analyses. For the silicon shift-up experiment, cultures were sampled right before Si addition, and then every hour or every half hour as the biomass began to increase. Based on the time course of the culture, the time points -0.25 (-15 min, control), 0.25, 0.5, 1, 2, 4, 6, and 8 hours relative to the silicate shift-up were selected for further analyses.

first: Tore

last: Brembu

first: Matilde

last: Chauton

first: Olav

last: Vadstein

first: Torfinn

last: Sparstad

first: Atle

middle: M

last: Bones


title: Differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24

first: Renate

last: Schmidt

overall_design: Expression data for the two accessions were compared for developing seeds of the same stage. For each of the accessions gene expression at the different developmental stages was also compared.

first: Anastassia

last: Boudichevskaia


title: Programmed death 1 receptor blockade and immune-related gene expression profiling in non-small cell lung carcinoma, head and neck squamous cell carcinoma and melanoma

status: Public on May 15 2017

city: Barcelona

first: Tomás

last: Pascual

address: Villarroel 170

department: Medical Oncology

institute: Hospital Clinic de Barcelona

summary: RNA from tumor samples from 65 patients with melanoma, lung cancer, head and neck treated  anti-PD1was analyzed on the nCounter system using the PanCancer 730-Immune Panel.

overall_design: Twenty-three immune-related genes or signatures were linked to response. The intra- and inter-biopsy variability of PD1, PDL1, CD8A and CD4 mRNA.

first: Aleix

last: Prat


title: Microarray analysis of xenograft model to characterize the CNS leukemia

status: Public on May 17 2017

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: We present a detailed genetic, transcriptional and physiological study of leukemic cells isolated from the CNS and bone marrows (BM) of both affected children and xenograft model of B-ALL which recapitulate the key features of CNS involvement. We reveal that leukemic cells in CNS possess distinct hypoxic signature such as proliferation suppression, decrease of mitochondrial oxidative phosphorylation and increase of glycolysis compared with leukemic cells in BM.

overall_design: We compared the gene expression profiles of leukemic cells isolated from organs of xenograft recipients from 4 patients (ALL#1-4) with microarrays.

first: Itaru

last: Kato

first: Hiroki

last: Ozawa

first: Dapeng

last: Wang

first: Masahiro

last: Nakamura


title: Expression data of nuclear mRNA export mutant rae1-167 cells

city: Kagamiyama, Higashi-Hiroshima

first: MUNEYOSHI

last: KANAI

institute: National Research Institute of Brewing

summary:
rae1 is an essential gene and encodes one of nuclear pore complex. rae1-167 mutant cells show rapid accumulation of polyA-RNA in the nucleus at 36°C followed by protein accumulation, suggesting that accumulated nuclear mRNA influences nucelar cytooplasmic transport.
We used microarrays to compare the overall gene expression of rae1-167 cells grown at 36°C with that at 25°C.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: rae1-167 cells grown in YE4S medium were harvested for RNA extraction and hybridization on Affymetrix microarray. In order to characterize transcriptional profiling of rae1-167 cells at 36°C, we carried out the genome-wide gene expression analysis of rae1-167 cells.

first: Kazunori

last: Kume

first: Muneyoshi

last: Kanai


title: Expression data from BIG LEAF

status: Public on May 11 2017

city: Charleston

first: Yordan

last: Yordanov

state: IL

address: 600 Lincoln ave

department: Department of Biological Sciences

institute: Eastern Illinois University

summary:
We study differences in gene expression between Populus P35S::BL (BL-oe)  lines and control, affecting plant growth and differentiation, and dormancy. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes droved by overexpression of BL gene.
We identified an activation tagging mutant with increased leaf size and correspondingly name it BIG LEAF (BL). We positioned the tag, localized a putative candidate gene and verified transcription activation. The activated gene encodes a WD40 putative transcription regulator similar to the Arabidopsis thaliana STERILE APETALA (SAP). We recapitulated the phenotype by overexpression of the gene into the same genotype under strong constitutive promoter (P35S::BL, BL-oe). Transgenic up-regulation of the BL gene caused enhanced leaf size, early bud-break, and suppression of secondary growth. BL transcript abundance in wild type plants is in apical tissues, mostly in shoot meristem, leaf primordia and axillary meristem. Our data indicates that BL plays an important role in the process of tree growth.

overall_design: Poplar apex, secondary stem (30th internode), and leaves (at 30 node) was selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain expression of affected genes in P35S::BL lines and control wild type (WT-717), in order to increase the resolution of expression profiles inducing the developmental changes in P35S::BL. To do that, we selected apex, stem and leaf tissue from greenhouse healthy plants.

first: Victor

middle: B

last: Busov


title: Novel surrogate markers for reflux esophagitis using exosomal microRNAs in rats

status: Public on Mar 15 2017

city: Osaka-city

first: Risa

last: Uemura

address: 1-4-3 asahimachi, abeno-ku

department: Gastroenterolgy

institute: Osaka city university Graduate School of Medicine

summary: There is no useful biomarker for reflux esophagitis. The aim of this study is to establish novel diagnosis marker for RE by using miRNA.

overall_design: In this study, acid reflux esophagitis was induced in rats. Rats were killed day 21 (chronic phase) after induction of RE. Shapm operation rats were used as control. Exosomes were extracted from serum, and the expression patterns of serum miRNAs during the RE chronic phase were analyzed via microarray.

first: Yoshikii

last: Murakami

first: Yasuhiro

last: Fujiwara


title: S-adenosylmethionine decarboxylase-dependent gene expression in planktonic Bacillus subtilis NCIB3610

status: Public on Mar 24 2017

city: Dallas

first: Anthony

middle: John

last: Michael

state: Texas

address: 6001 Forest Park

department: Pharmacology

institute: UT Southwestern Medical Center, Dallas

summary: The polyamine spermidine is not required for normal planktonic growth of Bacillus subtilis but is essential for robust biofilm formation. In a spermidine-deficient mutant of B. subtilis, the structural analogue norspermidine but not homospermidine restored biofilm formation. Intracellular biosynthesis of another spermidine analogue aminopropylcadaverine from exogenously supplied homoagmatine also restored biofilm formation. The differential ability of C-methylated spermidine analogues to replace the function of spermidine in biofilm formation indicated that the aminopropyl side of spermidine is more sensitive to C-methylation. Together, these data indicate that the aminopropyl side of spermidine is essential for its function in biofilm formation, and that the length and symmetry of the molecule is not critical. Transcriptomic analysis of a spermidine-depleted speD mutant of B. subtilis uncovered a nitrogen, methionine and S-adenosylmethionine sufficiency response, resulting in repression of gene expression related to purine catabolism, methionine and S-adenosylmethionine biosynthesis, methionine salvage, and there were indications that membrane status was altered. Consistent with the requirement for spermidine in biofilm formation, expression of the operons for production of the exopolysaccharide and TasA protein components of the biofilm matrix was reduced, as was expression of regulator SinR antagonist slrR. Single-cell analysis indicated that the effect of spermidine depletion was to decrease the number of cells expressing the biofilm matrix operons. Deletion of sinR or ectopic expression of slrR in the spermidine-deficient ΔspeD background restored biofilm formation, indicating that spermidine is required to promote expression of the biofilm regulator slrR.

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: The study consists of two identical experiments separated in time by one week. The first experiment consists of a comparison of gene expression of the parental Bacillus subtilis NCIB3610 strain with a speD mutant (S-adenosylmethionine decarboxylase) that produces a spermidine auxotrophic strain. Both strains were grown in MSgg polyamine-free minimal medium at 37C to an OD of 0.5. For each strain, three independent biological replicates were grown (3610-1, 3610-2, 3610-3 and speD-1,speD-2, speD-3) and analyzed separately. The second experiment was identical and performed one week later with samples 3610-4, 3610-5, 3610-6, speD-4, speD-5 and speD-6.


title: Global transcriptional changes during S. mutans biofilm dispersal

status: Public on Feb 27 2017

city: Guangzhou

first: Jia

last: Liu

state: Guangzhou

address: 74 Zhong Shan Er Road,

institute: Sun Yat Sen University

summary: We used whole-genome microarrays to identify the global transcriptional changes during biofilm dispersal and also to investigate the molecular mechanism that regulating biofilm dispersal.

overall_design: S. mutans biofilms at different dispersal stages were collected for microarray analysis

first: Xi

last: Wei


title: Methylated CpG Island Recovery Assay (MIRA)-chip from Sirt1 wild-type (Sirt1+/+) and knock-out (Sirt1-/-) murine embryonic stem cells (ESCs)

status: Public on Feb 20 2017

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

institute: University of Ulsan College of Medicine

summary:
Proper DNA-methylation is inevitable for normal development and this epigenetic program is dynamically reprogrammed especially around embryo implantation. Accordingly, embryonic stem cells (ESCs) derived from inner cell mass in pre-implantation embryo exhibit the lowest DNA methylation level compared with differentiated tissue cells to ensure their pluripotency and germ-line potency.
Methylated CpG Island Recovery Assay (MIRA) coupled chip DNA methylome analysis demonstrated that Sirt1 deficiency increases the abnormal DNA methylation especially on the a subtype of imprinted and germ-line development genes.

overall_design: Comparison of DNA methylome between Sirt1+/+ and Sirt1-/- murine ESCs

first: Dong-Myung

last: Shin

first: Mariusz

last: Ratajczak


title: Gene expression profiles of mesenterial adipose tissue of newborn rats from dams that were either fed a vitamin D adequate (1,000 IU vitamin D/kg diet) or a vitamin D deficient diet (0 IU vitamin D/kg diet)

status: Public on Dec 31 2016

city: Halle

first: Alexandra

last: Schutkowski

address: von Danckelmann Platz 2

institute: MLU Halle-Wittenberg

summary: The aim of the study was to investigate the role of vitamin D on adipocyte development. To this end, rat dams (Sprague-Dawley rats ) were fed diets with 0 or 1,000 IU vitamin D3 per kg diet 5 weeks prior to conception until the end of lactation. By using high-density DNA microarrays, we analyzed the gene-expression profile of mesenterial adipose tissue of both groups of newborn rats.

overall_design: RNA was extracted from mesenterial adipose tissue and analyzed with Affymetrix GeneChip Rat Genome 230 2.0 Array

first: Daniela

last: Max

first: Markus

last: Bönn

first: Corinna

last: Brandsch

first: Sarah

last: Grundmann

first: Frank

last: Hirche

first: Hagen

last: Kühne

first: Martin

middle: S

last: Staege

first: Gabriele

middle: I

last: Stangl


title: Expression Data from ALDH1+ breast cancer stem cells

city: Ribeirão Preto

first: Daniel

middle: Guimarães

last: Tiezzi

state: São Paulo

address: Av. Bandeirantes, 3900 - Monte Alegre

department: Gynecology and Obstetrics

institute: Ribeirão Preto Medical School - University of São Paulo

summary: Breast cancer is the most common cancer in women worldwide and metastatic dissemination is the principal factor related to death by this disease. Breast cancer stem cells, are thought to be responsible for metastasis and chemoresistance.. In this study, based on whole transcriptome analysis from putative breast CSCs and reverse-engineering of transcription control networks, we were able to identify two networks associated to this phenotype.

overall_design: Using samples acquired before the chemotherapy, Breast cancer cells from patient were sorted using flow cytometry to select for ALDEFLUORhigh cells. Gene expression profiles of these cells were compared with their matched tumor samples.

middle: G

first: Willian

last: Silveira

first: Patrícia

middle: P

last: Palma

first: Renata

middle: D

last: Sicchieri

first: Larissa

last: Mandanaro

first: Tatiane

last: Oliveira

first: Jurandyr

last: Andrade

first: Silvia

last: Rogatto

first: Rolando

last: Villacis


title: P53 regulated microRNAs in the presence/absence of caesin kinase 1 alpha (CK1alpha)

status: Public on Feb 16 2017

city: Heidelberg

first: Mohammed

last: Abba

address: Im Neuenheimer Feld 280

department: Molecular Oncology of Solid Tumors

institute: German Cancer Research Center (DKFZ)

summary: To evaluate the differential expression of mature miRNAs in the presence and absence of P53 using RKO isogenic cell lines. Additionally, we also wanted to study the imapct of CK1alpha on the regulation of these miRNAs

overall_design: RKO P53 isogenic cell lines with/without validated CK1apha siRNA transfected at an end concentration of 100nM

first: Nitin

last: Patil


title: Expression data from  control and demylination zebrafish at 10dpf

status: Public on Oct 27 2016

city: Tianjin

first: Xudan

last: Lei

address: Weijin Road 94

department: Medical College

institute: nankai University

summary:
Zebrafish is ideal model organism to study myelination and demyelination. We could use this model to screen demylination relative genes and provide a new idea for clinic therapy.
We used microarrays to identify the genes involved in the demyelination of our zebrafish model, and screen alteration gene relative to demylination disease

overall_design: First, we generated the Tg (mbp:nfsB-egfp) transgenic line using nitroreductase / metronidazole cell ablation technology. Second, we used metronidazole to  treat zebrafsih and contrbuting to demyelination. Third,  Control group and demylination zebrafih were selected at 10 day after fertilization for RNA extraction and hybridization on Affymetrix microarrays. At last, we used microaarray to obtain demyelination disease relative genes.

first: Yuhao

last: Li

first: Yangwu

last: Fang


title: Expression data from single embryonic chick retinal cells

status: Public on May 09 2017

city: Ames

first: Jeff

last: Trimarchi

state: IA

address: 2437 Pammel Drive

department: Genetics, Development and Cell Biology

institute: Iowa State University

summary: This study aimed to characterize the transcriptomes of developing neurons from the chicken retina.

overall_design: We examined 39 single cells isolated at timepoints ranging from E3-E15.

first: Lauren

last: Laboissonniere

first: Gregory

last: Martin

first: Jillian

middle: J

last: Goetz

first: Brock

last: Pope

first: Kallie

last: Weinand

first: Laura

last: Ellson

first: Diane

last: Fri

first: Miranda

last: Lee

first: Andrea

last: Wester

first: Jeffrey


title: Transcriptome-wide analysis of xylogenesis during growing season in Pinus canariensis

status: Public on Sep 01 2016

city: Göttingen

first: Victor

last: Chano

address: Buesgenweg 2

department: Forest Genetics and Forest Tree Breeding

institute: University of Göttingen

summary:
Wood in conifers is mainly composed of tracheids. Some taxa, such as Pinus, present tracheids also in the rays, but are axial tracheids which constitute the vast majority of secondary xylem. Nevertheless, radial and axial parenchyma surrounding constitutive and traumatic resin ducts is known to serve as crucial reserve storage. These reserves are mobilized in response to traumatism, insect and pathogen attacks and defoliation, allowing the synthesis of resin, healing and, in few taxa, even resprouting. However, due to the low proportion of parenchymatic cells in secondary xylem relevant genes involved in their differentiation may have been missed in studies of transcriptomics of conifer wood formation. In this study we have used Pinus canariensis as a model species, given its comparatively high proportion of axial parenchyma. We have prepared two normalized libraries from its cambial zone, covering early- and late-wood differentiation. We have de novo assembled a transcriptome, and have analyzed the transcriptional profiles during the growing season, getting a more complete picture of wood formation in conifers.

SUBMITTER_CITATION: Chano, V., López de Heredia, U., Collada, C., et al. (2017). Transcriptomic analysis of juvenile wood formation during the growing season in Pinus canariensis. Holzforschung, 0(0), pp. -. Retrieved 8 Aug. 2017, from doi:10.1515/hf-2017-0014

overall_design: mRNA samples were collected at 6 dates during the growing season in Pinus canariensis, supported by microscopical observation of cambial activity: March, April, May, June, July and September. Three biological replicates were collected for each time sampled, and therefore 18 mRNA samples were hybridazed in a one-color microarray experiment.

first: Unai

last: Lopez de Heredia

first: Carmen

last: Collada

first: Alvaro

last: Soto


title: BBr003: Characterization of bovine embryos cultured under conditions appropriate for sustaining human naïve pluripotency

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: In mammalian preimplantation development, pluripotent cells are set aside from cells that contribute to extra-embryonic tissues. Although the pluripotent cell population of mouse and human embryos can be cultured as embryonic stem cells, little is known about the pathways involved in formation of a bovine pluripotent cell population, nor how to maintain these cells in vitro. The objective of this study was to determine the transcriptomic profile related to bovine pluripotency. Therefore, in vitro derived embryos were cultured in various culture media that recently have been reported capable of maintaining the naïve pluripotent state of human embryonic cells. Gene expression profiles of embryos cultured in these media were compared using microarray analysis and quantitative RT-PCR. Compared to standard culture conditions, embryo culture in 'naïve' media reduced mRNA expression levels of the key pluripotency markers NANOG and POU5F1. A relatively high percentage of genes with differential expression levels were located on the X-chromosome. In addition, reduced XIST expression was detected in embryos cultured in naïve media and female embryos contained fewer cells with H3K27me3 foci, indicating a delay in X-chromosome inactivation. Whole embryos cultured in one of the media, 5iLA, could be maintained until 23 days post fertilization. Together these data indicate that 'naïve' conditions do not lead to altered expression of known genes involved in pluripotency. Interestingly, X-chromosome inactivation and development of bovine embryos were dependent on the culture conditions.

overall_design: Microarrays used were bovine whole genome gene expression microarrays V2 (Agilent Technologies) representing 43,653 Bos taurus 60-mer oligos in a 4x44K layout. Four sets of RNA samples isolated from dissected ICMs cultured in SOF or NHSM were compared in a direct experiment design using 4 dual-channel microarrays. Within each group of two microarrays for each treatment, sample (NHSM) versus control (SOF) hybridizations were performed in balanced dye-swap.

first: Bas

last: Brinkhof

first: Helena

middle: T

last: van Tol

first: Henk

last: Haagsman

first: Bernard

last: Roelen


title: Ileal expression data of mice fed with diet containing protein from various sources

status: Public on Aug 24 2016

city: Wageningen

first: Soumya

middle: Kanti

last: Kar

state: I am not in the U.S. or Canada

address: De Elst1

department: Animal Science Group

institute: WUR

summary:
This study was designed to address key questions concerning the use of alternative protein sources for animal feeds and addresses aspects such as their nutrient composition and impact on gut function, the immune system and systemic physiology. We used casein (CAS), partially delactosed whey powder (DWP), spray dried porcine plasma (SDPP), soybean meal (SBM), wheat gluten meal (WGM) and yellow meal worm (YMW) as protein sources.
We investigated the effects of feeding mice during a period of four weeks on semi-synthetic diets containing 30% of six different protein sources. Microarrays were used to detail the global gene expression in the ileal mucosae of mice.

overall_design: Male C57BL/6J mice were stratified according to bodyweight and litter of origin into six dietary treatment groups. These mice were fed for four weeks with semi-synthetic diets containing one of the following protein sources. At the end of four weeks, mice were sacrificed by euthenesia and ileal tissue samples (scrapings) were collected for RNA extraction and hybridization on Affymetrix microarrays. Soybean meal (SBM) diet group served as reference to make comparisons with other experimental diets.

first: Hooiveld

last: Guido

first: Dirkjan

last: Schokker


title: Dormant and after-ripened seeds are distinguished by early transcriptional differences in the imbibed state

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

institute: Wageningen University

summary:
We analyzed the transcriptome of dormant and after-ripened imbibed seeds of the Arabidopsis accession Cape verde Islands.
We analyzed the transcriptional changes in temporal and spatial detail by sampling at four imbibition time-points (3, 7, 12 and 24 hours after sowing) and two seed compartments (RAD and MCE).

overall_design: Gene expression in imbibed dormant and after-ripened seeds was compared. For each sample three replicates were used.

last: Dekkers

first: Simon

last: Pearce

first: Marieke

last: van Bolderen-Veldkamp

first: Michael

last: Holdsworth


title: Gene expression profile of biochemically recurrent prostate cancer

status: Public on May 01 2017

city: Vilnius

first: Kristina

last: Daniunaite

address: Sauletekio Ave. 7

department: Institute of Biosciences

country: Lithuania

institute: Vilnius University

summary: Prostate cancer (PCa) is the second most common solid tumor type in men with high mortality rates. This study specifically aimed at identification of molecular biomarkers of PCa showing clinically aggressive course of the disease. Transcriptome analysis of PCa cases with biochemical progression (BCR) and No-BCR cases was performed with human gene expression microarrays. Expression levels of the selected genes were validated by real-time PCR in two independent cohorts of PCa cases (N = 55 and N = 53) and non-cancerous control tissues (NPT; N = 12). Comparison of gene expression profile of BCR and No-BCR cases revealed significant changes in expression levels of 455 genes, and the vast majority of the genes were down-regulated in the recurrent PCa. Quantitative evaluation of gene expression levels identified down-regulation of MT1E and GPR52 expression and up-regulation of EZH2 as the specific biomarkers of PCa progression, but only MT1E expression retained the independent prognostic value in a multivariate model. Aberrant methylation of the two fragments of MT1E promoter was frequent (71% and 60%) in PCa tissues as compared to NPT (p < 0.001) and was significantly associated with decreased expression in one of the PCa cohorts (p < 0.050). In conclusion, the data of our study suggest epigenetic inactivation of MT1E expression as the specific feature of PCa showing the tendency to progress.

overall_design: Gene expression profile was analyzed in 8 PCa cases with BCR and compared to 8 BCR-free cases. No biological replicates were performed.

first: Sonata

last: Jarmalaite


title: Cumene hydroperoxide stimulon and OhrR regulon in Chromobacterium violaceum

city: Ribeirao Preto

first: Jose

middle: Freire

last: da Silva Neto

state: Sao Paulo SP

address: Av Bandeirantes 3900

department: Biologia Celular e Molecular e Bioagentes Patogenicos

institute: Universidade de Sao Paulo

summary: In this study, we used transcriptional profiling to define the adaptive response of C. violaceum to oxidative stress induced by cumene hydroperoxide (CHP) and to identify the OhrR regulon. DNA microarray and northern blot analysis revealed that in CHP-treated cells occur strong upregulation of genes involved in many pathways for stress protection, including antioxidant enzymes (catalase and peroxidases), thioredoxin, glutaredoxin and lipoyl-dependent reducing systems, DNA repair enzymes, heat shock response (σ32 regulon), iron limitation (Fur regulon) and nitrogen starvation. Genes encoding glyoxalases, glutathione S-transferases and oxygenases were also induced, suggesting further catabolism of the aromatic compound CHP. Pathways downregulated by CHP stress include electron transport chain, nucleotide biosynthesis and unsaturation of fatty acids. Further, we identified two upregulated genes (OhrA and a protein with GGDEF domain for c-di-GMP synthesis) and three downregulated genes (hemolysin, chitinase and collagenase) in the ohrR mutant. Using a mouse infection model, we demonstrate that the ohrR mutant, but not the ohrA mutant, is attenuated for virulence and showed a decreased bacterial burden in the liver. Therefore, we have defined the CHP stimulon and determined that C. violaceum uses the organic hydroperoxide sensor OhrR for regulate expression of genes required to antioxidant defense and to modulate virulence in its interaction with the host.

overall_design: Two experimental procedures comparing WT control vs. WT CHP or WT control vs. ohrR mutant. Each comparison was performed using three biological replicates.

first: Maristela

last: Previato

first: Diogo

middle: A

last: Meireles

first: Luis

middle: E

last: Netto

first: José

middle: F


title: Chicken brain and lung gene expression profiles following infection with two recombinant H5N3 avian influenza viruses - rH5N3 Ori (P0) and rH5N3 P6

status: Public on Mar 22 2017

city: Winnnipeg

first: John

last: Pasick

state: Manitoba

address: 1015 Arlington Street

department: NCFAD

institute: CFIA

overall_design:
Groups of 6 specific pathogen free Leghorn chickens were infected oronasally with 4.0 x 10e4 pfu of rH5N3 Ori, 4.0 x 10e4 rH5N3 P6, or sterile PBS. At 1 and 3 days post-inoculation 3 birds from each group were humanely euthanized and RNA extracted from brain and lung samples.
100 mg of each tissue was homogenized in 1 ml of TriPure isolation reagent with 1.0 mm zirconia/silica beads. This was followed by the addition of 0.2 ml chloroform, thorough vortexing and phase separation by centrifugation. The aqueous phase was mixed with an equal volume of 75% ethanol and passed through an RNeasy column (Qiagen). The column was washed once with RW1 and twice with RPE buffer before eluting the RNA in nuclease free water. OD260, OD280 and RNA concentration were determined on a NanoDrop ND-1000 spectrophotometer. RNA concentration and integrity were further assessed using a eukaryotic total RNA nanochip and an Agilent Bioanalyzer 2100.

first: Sandra

last: Diederich

first: Yohannes

last: Berhane


title: circRNA expression profiles for 10 human samples derived from patients with hepatocellular carcinoma

status: Public on Apr 20 2017

city: Ningbo

first: liyun

last: fu

address: ningbo xibei street No.41, zhejiang province

department: Department of Hepatology

institute: HwaMei Hospital, University of Chinese Academy of Sciences (Ningbo No.2 hospital)

summary: Investigation of circRNA expression profile of  hepatocellular carcinoma

overall_design: A ten chip study using total RNA extracted from five hepatocellular carcinoma tissues and three paracancerous tissues


title: Transcriptome profiling of spleen, blood and hemi-brain of social stressed C57B6 mice exhibiting PTSD like features

status: Public on Dec 31 2015

city: Fort Detrick

first: seid

last: muhie

state: MD

address: 568 Doughten Dr

department: Systems Biology Enterprise

institute: USACEHR

summary: Social stress mouse models were used to simulate human post-traumatic stress disorder (PTSD). C57B/6 mice exposed to SJL aggressor mice exhibited behaviors accepted as PTSD-in-mouse phenotype: 'frozen' motion, aggressor's barrier avoidance, startled jumping, and retarded locomotion. Transcripts in spleen, blood and hemi-brain of stressed and control C57B/6 mice were analyzed using Agilent's mouse genome-wide arrays.

overall_design:
C57B6 mice were exposed to SJL aggressor mice for periods of 5 days and 10 days (6 hours each day) to induce anxiety/stress which parallels to PTSD in human.
Organs, blood and brain regions were collected after 24 hours and 1.5 week of post 5 days social defeat period; and 24 hour and 6 weeks post 10 days social stress period.

first: Seid

last: Muhie

first: Rasha

last: Hammamieh

first: Marti

last: Jett


title: The microRNA expression profile of mouse Muller glia in vivo and in vitro

status: Public on Feb 11 2017

city: New York

first: Stefanie

last: Wohl

state: NY

address: 33w 42nd Street

department: Biological and Vision Sciences

institute: SUNY Optometry

summary:
In order to identify the miRNAs in adult and young (postnatal day 11/12) Müller glia of the neural retina, we isolated the Müller glia from Rlbp-CreER: Stopf/f-tdTomato mice by means of fluorescent activated cell sorting and analyzed their miRNAs using NanoStrings Technologies®.
We next compared miRNA expression of acutely isolated Müller glia with those that were maintained in dissociated culture for 8 and 14 days. We found that most miRNAs declined in vitro. Interestingly, some miRNAs that were not highly expressed in adult Müller glia increased in cultured cells. Our results thus show the miRNA profile of adult Müller glia and the effects of cell culture on their levels.

overall_design:
We used fluorescence activated cell sorting (FACS) to purify adult MG (pooled from 40 retinas), using an MG specific cre-lox labeling strategy by crossing Rlbp-CreER mice with stopf/f-tdTomato mice. The RNA was extracted from purified MG (tdTomato+) and retinal neurons (tdTomato−) and miRNA expression was analyzed by means of a recently developed molecular barcode technology called NanoStrings®. The miRNAs of freshly isolated P11/12 (pooled from 32 retinas) and adult Muller glia and cultured Muller glia (8 and 14 days in vitro, 20 retinas total) were analyzed using NanoString and nCounter Technologies ®.

[1] Values from adult MG, adult neurons, P11 MG and P11 neurons were normalized against 4 housekeeping genes (β -actin, GAPDH, Rpl19, and B2m), 8 negative controls, and 6 positive controls that were run simultaneously with the samples.

[2] Values from adult MG, P11 MG and cultured MG for 8 DIV or 14 DIV were normalized against 4 housekeeping genes (β -actin, GAPDH, Rpl19, and B2m), 8 negative controls, and 6 positive controls that were run simultaneously with the samples.

This work was funded by these additional grants:

Grant Number: Wo 2010/1-1
Source: DFG scholarship for S.G. Wohl, German Research Foundation (DFG)

Grant Number: TA-RM-0614-0650
Source: for  T.A. Reh, Foundation Fighting Blindness (FFB)

Grant Number: P30EY01730
Source: Vision Core Grant for the use of imaging facilities

first: Thomas

last: Reh