title: Copy number variation analysis of human Barrett's esophagus stem cells (HumanOmniZhongHua-8 v1.1 Beadchip)


title: LNCRNAs and mRNAs in a Gynecological Disease

status: Public on Jan 26 2016

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: sun yat sen university

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

summary:
Increasing evidence indicates that long non-coding RNAs (lncRNAs) play important roles in human diseases. This study aimed to investigate the tissue and serum lncRNAs that are differentially expressed between patients with endometriosis, a gynecological disease, to evaluate the potential of these lncRNAs as non-invasive markers for the disease.
Genome-wide profiling of lncRNA expression patterns revealed that many lncRNAs were abnormally expressed between sera and tissues of the patient samples.

overall_design: the Glue Grant Human Transcriptome Array, which contained approximately 39,223 lncRNAs. The arrays were performed with 5 sets of pooled samples, including a pool of 10 endometriosis serum samples, a pool of 10 control serum samples, a pool of 5 eutopic (EU) endometrium tissue samples, a pool of 5 ectopic (EC) endometrium tissue samples and a pool of 5 negative tissue controls.

first: Yue-Qin

last: Chen


title: Copy number variation analysis of human Barrett's esophagus stem cells

status: Public on Jan 13 2016

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

country: USA

institute: University of Houston

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

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

overall_design: Refer to individual Series


title: 244K array Comparative Genomic Hybridization for the characterization of CNVs among inbred Fayoumi, inbred Leghorn, Line A broiler, and Line B broiler chicken

status: Public on Feb 11 2016

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

type: Genome variation profiling by genome tiling array

summary: Chromosomal structural variation can cause alterations in gene dosage and gene regulation between genomes. Structural variants producing a change in the number of copies of a genomic region are termed copy number variants (CNVs). CNVs have been demonstrated to have causative effects on both Mendelian and complex traits, including susceptibility to infectious diseases. We are interested in mapping CNVs to domesticated chicken breeds to help determine structural variation between genomes that influences economically important traits. For this study, Fayoumi, Leghorn, Line A broiler and Line B broiler chicken were chosen.  Fayoumi and Leghorn chickens were selected as these two breeds harbor different responses certain pathogens like Avian Influenza Virus and coccidiosis; Broiler Line A and Line B indivduals were chosen as they harbor different intestinal colonization loads to the bacterium Campylobacter jejuni. Campylobacter genetic Line A and genetic Line B are from a commercial producer have been previously described as either resistant (Line A) or susceptible (Line B). Highly inbred chicken lines Fayoumi M15.2 (n=6) and Leghorn GHs6 (n=6) and broilers from Line A (n=24 individuals in pools of 4) and Line B (n=24 individuals in pools of 4)were subjected to array Comparative Genomic Hybridization (aCGH). Each sample was normalized to a Red Jungle Fowl reference. CNVs for each individual and between lines were determined. The major goal of this study was to discover and characterize CNVs in chickens to further narrow in on Quantitative Trait Loci (QTLs) affecting disease response.

overall_design: For the test DNA in Fayoumi and Leghorn, samples from 6 inbred Fayoumi and 6 inbred Leghorn individuals were used; For the test DNA in the Campylobacter genetic lines, samples from 24 individual broilers of Line A (in pools of 4) and 24 individual broilers of Line B (in pools of 4) were used. For the reference DNA, Red Jungle Fowl line UCD001 was used from a self-self hybridization.

first: Huaijun

last: Zhou


title: Post-pollination carpels of S. pennellii introgression lines

status: Public on Jan 27 2016

city: Bloomington

first: Rafael

middle: F

last: Guerrero

state: IN - Indiana

address: 1001 E 3rd St

department: Biology

institute: Indiana University

summary: Expression in carpels of three pennellii NILs were contrasted to the recurrent parent (S. lycopersicum)

sample_organism: Solanum lycopersicum x Solanum pennellii

overall_design: Each of 3 hybrids is compared to the control

first: Guerrero

last: Rafael


title: BMP-2 response pattern in human lung fibroblasts predicts outcome in lung adenocarcinomas

status: Public on Feb 19 2016

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich


title: Pre-anthesis anthers of S. pennellii introgression lines

summary: Expression in pollen of four pennellii NILs were contrasted to the recurrent parent (S. lycopersicum)

overall_design: Each of 4 hybrids is compared to the control


title: Lactococcus lactis MG1363 ∆guaA versus L. lactis MG1363 (wt)

status: Public on Jan 12 2016

city: Groningen

first: Ana

last: Solopova

address: Nijenborgh 7

department: MolGen

country: Netherlands

institute: RUG

summary: Gene expression in Lactococcus lactis MG1363 was compared to that of L. lactis MG1363 ∆guaA in rich GM17 medium.

platform_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: One condition design comparison of two strains

first: Cécile

last: Formosa-Dague

first: Pascal

last: Courtin

first: Sylviane

last: Furlan

first: Patrick

last: Veiga

first: Julija

last: Armalyte

first: Mikas

last: Sadauskas

first: Jan

last: Kok

last: Hols

first: Yves

last: Dufrêne

first: Oscar

middle: P

last: Kuipers

first: Marie-Pierre

last: Chapot-Chartier

first: Saulius

last: Kulakauskas


title: MiR-193b promotes autophagy and non-apoptotic cell death in oesophageal cancer cells

status: Public on Jan 23 2016

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

institute: Erasmus University Medical Center

summary:
Background: Successful treatment of oesophageal cancer is hampered by recurrent drug resistant disease. We have previously demonstrated the importance of apoptosis and autophagy for the recovery of oesophageal cancer cells following drug treatment. When apoptosis (with autophagy) is induced, these cells are chemosensitive and will not recover following chemotherapy treatment. In contrast, when cancer cells exhibit only autophagy and limited Type II cell death, they are chemoresistant and recover following drug withdrawal.
Methods: MicroRNA (miRNA) expression profiling of an oesophageal cancer cell line panel was used to identify miRNAs that were important in the regulation of apoptosis and autophagy. The effects of miRNA overexpression on cell death mechanisms and recovery were assessed in the chemoresistant (autophagy inducing) KYSE450 oesophageal cancer cells.
Results: MiR-193b was the most differentially expressed miRNA between the chemosensitive and chemoresistant cell lines with higher expression in chemosensitive apoptosis inducing cell lines. Colony formation assays showed that overexpression of miR-193b significantly impedes the ability of KYSE450 cells to recover following 5-fluorouracil (5-FU) treatment. The critical mRNA targets of miR-193b are unknown but target prediction and siRNA data analysis suggest that it may mediate some of its effects through stathmin 1 regulation. Apoptosis was not involved in the enhanced cytotoxicity. Overexpression of miR- 193b in these cells induced autophagic flux and non-apoptotic cell death.
Conclusion: These results highlight the importance of miR-193b in determining oesophageal cancer cell viability and demonstrate an enhancement of chemotoxicity that is independent of apoptosis induction.

overall_design: The miRNA expression profile was determined of four human oesophageal cancer cell lines OE19, OE21, OE33 and KYSE450. The miRNA expression of each cell line was analyzed in triplicate.

first: Michelle

middle: J

last: Nyhan

first: Tracey

middle: R

last: O'Donovan

first: Antonius

middle: W

last: Boersma

middle: A

first: Sharon

middle: L

last: McKenna


title: Genomic profiling of pancreatic cancer cell lines by array-based comparative genomic hybridization

status: Public on Jan 22 2016

city: Yufu

first: Naoki

last: Hijiya

state: Oita

address: 1-1, Idaigaoka Hasama-machi

department: Medicine

country: Japan

institute: Oita University

summary: In this study, we determined the genomic profiles of pancreatic cancer cell lines.

overall_design: 12 pancreatic cancer cell lines vs control (genomic DNA of human peripheral blood mononuclear cells from 8-healthy donors).

first: Yoshiyuki

last: Tsukamoto

first: Chisato

last: Nakada

first: Nguyen

last: Lam Tung

first: Tomoki

last: Kai

first: Keiko

last: Matsuura

first: Kohei

last: Shibata

first: Masafumi

last: Inomata

first: Tomohisa

last: Uchida

first: Akinori

last: Tokunaga

last: Amada

first: Kuniaki

last: Shirao

first: Yasunari

last: Yamada

first: Hiromu

last: Mori

first: Ichiro

last: Takeuchi

first: Masao

last: Seto

first: Masahiro

last: Aoki

first: Mutsuhiro

last: Takekawa

first: Masatsugu

last: Moriyama


title: Targeting the lineage-specific long non-coding RNA LINC01212 as an effective anti-melanoma therapeutic strategy [1]

status: Public on Jan 15 2016

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

summary: Focal amplifications of 3p13-3p14 occur in about 10% of melanoma and are associated with poor prognosis. The melanoma-specific oncogene MITF resides at the epicenter of this amplicon1. However, whether other loci present in this amplicon also contribute to melanomagenesis is unknown. Here we show that the recently annotated long non-coding RNA gene LINC01212 is consistently co-gained with MITF. In addition to being amplified, LINC01212 is a target of the lineage-specific transcription factor SOX10 and, consequently, it is expressed in more than 90% of human melanomas, but not in normal adult tissues. Whereas exogenous LINC01212 functions in trans to increase melanoma clonogenic potential LINC01212 knock-down dramatically decreases the viability of melanoma cells irrespective of their transcriptional cell state, BRAF, NRAS or TP53 status, diminishes melanoma growth and increases their sensitivity to MAPK-targeting therapeutics both in vitro and in patient-derived melanoma xenograft mouse models. Mechanistically, LINC01212 functions as a lineage addiction oncogene by interacting with and modulating the cellular localization and function of two proteins, XRN2 and p32, involved in nucleolar and mitochondrial rRNA processing, ribosome biogenesis and protein synthesis. LINC01212 targeting, especially in combination with BRAFV600E-inhibitors, is expected to deliver highly effective and tissue-restricted antimelanoma therapeutic responses.

overall_design: LINC01212 knockdown or overexpression in 4 and 1 cell line respectively. Depending on the cell line, 3-4 replicates per condition are included.

last: Mestdagh

first: Jo

last: Vandesompele

first: Eleonora

last: Leucci

first: Jean-Christophe

last: Marine


title: microRNA expression in hematopoietic-associated populations differentiated from induced pluripotent stem cells

city: Bethesda

first: Colin

last: Sweeney

state: MD

address: Building 10-CRC, Room 5-3888, 10 Center Drive

department: NIAID - Genetic Immunotherapy Section

institute: NIH

summary: In vitro generation of mature neutrophils from human induced pluripotent stem cells (iPSCs) requires hematopoietic progenitor development followed by myeloid differentiation. The purpose of our studies was to extensively characterize this process, focusing on the critical window of development between hemogenic endothelium, hematopoietic stem/progenitor cells (HSPCs), and myeloid commitment, to identify associated regulators and markers that might enable the stem cell field to improve the efficiency and efficacy of iPSC hematopoiesis. We utilized a 4-stage differentiation protocol involving: embryoid body (EB) formation (Stage-1); EB culture with hematopoietic cytokines (Stage-2); HSPC expansion (Stage-3); and neutrophil maturation (Stage-4). CD34+CD45- putative hemogenic endothelial cells were observed in Stage-3 cultures, and expressed VEGFR-2/Flk-1/KDR and VE-cadherin endothelial markers, GATA-2, AML1/RUNX1, and SCL/TAL1 transcription factors, and endothelial/HSPC-associated microRNAs miR-24, miR-125a-3p, miR-126/126*, and miR-155. Upon further culture, CD34+CD45- cells generated CD34+CD45+ HSPCs that produced hematopoietic CFUs. Mid-Stage-3 CD34+CD45+ HSPCs exhibited increased expression of GATA-2, AML1/RUNX1, SCL/TAL1, C/EBPα, and PU.1 transcription factors, but exhibited decreased expression of HSPC-associated microRNAs, and failed to engraft in immune-deficient mice. Mid-stage-3 CD34-CD45+ cells maintained PU.1 expression and exhibited increased expression of hematopoiesis-associated miR-142-3p/5p and a trend towards increased miR-223 expression, indicating myeloid commitment. By late Stage-4, increased CD15, CD16b, and C/EBPε expression were observed, with 25-65% of cells exhibiting morphology and functions of mature neutrophils. These studies demonstrate that hematopoiesis and neutrophil differentiation from human iPSCs recapitulates many features of embryonic hematopoiesis and neutrophil production in marrow, but reveals unexpected molecular signatures that may serve as a guide for enhancing iPSC hematopoiesis.

overall_design: miRNA expression profiles were analyzed in iNC-01-3 and iNC-01-4 induced pluripotent stem cell lines at day 0 (undifferentiated iPSCs), day 18 of differentiation (embryoid bodies), and in 3 FACS-sorted cell populations at day 22 of differentiation (CD34+CD45- cells, CD34+CD45+ cells, and CD34-CD45+ cells). Comparative CT analysis was normalized to U6 snRNA and RNU48 control RNAs relative to expression in undifferentiated iPSCs. Data includes 2 files for each sample, one for the card A array and one for the card B array. This includes a total of 32 data files consisting of: 5 replicates for undifferentiated iPSCs (10 files), 2 replicates for EB (4 files), 3 replicates for CD34+CD45- (6 files), 3 replicates for CD34+CD45+ (6 files), and 3 replicates for CD34-CD45+ (6 files).


title: Role of IRF7 in airway epithelial cell responses to human rhinovirus infection.

status: Public on Jan 10 2016

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

summary:
Primary human bronchial epithelial cells were transfected with siRNA to knockdown IRF7 gene expression, allowed to recover, and then infected with human rhinovirus.
At 24 hrs post rhinovirus infection, gene expression patterns were profiled on microarrays.

overall_design: The study design consisted of five donors, two transfection conditions (all-star negtaive control siRNA; IRF7-specific siRNA), and two culture conditions (medium control, rhinovirus-16).

first: Shahina

last: Wiehler

first: David

last: Proud


title: The Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance (pooled shRNA screens)

status: Public on Jan 14 2016

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

summary:
Large-scale genomic studies have identified multiple somatic aberrations in breast cancer, including copy number alterations, and point mutations. Still, identifying causal variants and emergent vulnerabilities that arise as a consequence of genetic alterations remain major challenges. We performed whole genome shRNA "dropout screens" on 77 breast cancer cell lines. Using a hierarchical linear regression algorithm to score our screen results and integrate them with accompanying detailed genetic and proteomic information, we identify vulnerabilities in breast cancer, including candidate "drivers," and reveal general functional genomic properties of cancer cells. Comparisons of gene essentiality with drug sensitivity data suggest potential resistance mechanisms, effects of existing anti-cancer drugs, and opportunities for combination therapy.  Finally, we demonstrate the utility of this large dataset by identifying BRD4 as a potential target in luminal breast cancer, and PIK3CA mutations as a resistance determinant for BET-inhibitors.

The T0 measurements for the EFM19, HCC1954, HCC38 screens were omitted for technical reasons. T0 measurements, regardless of cell line, represent the initial abundance of shRNAs before cell line-specific selection effects, leading to highly correlated T0 measurements across cell lines. Our analyses showed a median correlation of 0.92 between pairs of T0 arrays from different cell lines, compared to correlations of 0.94-0.97 for replicate arrays within a cell line, a median correlation of 0.79 between T1 arrays of different cell lines and median correlation of 0.68 between T2 arrays from different cell lines.

As a result, we used to T0 measurements of the MCF7 screen to provide initial shRNA abundance measurements for the HCC1954 and HCC38 screens, and T0 measurements from the SW527 screen to provide initial measurements for the EFM19 screen.

Additional formatted data can be found at http://neellab.github.io/bfg/.
Code and tutorials for the siMEM algorithm can be found at http://neellab.github.io/simem/.

overall_design: Pooled shRNA screens of 77 cell lines, with dropout trends for each screen measured in triplicate across 3 time-points (with a few exceptions), resulting in 8-9 arrays per screen, and a total of 621 arrays.

first: Azin

last: Sayad


title: Microarray of NFAT1-shRNA (KD) vs Non-targeting shRNA (NT) metastatic melanoma cell line

status: Public on Jan 06 2016

first: Menashe

last: Bar-Eli

address: 1515 Holcombe blv.

institute: M.D. Anderson

summary: The metastatic melanoma cell line A375SM was stably transduced with NFAT 1 shRNA utilizing the pSIH-HI-  5     copGFP lentiviral vector. A non-targeting (NT) shRNA construct with no known homology to any human gene was was created and transduced into A375SM cells as a control. These two sets of cells were then subjected to microarray profiling using the Human OneArray microarray (version HOA 6.1, GEO Platform GPL19137) from Phalanx Biotech Group.

overall_design: NFAT shRNA A375SM cells vs. NT-shRNA A375SM cells were subjected to microarray analysis. 3 biological replicates for each cell type were used.

first: Einav

last: Shoshan


title: Vibrio cholerae lon protease mutant microarray analysis

city: Santa Cruz

first: Sinem

last: Beyhan

state: CA

address: 1156 High Street

department: Microbiology and Environmental Toxicology

institute: University of California, Santa Cruz

summary: Lon protease is known to regulate various transcriptional regulators in other bacterial organisms. To understand whether lon protease is involved in transcriptional changes in Vibrio cholerae, wholel-genome level transcriptional profiling was performed using custom microarrays. Transcriptomes of lonA mutant and wild-type strains were compared in this study.

overall_design: Three biological replicates of wild-type and lonA mutant strains were used for this study. Reference RNA sample was harvested from wild-type strain.

first: Andrew

last: Rogers

first: Loni

last: Townsley

first: Ana

last: Gallego-Hernandez

first: Laura

last: Kwuan

first: Fitnat

middle: H

last: Yildiz


title: Dynamic membrane depolarization is an early regulator of ependymoglial cell response to spinal cord injury in axolotl

status: Public on Jan 03 2016

city: Woods hole

first: Karen

last: Echeverri

state: MA

address: 7 MBL ST

department: Eugene Bell Center for Regeneration Biology and Tissue Engineering

institute: MARINE BIOLOGICAL LAB

summary:
Salamanders, such as the Mexican axolotl, are some of the few vertebrates fortunate in their ability to regenerate diverse structures after injury. Unlike mammals they are able to regenerate a fully functional spinal cord after injury. However, the early signals required to initiate a pro-regenerative response after spinal cord injury is not well understood.
To address this question we developed a spinal cord injury model in axolotls and used in vivo imaging of ion sensitive dyes and determined that spinal cord injury induces a rapid and dynamic change in the resting membrane potential of ependymoglial cells. Prolonged depolarization of ependymoglial cells after injury inhibits glial cell proliferation and subsequent axon regeneration. Using transcriptional profiling we identified c-Fos as a key voltage sensitive early response gene that is expressed specifically in the ependymoglial cells after injury. This data establishes that dynamic changes in the membrane potential after injury are essential for regulating the specific spatiotemporal expression of c-Fos that is critical for promoting faithful spinal cord regeneration in axolotl.

overall_design:
All axolotls used in these experiments were bred in the axolotl facility at the University of Minnesota under the IACUC protocol #1201A08381. Axolotls of 2–3 cm were used for all in vivo experiments, and animals were kept in separate containers and fed daily with artemia; water was changed daily. Animals were anesthetized in 0.01% p-amino benzocaine (Sigma) before microinjection was performed.
Experimental Design: Ivermectin injection
Ivermectin or vehicle only (water) was pressure injected into the central canal of the spinal cord, and this was visualized by the addition of Fast Green into the solution. Directly after injection, a portion of the spinal cord was surgically removed and the animals were placed back into water in individual containers. One day post injury (1dpi) animals were anesthetized again and the area of the injury was removed. Tissue from 10 animals were pooled for each microarray replicate.

first: Keith

last: Sabin

first: Tiago

last: Santos-Ferreria

first: Jaclyn

last: Essig

first: Sarah

last: Rudasill


title: Genome-wide analyses in neuronal cells reveal that USF transcription factors regulate lysosomal gene expression [ChIP-chip]

status: Public on Jan 08 2016

city: Niigata

first: Tomoyuki

last: Yamanaka

address: 1-757 Asahimachidori, Chuo-ku

department: Brain Research Institute

institute: Niigata University

type: Genome binding/occupancy profiling by genome tiling array

summary:
The upstream stimulating factors (USFs) USF1 and USF2 are ubiquitously expressed transcription factors characterized by a conserved basic helix-loop-helix leucine zipper DNA-binding domain. They form homo- or heterodimers and recognize E-box motifs to modulate gene expression. They are known to regulate diverse cellular functions including the cell cycle, immune response and glucose-lipid metabolism, but their roles in neuronal cells remain to be clarified. Here, we performed chromatin immunoprecipitation of USF1 from mouse brain cortex preparations. Subsequent promoter array analysis (ChIP-chip) indicated that USF1 exclusively bound to the CACGTG E-box motifs in the proximal promoter regions. Importantly, functional annotation of the USF1-binding targets revealed an enrichment of genes related to lysosomal functions. Gene expression arrays using a neuronal cell line subsequently revealed that knockdown of USFs deregulated lysosomal gene expression. Altered expression was validated by quantitative RT-PCR, supporting the conclusion that USFs regulate lysosomal gene expression. Furthermore, USFs knockdown slightly increased LysoTracker staining, implying a role for USFs in modulating lysosomal homeostasis. Together, our comprehensive, genome-scale analyses identified lysosomal genes as targets of USFs in neuronal cells, suggesting a potential additional pathway of lysosomal regulation.
ChIP-chip analysis of USF1 and NF-Y in mouse brain cortex.

overall_design: To identify downstream targets of USF1 and NF-Y in neuronal cells, they were chromatin-immunoprecipitated from mouse brain cortical lysates. The obtained chromatin DNAs were labeled with biotin and hybridized on Affymetrix Mouse Promoter 1.0R Array.

first: T

first: N

last: Nukina


title: Translational control of autophagy by Orb in the Drosophila germline [mature]

status: Public on Jan 01 2016

city: MONTPELLIER

first: Simonelig

last: Martine

address: 141, rue de la Cardonille

department: Genetics and Development

country: France

institute: Institut de Genetique Humaine - CNRS

summary: Drosophila Orb, the homologue of vertebrate CPEB is a key translational regulator involved in oocyte polarity and maturation through poly(A) tail elongation of specific mRNAs. orb has also an essential function during early oogenesis which has not been addressed at the molecular level. Here, we show that orb prevents cell death during early oogenesis, thus allowing oogenesis to progress. It does so through the repression of autophagy, by directly repressing, together with the CCR4 deadenylase, the translation of Autophagy-specific gene 12 (Atg12) mRNA. Autophagy and cell death observed in orb mutant ovaries are reduced by decreasing Atg12 or other Atg mRNA levels. These results reveal a role of Orb in translational repression and identify autophagy as an essential pathway regulated by Orb during early oogenesis. Importantly, they also establish translational regulation as a major mode of control of autophagy, a key process in cell homeostasis in response to environmental cues.

overall_design: Orb RIP-chip vs mock IP on ovaries from mature 3-5 day old females.

first: I

last: Busseau

first: D

last: Séverac

first: C

last: Dantec

first: S

last: Pierson

first: P

last: Rojas-Rios

first: A

last: Chartier

first: M

last: Simonelig


title: Translational control of autophagy by Orb in the Drosophila germline


title: Expression profile of EV71-infection-responsive miRNAs

city: Taoyuan

first: Wen-Fang

last: Tang

address: No.259, Wenhua 1st Rd., Guishan Dist.

department: Biochemistry and Molecular Biology

country: Taiwan

institute: Chang Gung University

summary: We attempted to identify potential miRNAs that can regulate viral replication by screening host miRNAs in EV71-infected RD cells. To compare the differential expression of miRNAs in EV71-infected cells at different time points, miRNA expression profiles were analyzed using Agilent Human MicroRNA Array chips. At 5 h p.i., the expression levels of most miRNAs in EV71-infected cells were not different from those of mock-infected cells. However, five miRNAs (miR-574-3p, miR-574-5p, miR-181d, miR-197, and miR-939) showed a miRNAs (miR-193a-3p and miR-324-5p) exhibited a increase in expression level in response to EV71 infection at 10 h p.i.

overall_design: RD cells were seeded (2*106 cells) in 10 cm dishes and incubated overnight. The cells were infected with EV71 (strain 2231) on ice at an M.O.I. of 10. After adsorption for 1 h, the virus suspension was replaced with DMEM containing 2% FBS, and the cells were harvested at the indicated times. Total cellular RNA extraction and miRNA microarray analyses were performed  using the Agilent Human MicroRNA Array V2 chip, which contains 723 human and 76 viral miRNAs, each with 16 duplicates. Total gene signals were detected and analyzed using the GeneSpring 7.3.1 software and were normalized to the 75th percentile.

first: Jim-Tong

last: Horng


title: Translational control of autophagy by Orb in the Drosophila germline [early]

overall_design: Orb RIP-chip vs mock IP on ovaries from newly eclosed females.


title: Changes in exosomal circulating microRNAs in grazing cattle

city: Tsukuba

first: Susumu

last: Muroya

state: Ibaraki

address: Ikenodai 2

department: Animal Products Research Division

institute: NARO Institute of Livestock and Grassland Science

summary: To investigate the potential effect of grazing movement on miRNA circulation in cattle, here we profiled miRNA expression in centrifugally prepared exosomes from the plasma of both grazing and housed Japanese Shorthorn cattle. Microarray analysis of the c-miRNAs resulted in detection of a total of 231 bovine exosomal miRNAs in the plasma, with a constant expression level of let-7g across the duration and cattle groups. Expression of muscle-specific miRNAs such as miR-1, miR-133a, miR-206, miR-208a/b, and miR-499 were undetectable, suggesting the mildness of grazing movement as exercise.

overall_design: Changes in miRNA expression in plasma exosome of cattle was measured at during 0, 1, 2 and 4 months of grazing or housing. Plasma exosome samples prepared from three cattle for each treatment were collected and mixed within the treatment at each time for microarray analysis .


title: Cytokeratin-19 positivity is acquired along cancer progression and does not predict cell origin in rat hepatocarcinogenesis (II)

city: CAGLIARI

first: AMEDEO

last: COLUMBANO

address: VIA PORVELL 4

department: DIPARTIMENTO DI SCIENZE BIOMEDICHE

country: Italy

institute: UNIVERSITA' DEGLI STUDI DI CAGLIARI

summary: Analysis of early changes in the R-H model of carcinogenesis in order to investigate the relationship between oval cell proliferation and preneoplastic foci

overall_design: 5 controls, 5 CK-19-negative preneoplastic nodules, 5 CK-19-positive preneoplastic nodule, 5 Preneoplastic foci

first: Pia

last: Sulas


title: Parental Effects on Seed Transcriptome-Metabolome

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

institute: Wageningen University

summary:
Transcriptome analyses on seeds developed in different parental conditions
investigating the effect of the parental environment on the transcriptome of dry seeds of three different genotypes

overall_design:
RNA isolated from freshly harvested dry seed of three genotypes, the near isogenic line of DELAY OF GEMRMINATION 1 (DOG1), DOG3 and DOG6, grown in 15°C, 20°, low nitrate (N0), low light (LL) and SL (standard light).
Please note that SL (standard light) is the control for the LL (low light), and  20C  is the control for both 15C and low nitrate (N0).

first: Hanzi

last: He

first: Leo

last: Willems

first: Albert

last: Batushansky

first: Aaron

last: Fait

first: Johannes

last: Hanson

first: Harm

last: Nijveen

first: Henk

last: Hilhorst


title: Brassica napus differentially expressed genes in seeds and silique walls

city: Wuhan

first: yongming

last: zhou

state: Hubei

address: No.1,Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: Identification of differentially expressed genes in seeds and silique walls at the seed-filling stage in Brassica napus through transcriptional profiling

overall_design: Two tissues, three biological replicates, one  biological duplicate with two technical replicates

first: Qingyong

last: Yang

first: Han

last: Liu

first: Chuchuan

last: Fan

first: Yongpeng

last: Li

first: Xuemin

last: Wang

first: Yongming

last: Zhou


title: Investigation of differential gene expression in menthol treated and control (untreated) cell lines in  CaCO2 human cell line during apoptosis

city: Lucknow

first: Ajit

middle: K.

last: Shasany

state: Uttar Pradesh

address: P.O. CIMAP

department: Biotechnology Division

country: India

institute: CSIR-Central Institute of Medicinal and Aromatic Plants

summary: To identify changes in gene expression with apoptosis, we investigated differential gene expression in a colon carcinoma model established in human cell line CaCO2. We arrayed 384 oligos (representing 384 genes including positive and negative controls) related with Apoptosis for detection of differences at gene expression levels in some of the very important apoptotic biomarkers

overall_design: We arrayed 384 genes related with Apoptosis including control for detection of differences at gene expression levels in some of the very important apoptotic biomarkers. Those arrayed oligos gene chip were co- hybridized with labeled cDNA probe prepared from total RNA isolated from menthol treated and untreated control cell lines to find out the differential behaviour of the genes related to Apoptosis. Two-condition experiment, Control (untreated vs menthol treated ) Human cell lines CaCO2.

first: Sunita

middle: S

last: Dhawan

first: Uzma

last: Faridi

first: A

middle: K

first: MP

last: Darokar


title: THE BILIARY EPITHELIUM GIVES RISE TO LIVER PROGENITOR CELLS BUT MAKES A MINOR CONTRIBUTION TO HEPATOCYTE REGENERATION AFTER LIVER INJURY

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: We previously showed that severe liver diseases are characterized by expansion of liver progenitor cells (LPC), which correlates with disease severity. However, the origin and role of LPC in liver physiology and in the hepatic response to injury remains a contentious topic. We have now used genetic lineage tracing of Hnf1β-expressing biliary duct cells to assess their contribution to LPC expansion and hepatocyte generation during normal liver homeostasis, and following different types of liver injury. We found that ductular reaction cells in human cirrhotic livers express HNF1β. However, HNF1β expression was not present in newly generated EpCAM-positive hepatocytes. Using a tamoxifen-inducible Hnf1βCreER/R26RYFP/LacZ mouse, we show that there is no contribution of the biliary epithelium to hepatocyte turnover during liver homeostasis in healthy mice. Moreover, after loss of liver mass, Hnf1β+ LPC did not contribute to hepatocyte regeneration. We also assessed the contribution of Hnf1β+ cells following acute and repeated liver injury. All animal models showed expansion of LPC, as assessed by immunostaining and gene expression profile of sorted YFP-positive cells. A contribution of Hnf1β+ LPC to hepatocyte generation was not detected in animal models of liver injury with preserved hepatocyte regenerative potential such as acute acetaminophen, carbon tetrachloride injury, or chronic diethoxycarbonyl-1,4-dihydro-collidin (DDC)-diet. However, in mice fed with choline-deficient ethionine-supplemented (CDE)-diet, which causes profound hepatocyte damage and arrest, a small number of hepatocytes were derived from Hnf1β+ cells. Conclusion: Hnf1β+ cells do not participate in hepatocyte turnover in the healthy liver or during liver regeneration after partial hepatectomy. After liver injury, LPC arise from the biliary duct epithelium, which gives rise to a limited number of hepatocytes only when hepatocyte regeneration is compromised.

overall_design: Transcriptomic profile using MoGeneST-2.0 chip from 3 samples of YFP+ CDE, 3 samples of YFP+ DDC, 2 samples of YFP+ UTR and 3 samples YFP-

first: D

last: Rodrigo-Torres

first: S

last: Affo

first: M

last: Coll

first: P

last: Sancho

first: J


title: H3K27me3 profiles along the length of the  X chromosome in trophoblast stem (TS) cells showing inverted X-inactivation profiles, ChIP-chip

city: Paris

first: Celine

last: Morey

address: 35 rue Hélène Brion

department: University Paris 7

institute: UMR7216-Epigenetics and stem cell

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This analysis includes H3K27me3 profiles along the length of the X-chromosome in male (F2) and female (F3) TS cells and in female TS cells showing a complete reversal of X-chromosome inactivation (F3 clone1#A).

overall_design: Analysis of H3K27me3 profiles in three different cell populations. Two independent biological replicates for each cell population are provided. The array includes approx. 162,5 Mb of the X chromosome and approx. 14,6 Mb of chromosome 17 as a control.

first: Julie

last: Prudhomme

first: Agnes

last: Dubois

first: Pablo

last: Navarro

first: Philip

last: Avner

first: Céline


title: Transcriptional analysis of temperature regulation in Yersinia pestis

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

summary: Temperature is a key environmental factor for facultative pathogens during the host adaptation response. To assess the functional role of temperature in Yersinia pestis, a microarray study was conducted comparing the Δpgm (pigmentation-negative) R88 strain grown at 37°C or 30°C.

overall_design: Six independent RNA samples from 37°C cultures were paired with six independent RNA samples from 30°C cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

first: Jing

last: Yu


title: 3 quorum sensing signals add in microarray comparison in Yersinia pestis at 30°C

summary: The quorum-sensing system has been linked to diverse phenotypes and regulatory changes in pathogenic bacteria. In strain CO92, the AI-2 signal is produced in a luxS-dependent manner, reaching maximal levels of 2.5 μM in late logarithmic growth, and both wild type and pigmentation mutant strains made equivalent levels of AI-2. Yersinia pestis CO92 possesses a chromosomal lsr locus encoding factors involved in the binding and import of AI-2, and confirming this assignment, an lsr deletion increased extracellular pools of AI-2. To assess the functional role of 3 quorum sensing singlas in Y. pestis, microarray study was conducted comparing the 3 quorum sensing signals added in to control at 30°C to mimic the flea gut. Here, the ΔPgm (pigmentation-negative) R88 strain was used. The three signals are one AI-2 and two AHLs (N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone).The control consisted of cells grown and treated under the same conditions without added signals.

overall_design: Six independent RNA samples from 3 signals add in cultures were paired with six independent RNA samples from control cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.


title: Transcriptional analysis of quorum sensing null strain in Yersinia pestis CO92 at 30°C

summary: Yersinia pestis is the etiology of plague that is able to sense cell density by quorum sensing. The function of quorum sensing in Y.pestis is not clear. Here, the process of quorum sensing was investigated by comparing transcript profiles when three quorum sensing synthase genes are knocked out. Two strains, ∆pgm (pigmentation-negative) mutant R88 as treatment and 3XQS mutant with mutation (∆pgm, ∆ypeIR, ∆yspIR, and ∆luxS) R115 as control are used in this analysis.

overall_design: Six independent RNA samples from R115 cultures were paired with six independent RNA samples from R88 cultures for hybridization to six two-color microarrays. Dye-swap design was used to remove the Cy5 and Cy3 dye bias.

first: Minion

last: Chris

first: Yu

last: Jing


title: Irp2 mediates cigarette smoke-induced bronchitis and emphysema via regulation of cytochrome c oxidase and mitochondrial iron loading.

city: New York

first: Augustine

middle: MK

last: Choi

state: NY

address: 525 East 68th Street, Room M-522, Box 130

department: Department of Medicine

institute: Weill Cornell Medical College

summary:
Chronic obstructive pulmonary disease (COPD), the fourth leading cause of death globally, is influenced by both cigarette smoking and genetic determinants.  We have previously identified iron-responsive element binding protein 2 (IRP2) as a candidate COPD susceptibility gene based on genetic association studies, with IRP2 increased in the lungs of COPD patients. Here we demonstrate that mice deficient in IRP2 are protected from cigarette smoke (CS)-induced COPD. Using RIP-Seq, RNA-Seq, gene expression and pathway analysis, we identify IRP2 as a regulator of mitochondrial function in the lung. We show that an increase in IRP2 results in a cytochrome c oxidase (COX)-dependent alteration in oxidative capacity and mitochondrial-iron dysfunction involving frataxin. We demonstrate that mice with impaired COX or frataxin activity have altered responses to CS and show that overexpressing IRP2 in vivo alters mitochondrial dynamics. These data suggest a critical role of the mitochondria-iron axis in mediating the pathogenesis of COPD.
We used microarrays to compare the global programme of gene expression in the lungs of WT mice compared ot the lungs harvested from Irp2-/- mice.

overall_design: n=6 Wildtype C57/BL6 mice (n=3 males, 3 females), n=5 (n=2 males, n =3 females) Irp2-/- C57/BL6 mice, approx 28-32 weeks were sacrificied, lungs removed and snap forzen. RNA isolated after one freeze thaw cycle using the Qiagen RNeasy Kit.

first: Suzanne

last: Cloonan

first: Kimberly

last: Glass


title: Cytokeratin-19 positivity is acquired along cancer progression and does not predict cell origin in rat hepatocarcinogenesis

first: AMEDEO

last: COLUMBANO

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

overall_design: Refer to individual Series


title: Integrating high-dimensional transcriptomics and image analysis tools into early safety screening (III)

status: Public on Dec 31 2015

city: Beerse

first: Steven

last: Osselaer

address: Turnhoutseweg 30

institute: Janssen Pharmaceutica NV

summary:
In this paper we demonstrated the potential to flag toxicity issues by utilizing data from exploratory experiments which are typically generated for target evaluation purposes during early drug discovery
During drug discovery and development, the early identification of adverse effects is expected to reduce costly late stage failures of candidate drugs.
As risk/safety assessment takes place rather late during the development process and due to the limited predictivity of animal models to the human situation, modern unbiased high-dimensional biology read-outs are sought, such as molecular signatures of in vivo response using high-throughput cell-based assays.
In this theoretical proof-of-concept we provide findings of an in-depth exploration of a single chemical core structure.
Via transcriptional profiling we identified a subset of close analogs which commonly down-regulate tubulin genes across cellular contexts, suggesting possible spindle poison effects.
Confirmation via a qualified toxicity assay (in vitro micronucleus test) and the identification of a characteristic aggregate-formation phenotype via exploratory high content imaging validated the inititial findings.
SAR analysis triggered the synthesis of a new set of compounds and allowed us to extend the series showing the genotoxic effect.
We demonstrate the potential to flag toxicity issues by utilizing data from exploratory experiments which are typically generated for target evaluation purposes during early drug discovery.
We  share our thoughts on how this approach may be incorporated into drug development strategies.

overall_design: Cells were cultured using standard protocols, seeded in 96 well plate, cultured for 8 hours before treatment with a number of inhouse synthesized compounds. The treatments represent different chemical structures/small molecules that have been synthesized in the context of developing a new drug targeting PDE10A.

first: Bie

middle: M

last: Verbist

first: Geert

last: Verheyen

first: Liesbet

last: Vervoort

first: Marjolein

last: Crabbe

first: Dominiek

last: Beerens

first: Cindy

last: Bosmans

first: Steffen

last: Jaensch

first: Willem

last: Talloen

first: Ilse

last: Van den Wyngaert

last: Van Hecke

first: Dirk

last: Wuyts

first: Freddy

last: Van Goethem

first: Hinrich

last: Göhlmann


title: Transcriptional analysis of AHLs signals add in experiment inYersinia pestis CO92 at 37°C

first: Chris

last: Minion

summary: Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of AHL quorum sensing was investigated by comparing transcript profiles when two AHL quorum-sensing signals are added in. The strain ∆pgm (pigmentation-negative) mutant R88 was called wild type. The two AHLs signals are N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone.The control consisted of cells grown and treated under the same conditions without added signals.

overall_design: Six independent RNA samples from R88 cultures were paired with six independent RNA samples from two AHLs added cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

first: Jing

last: Yu


title: LuxS/AI-2 quorum sensing microarray comparison in Yersinia pestis at 30°C

summary: The AI-2 quorum-sensing system has been linked to diverse phenotypes and regulatory changes in pathogenic bacteria. In strain CO92, the AI-2 signal is produced in a luxS-dependent manner, reaching maximal levels of 2.5 μM in late logarithmic growth, and both wild type and pigmentation mutant strains made equivalent levels of AI-2. Y. pestis CO92 possesses a chromosomal lsr locus encoding factors involved in the binding and import of AI-2, and confirming this assignment, an lsr deletion increased extracellular pools of AI-2. To assess the functional role of AI-2 sensing in Y. pestis, microarray study was conducted comparing the ∆Pgm strain R88 to a ∆Pgm ∆luxS mutant at 30°C to mimic the flea gut.

overall_design: Six independent RNA samples from Y. pestis CO92 ΔPgm cultures were paired with six independent RNA samples from ΔPgm ΔluxS cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.


title: Integrating high-dimensional transcriptomics and image analysis tools into early safety screening (II)


title: Effects of Morus alba L. (Mulberry) Leaf Extract in Hypercholesterolemic Mice on Suppression of Cholesterol Synthesis

city: Minato-ku

first: Yukihiro

last: Kobayashi

state: Tokyo

department: Department of Marine Biosciences

institute: Tokyo University of Marine Science and Technology

summary:
To investigate effects of intake of mulberry leaf extracts on hypercholesterolemia, we performed gene expression profiling on rat liver by microarray analysis.
Microarray analysis revealed that mulberry leaf extracts up-regulated the gene expression involved in suppression of cholesterol synthesis and stimulation of innate-adaptive Immunity.

overall_design: Mice were fed a high-cholesterol diet without/with orally administration of mulberry leaf extracts for 4 weeks. Livers were taken for RNA extraction and hybridization on Agilent microarrays.

first: Maki

last: Miyazawa

first: Mayumi

last: Araki

first: Asuka

last: Kamei

first: Keiko

last: Abe

first: Tetsuya

last: Hiroi

first: Takahiko

last: Hirokawa

first: Nobuyoshi

last: Aoki

first: Toshiyuki

last: Ohsawa

first: Takashi

last: Kojima


title: DNA microarray for STD pathogen detection

city: Tianjin

first: Boyang

last: Cao

address: #23 HongDa Street

institute: Nankai Univ

summary: This work describes the development of the first microarray detection system that simultaneously identifies common pathogens associated with STDs from clinical samples, and paves the way for establishing a time-saving, accurate and high-throughput diagnostic tool.

sample_organism:
Neisseria gonorrhoeae
Chlamydia trachomatis
Mycoplasmoides genitalium
Metamycoplasma hominis
Ureaplasma
Human alphaherpesvirus 1
Human alphaherpesvirus 2
human papillomavirus 11
human papillomavirus 31
human papillomavirus 33
human papillomavirus 35
human papillomavirus 39
human papillomavirus 58
Human papillomavirus type 6
Human papillomavirus 16
human papillomavirus 18
Alphapapillomavirus 13

platform_organism:
Neisseria gonorrhoeae
Chlamydia trachomatis
Mycoplasmoides genitalium
Metamycoplasma hominis
Ureaplasma
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human papillomavirus

overall_design: The target genes are 16S rRNA gene for N. gonorrhoeae, M. genitalium, M. hominism, and Ureaplasma, the major outer membrane protein gene (ompA) for C. trachomatis, the glycoprotein B gene (gB) for HSV; and the L1 gene for HPV. 34 probes that reproducibly detected multiple Legionella species with high specificity were included in the array.

first: Pinliang

last: Hu

first: Suwei

last: Wang

first: Zhenyang

last: Tian


title: CodeLink Mouse Whole Genome Bioarray data from hematopoietic stem cells (HSCs) of miR-125a (+/+) wild-type and miR-125a knockout mice with myeloproliferative disorder (MPD)

city: Suita

first: Naoya

last: Tatsumi

state: Osaka

address: 1-7 Yamada-Oka

department: Functional Diagnostic Science

institute: Osaka University Graduate School of Medicine

summary: miR-125a knockout mice develop myeloproliferative disorder (MPD). To investigate the molecular mechanisms of MPD induced by the loss of miR-125a, gene expression profiling on hematopoietic stem cells of miR-125a (+/+), (+/-) MPD, and (-/-) MPD mice was performed by using CodeLinkTM Whole Genome DNA array analysis.

overall_design: CodeLink Mouse Whole Genome Bioarrays were performed according to the manufacturer’s instruction on total RNA extracted from hematopoietic stem cells of miR-125a (+/+) wild-type mouse, miR-125a (+/-) heterozygous mouse with MPD, and miR-125a (-/-) homozygous mouse with MPD. One replicate per array.


title: MicroRNAs among esophageal cancer cell sublines with different migration ability

city: Beijing

first: Zhihua

last: Liu

address: No.17, Panjiayuannanli, Chaoyang District

department: Cancer Institute & Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary:
Cellular directed migration is critical to invasion-metastasis cascade of cancer cells. We used in vitro transwell model to screen two esophageal cancer cell lines (KYSE30/180) and obtained two pairs of subpopulations with distinc motiliyt ability.
Then we used microarrays to detail the differentially expressed genes and microRNAs between these two cell sublines (30U/D and 180U/D) to identify those responsible for ESCC motility.

overall_design: KYSE30/180 cells were subject to four successive selections using transwell (CORNING, USA). Subpopulations penetrated through membrane (D) or not (U) were harvested respectively for RNA extraction and hybridization on Affymetrix genome and LC Sciences microRNA microarrays

first: Gang

last: Ma

first: Chao

last: Jing


title: Integrating high-dimensional transcriptomics and image analysis tools into early safety screening (I)

first: Steven

last: Osselaer

first: Bie

last: Verbist

first: Geert

last: Verheyen

first: Liesbet

last: Vervoort

first: Marjolein

last: Crabbe

first: Dominiek

last: Beerens

first: Cindy

last: Bosmans

first: Steffen

last: Jaensch

first: Willem

last: Talloen

first: Ilse

last: Van den Wyngaert

last: Van Hecke

first: Dirk

last: Wuyts

first: Freddy

last: Van Goethem

first: Hinrich

last: Göhlmann


title: Transcriptional analysis of AI-2 treatment in Yersinia pestis at 30°C

first: Chris

last: Minion

summary: Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of autoinducer-2 (AI-2) quorum sensing was investigated by comparing transcript profiles when AI-2 quorum-sensing signal is added in to control. The strain Δpgm (pigmentation-negative) mutant was used as wild type.The control consisted of cells grown and treated under the same conditions without added signals.

overall_design: Six independent RNA samples from Y. pestis CO92 Δpgm cultures were paired with six independent RNA samples from AI-2 signal added in cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

first: Jing

last: Yu


title: Expression data from OSKM-mediated 2nd reprogramming cells and the corresponding iPS cell line

city: Shanghai

first: Min

last: Li

address: 1239 Siping Road, Yangpu District

institute: Tongji University

summary:
Forced expression of four transcription factors Oct4,Sox2, Klf4 and Myc (OSKM) induces somatic cell reprogramming towards pluripotency. Major efforts have been made to characterize the molecular events involved in this process. Yet, it remains elusive how gene expression change, epigenetic landscape remodelling and cell fate conversion are triggered by expression of these Yamanaka factors. To address this gap, we utilized a secondary inducible reprogramming system and performed genome-wide profilings of Oct4 binding, histone modification (H3K4me3/H3K27me3/H3K4me1/H3K27ac), and gene expression analysis during this process. Through integrative analysis, we revealed stage-specific Oct4 binding and enhancer signatures in consistence with gene expression changes, in which the initial regression of somatic program is followed by the gradual acquisition of pluripotent program. Oct4 preferatially binds to H3K4me1 marked enhancer regions and Oct4 binding is positively correlated with active mark H3K27ac. Moreover, we observed significant enhancer activation of epigenetic related genes, especially acetylation associated genes, prior to pluripotency network activation, suggesting a pivotal role of epigenetic remodelling in the process of pluripotency acquisition and maintenance.
We used microarrays to explore the global changes of gene expression during OSKM-mediated somatic cell reprogramming.

overall_design: time series design with bulk population samples collected at different time point of 2nd reprogramming as well as a corresponding iPS cell line. Each sample include two replicates. 2nd mouse embryonic fibroblasts(sample day0) were treated with ES medium supplemented with 1µg/ml Doxcycline and 50µg/ml Vitamin C for 15 days (sample day1-day15); 72 hours after dox and Vc withdrawl, dox-independent iPS cells are collected(sample day18).


title: Comparing two intestinal porcine epithelial cell lines (IPECs): global expression patterns to characterise a in vitro model of intestinal physiology

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

summary: The intestinal epithelial cell lines 1 and J2 (IPEC-1, IPEC-J2) - spontaneously immortalised cell lines from the porcine intestine - are important tools for studying intestinal function. Microarrays (GeneChip Porcine Genome Array) were used to compare the expression pattern at basal in vitro conditions. Expression analyses complemented by morphological, functional and biochemical analyses revealed that IPEC-J2 is a morphologically and functionally more differentiated cell line in comparison to IPEC-1. In addition, IPEC-2 cells are a preferential tool for in vitro studies with the focus on metabolism.

overall_design: We compared the genome wide gene expression of untreated and IPEC 1 an dIPEC-J2 cells by the GeneChip® Porcine Genome Array of Affymetrix.

first: Constanze

last: Nossol

first: Anikó

last: Barta-Böszörményi

first: Stefan

last: Kahlert

first: Werner

last: Zuschratter

first: Heidi

last: Faber-Zuschratter

first: Nicole

last: Reinhardt

first: Siriluck

last: Ponsuksili

first: Anne-Kathrin

last: Diesing

first: Hermann-Josef

last: Rothkötter


title: Molecular response of bifidobacteria to a cholesterol rich environment

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

institute: University of Parma

summary: We investigated the capabilities of bifidobacteria to reduce the cholesterol level in the media, which clearly evidenced a high ratio of assimilation of this molecule by specific bifidobacterial strains including Bifidobacterium bifidum PRL2010. The transcriptomics of PRL2010 cells cultivated in the presence of cholesterol evidenced a significant higher expression of carriers as well as reductase encoding genes

overall_design: In order to investigate whether and how B. bifidum PRL2010 cells respond to cholesterol treatment, transcriptional profiling experiments were carried out. We first investigated the transcriptomes of PRL2010 cultures grown in only MRS representing the reference conditions. In addition, we investigated the transcriptomes of PRL2010 cells incubated with cholesterol in presence or absence of oxgall. Based on what previously described, the presence of oxgall in the culture medium mimics the intestinal environment. Two conditions were analysed, the former involving B. bifidum PRL2010 cells that were grown to an OD of 0.6, followed by the addition of cholesterol; the latter including 5% oxgall and 100µg/ml cholesterol and subsequent incubation for 180 minutes, after which RNA was harvested and labelled for microarray analysis. Every experiment was performed in duplicate.


title: Epigenome analysis of peripheral blood mononuclear cell (PBMC) samples from obstructive sleep apnea patients and healthy subjects

city: Hsinchu

first: Tingwen

last: Chen

address: No. 75, Boat Street, East District

institute: National Yang Ming Chiao Tung University

summary: Genome wide DNA methylation profiling of obstructive sleep apnea (OSA) patients and healthy subjects. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in peripheral blood mononuclear cell samples. Samples included 8 normal subjects and 16 patients with obstructive sleep apnea syndrome.

overall_design: Bisulphite converted DNA from the 21 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Yung-Che

first: Ting-Wen


title: Tonsil cancer compared with normal tonsil tissue

status: Public on Dec 23 2015

city: Sydney

first: Nham

last: Tran

state: NSW

address: Jones

department: CHT/FEIT

institute: UTS

summary:
To investigate miRNA expression in human tonsil squamous cell carcinoma (SCC) compared to normal tonsil tissue.
Two colour LNA Exiqon array. MicroRNAs were labeled at 3'-end with a P-CU-C3-Cy3 RNA linker. A mixture of 371 synthetic DNA reference oligonucleotides containing complementary sequences to all LNA probes was randomly labeled using the ULYSIS labeling kit.

sample_organism:
Homo sapiens
synthetic construct

overall_design: Two groups, tumor SCC and normal tissue samples were arrayed and then expression compared. HNxx identifiers with the same number are from the same patient, either tumor tissue (T) or adjacent normal tissue (N). Arrays were carried out in duplicate, denoted by 1 and 2.


title: miRNA expression profiling of 21 JMML patients and 4 healthy donors

city: Ghent

first: Hetty

middle: Hilde

last: Helsmoortel

address: De Pintelaan 185

department: Department of Pediatric Hematology-Oncology and Stem Cell Transplantation

institute: Ghent University

summary:
Juvenile myelomonocytic leukemia (JMML) is a very rare and aggressive stem cell disease that mainly occurs in young children. RAS activation constitutes the core component of oncogenic signaling. In addition, the leukemic blasts of a quarter of JMML patients present with monosomy 7 (-7), whereas more than half of the patients show enhanced age-adjusted fetal hemoglobin (HbF) levels. Hematopoietic stem cell transplantation is the current standard of care. This results in an event-free survival of 50 - 60%, indicating that novel molecular driven therapeutic options are urgently needed. Using gene expression profiling in an extensive series of 82 patient samples, we aimed at understanding the molecular biology behind JMML and identified a previously unrecognized molecular subgroup characterized by high LIN28B expression.
Interestingly, LIN28B overexpression was significantly correlated with higher HbF levels whereas patients with -7 seldom showed enhanced LIN28B expression. In line with LIN28B’s role as mediator of fetal hematopoiesis, this explains the biology behind the observation that patients with -7 are rarely diagnosed with high age-adjusted HbF levels. In addition, this new fetal-like JMML subgroup presented with reduced levels of most members of the let-7 microRNA family and showed characteristic overexpression of genes involved in fetal hematopoiesis and stem cell self-renewal. Finally, high LIN28B expression was associated with poor clinical outcome in our JMML patient series, but not independent from other prognostic factors such as age and age-adjusted HbF levels. In conclusion, we identified LIN28B as a crucial molecular player at the heart of a novel fetal-like subgroup in JMML.

overall_design: miRNA expression was measured on a qPCR-based platform in 21 JMML patients and 4 healthy donors in the discovery cohort. Corresponding mRNA and lncRNA expression data were measured on Agilent. All patient data can be found in Supplementary Table S1.


title: Gene expression profiling of 44 JMML patients and 7 healthy donors (discovery cohort)

overall_design: Gene expression was measured on Agilent in 44 JMML patients and 7 healthy donors in the discovery cohort. A validation cohort of 38 patients and 9 healthy donors was measured on Affymetrix. All patient data can be found in Supplementary Table S1.


title: Expression profiling of JMML patients and healthy donors

type:
Expression profiling by array
Expression profiling by RT-PCR


title: Expression profiles of 32-gene signature in liver tissue of obese subjects with NASH undergoing bariatric surgery.

status: Public on Dec 07 2015

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Background & Aims: Bariatric surgery is associated with improved outcomes in subjects with severe obesity. We aimed to determine the prognostic relevance of liver histology in a large cohort of obese patients undergoing bariatric surgery. Methods: In a single center cohort of 492 subjects undergoing Roux-en-Y gastric bypass bariatric surgery with routine perioperative liver biopsy at Geneva University Hospital between January 1997 to December 2004, clinical and histopathological variables were analyzed for association with overall survival. Survival of the cohort was compared to age- and sex-matched life tables from the Swiss general population and propensity score-matched subjects from the third National Health and Nutrition Examination Survey (NHANES III). A 32-gene signature was evaluated in the liver tissue of 47 non-alcoholic steatohepatitis (NASH) subjects. Results: Median body mass index was 43.6 kg/m2. Twenty-one patients (4.2%) died during a median follow-up of 10.3 years. At baseline liver histology, 12% and 16% of subjects had NASH, and fibrosis, respectively. In multivariable Cox regression, presence of NASH (hazard ratio [HR] 3.4, p=0.0087), age greater than 50 years (HR 2.7, p=0.044), hypertension (HR 3.8, p=0.021), and short-term postoperative complications (HR 2.8, p=0.048) were associated with overall survival. Compared to matched NHANES III subjects, bariatric surgery improved long-term survival (HR 0.54, p=0.035), although this benefit was not observed in the subgroup of NASH patients (HR 0.97, p=0.94). A 32-gene poor prognosis signature prediction was associated with worse overall survival within NASH subjects (n=47, HR = 7.7, p=0.03 ). Conclusions Histologically proven NASH was associated with increased long-term mortality in subjects undergoing bariatric surgery. Although survival benefit of bariatric surgery may be limited in obese patients with NASH, a 32-gene expression signature appears to predict long term mortality in these patients.

overall_design:
47 surgical liver biopsies of obese subjects with non-alcoholic steatohepatitis undergoing bariatric surgery
32-gene signature: FSHB, SH3GL2, RBM34, NCAPH, EGF, TRIO, COL6A3, ABLIM1, ITGA9, NTS, SERPINB2, MMP7, PRKG2, EDG4, NOS2A, EPHA4, SP100, FMO1, GPX2, RPS6KA5, PKLR, TMEM97, PPP1R1A, PSMB3, PTPN2, ADRA2B, ACSM3, PFKFB1, IMPA1, RLF, TTR, and ALDH9A1
--------------------------------------------------
The submitters of this dataset have not obtained permission to provide the relevant de-identified clinical outcomes.  Thus, the information accompanying this dataset is incomplete.

first: Nicolas

last: Goossens

first: Scott

last: Friedman

first: Minoa

last: Jung

first: Philippe

last: Morel

first: Shigeki

last: Nakagawa

first: Jean-Louis

last: Frossard

first: Laurent

last: Spahr

first: Francesco

last: Negro

first: Laura

last: Rubbia-Brandt

first: Emiliano

last: Giostra


title: Analysis of mature miRNA levels in the context of CHO cell proliferation

status: Public on Dec 10 2015

city: Vienna

first: Gerald

last: Klanert

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Biotechnology

summary: Mature microRNA transcripts were analyzed in 9 CHO cell lines growing at different proliferation rates. The goal was to identify microRNAs that correlate positively or negatively with CHO proliferation rates.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: A common reference design was chosen, where all samples were hybridized against a pool of all RNA samples.

first: Vaibhav

last: Jadhav

first: Vinoth

last: Shanmukam

first: Matthias

last: Hackl

first: Nicole

last: Borth


title: Gene networks linked to vitellogenin mRNA disruption

status: Public on Dec 28 2015

city: Piracicaba

first: Ana

middle: Durvalina

last: Bomtorin

state: São Paulo

address: R Ajudante Albano 847

country: Brazil

institute: Universidade de Sao Paulo

middle: D

first: Francis

last: Nunes

first: Angel

last: Barchuk

first: Zila

last: Simoes


title: Analysis of altered mRNA expression profiles in the genetic hypercalciuric stone-forming (GHS) rat compared to normal SD rat

status: Public on Dec 01 2015

city: Wuhan

first: Yuchao

last: LU

address: 1095# Jiefang Avenue

department: Urology

institute: Tongji Hospital of Tongji medical college, Huazhong University of Science &Technology

summary: Urolithiasis is a common desease to human beings, and idiopathic hypercalciuria (IH) is an important risk factor of calcium urolithiasis, previous studies strongly suggested that the decreased tubular Ca2+ reabsorption played a key role of hypercalciuria. However,the molecular mechanism of IH-urolithiasis formation is still not completely elucidated. GHS rat is regarded as an ideal animal model of calcium urolithiasis, reveals many identical pathophysiologic characteristics with IH patients . We analyzed mRNA expression profiles of the kidney of GHS rat in order to find out the target genes and signaling pathways in the pathogenesis of IH.

overall_design: The colony of GHS rats were created by the selective breeding of male and female SD rats with the highest 24 hour urine excretions (doi: 10.3390/ijms160716313). In the 28 generation, GHS rats have stabilized excreted significant higher level of urine calcium than wild-type normal SD rats, and reveals many identical pathophysiologic characteristics with IH patients, such as normal serum Ca2+, hypercalciuria, elevated intestinal Ca2+ resorption and a tendency to lose calcium from the bone. This present study examined the mRNAs expression of three pairs of GHS rats’ kidneys with normal SD rats by microarrays.

last: Lu

first: Shaogang

last: Wang


title: Plasma microRNA array analysis following polymicrobial sepsis

status: Public on Nov 13 2015

city: Charlestown

first: Yan

last: Feng

address: 149 13th Street, Rm4423

department: Anesthesia, Critical Care and Pain Medicine

institute: MGH

summary: In this study, total 68 immunolog-related miRNAs were detected

overall_design: Two groups: Sham and CLP

first: Lin

last: Zou

first: Wei

last: Chao


title: CodeLink™ Mouse Whole Genome Bioarray data from hematopoietic stem cells (HSCs) of miR-125a (+/+) wild-type mice and miR-125a (+/-) heterozygous mice with myeloproliferative disorder

status: Public on Jun 30 2015

first: Naoya

last: Tatsumi

summary: miR-125a knockout mice develop myeloproliferave disorder (MPD). To investigate the molecular mechanisms of MPD induced by the loss of miR-125a, gene expression profiling on hematopoietic stem cells of miR-125a (+/+) and (+/-) MPD mice was performed using CodeLink Whole Genome DNA array analysis.

overall_design: Codelink Mouse Whole Genome Bioarrays were performed according to the manufacturer’s instruction on total RNA extracted from hematopoietic stem cells of miR-125a (+/+) wild-type mice and miR-125a (+/-) heterozygous mice with MPD. One replicate per array.


title: Chimeric repressors of GLKs confer tolerance to air pollutant by closing stomata in Arabidopsis

status: Public on Oct 01 2015

city: Tsukuba

first: Nobutaka

last: Mitsuda

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: Regulation of stomatal movement is one of the effective strategies for developing resistant crops to air pollutant because stomata allows absorption of various air pollutants, such as ozone and sulfur dioxide. Transcription factor (TF) is a fascinating target of genetic manipulation for this end because TF regulates many genes simultaneously and methods of genetic manipulation are universally established. Here, we have screened transgenic Arabidopsis lines expressing chimeric repressor of TFs in high-concentration of ozone and found that the chimeric repressors of GOLDEN-LIKE1 (GLK1) and GLK2 (GLK1-SRDX and GLK2-SRDX) conferred strong tolerance to ozone. These 35S:GLK1/2-SRDX plants also showed sulfur dioxide tolerance. Their leaves showed lower rate of transpiration than wild type and a remarkable closed-stomata phenotype. The expression of the genes encoding K+ and water channels, including KAT1 and AKT1, which are involved in stomatal opening, was downregulated in 35S:GLK1-SRDX plants. Consistently, expression of GLK1-SRDX driven by the GC1 promoter, which has an activity only in guard cell, also induced closed-stomata and an ozone tolerant phenotype. On the contrary, 35S:GLK1/2 plants showed hypersensitivity to ozone and an opened-stomata phenotype. These data suggested that GLK1 and GLK2 have an ability to induce transcriptional change in guard cell and regulate stomatal movement. Our findings provide an effective tool to confer resistance to air pollutant by regulating stomatal aperture and improve crop productivity in future.

overall_design: Transcriptomes of 35S:GLK1-SRDX, glk1 glk2 double mutant and wild-type Arabidopsis seedlings were compared.

first: Nagatoshi

last: Yukari

first: Mitsuda

last: Nobutaka

first: Inoue

last: Shin-ichiro

first: Kubo

last: Akihiro

first: Saji

last: Hikaru

first: Kinoshita

last: Toshinori

first: Seo

last: Mitsuhiro

first: Ohme

middle: T

last: Masaru


title: Expression profiling of peripheral blood gene expression of women with hereditary breast cancer and controls (set 1)

status: Public on Oct 21 2015

city: Salt Lake City

first: Andrea

last: Bild

state: UT

address: 112 Skaggs Hall

department: Pharmacology and Toxicology

institute: University of Utah

summary:
We obtained peripheral blood samples for women from Utah (USA) and Ontario (Canada) who had a family history of breast cancer (or did not), who carried a BRCA1/2 mutation (or did not), and who had developed breast cancer (or had not).
We classified the women into two groups: [1] those who had a family history of breast cancer (irrespective of BRCA1/2 mutation status) and had developed an early-onset breast tumor and [2] those who had a family history of breast cancer but had not developed a breast tumor or who did not have a family history of breast cancer (some of whom had developed sporadic breast cancer and and others who had not). We then used machine-learning methods to assess how well we could classify these women into either group. The Utah samples served as a training set, and the Ontario samples served as an independent validation set from a geographically distinct population.

overall_design:
For the Utah cohort, there are 124 samples total: 16 who had a family history of breast cancer and carried a BRCA mutation and had developed breast cancer, 23 with a family history of breast cancer but did not carry a BRCA1/2 mutation and had developed breast cancer, 22 with a family history of breast cancer and carried a BRCA1/2 mutation but had not developed breast cancer, 22 with a family history of breast cancer but did not carry a BRCA1/2 mutation and had not developed breast cancer, 22 with no family history of breast cancer and had developed breast cancer, and 19 with no family history of breast cancer and had not developed breast cancer. The Ontario cohort included 73 samples: 11 who had a family history of breast cancer and carried a BRCA mutation and had developed breast cancer, 17 with a family history of breast cancer but did not carry a BRCA1/2 mutation and had developed breast cancer, 14 with a family history of breast cancer and carried a BRCA1/2 mutation but had not developed breast cancer, 18 with a family history of breast cancer but did not carry a BRCA1/2 mutation and had not developed breast cancer, 8 with no family history of breast cancer and had developed breast cancer, and 5 with no family history of breast cancer and had not developed breast cancer. 36 of the Ontario samples were scanned and processed at Duke University; the remaining 37 samples were handled at Boston University.

The batch-adjustment process was repeated twice independently: [1] all 124 Utah samples were adjusted jointly with the 36 Ontario samples that had been processed at Duke University (set 1) and [2] all 124 Utah samples were adjusted jointly with the 37 Ontario samples that had been processed at Boston University (set 2).
This dataset represents set 1.

first: Stephen

last: Piccolo


title: mRNA Expression data from rats treated with ANIT or vehicle

status: Public on Aug 26 2015

city: Little Rock

first: Alison

middle: Hege

last: Harrill

state: AR

address: 4301 W Markham Street Slot 820-11

institute: University of Arkansas for Medical Sciences

summary:
Adult Sprague Dawley rats were treated i.g. with 50 mg/kg alpha-naphthylisothiocyanate (ANIT) or vehicle (corn oil). Hepatobiliary liver injury occurred at 24 h postdose in ANIT rats with repair at 120h.
Livers were extracted from rats at 24h and 120 h post ANIT exposure. This study investigated differences in mRNA expression between the injury and repair phases in the context of ANIT exposure.

overall_design: 8 week male Sprague Dawley rats were administered ANIT or vehicle for quantification of hepatobiliary injury via clinical chemistry biomarkers and pathology between 6 and 168 h postdosing. Rats sacrificed at 24 h and 120h postdosing coincided with peak injury and injury resolution, respectively.

first: Rachel

last: Church


title: Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without iron.

status: Public on Jul 22 2015

city: Bloomington

first: Jason

middle: Eugene

last: Heindl

state: IN

address: 1001 E. 3rd St., Jordan Hall 142

department: Biology

institute: Indiana University

summary: The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. We demonstrate that A. tumefaciens biofilm formation is reduced under limiting iron conditions. Treatment of A. tumefaciens cultures with EDDHA, an iron-specific extracellular chelator, inhibited both planktonic growth rate and adherent biomass. These effects were reversed upon addition of exogenous ferrous iron. This reduced biofilm formation effect is independent of the known iron-responsive regulators Irr and RirA. Transcriptome analysis comparing gene expression under iron-replete versus iron-deficient conditions identified hundreds of genes that are differentially regulated. Downregulated genes suggest an iron sparing response.

overall_design: Four biological replicates, independent RNA preparations, one dye swap.

middle: E

first: Michael

last: Hibbing

first: Jing

last: Xu

first: Clay

last: Fuqua


title: Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without manganese

status: Public on Jul 24 2015

summary: The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. In several systems intracellular levels of the redox-active manganous (Mn2+) and ferrous (Fe2+) ions are interrelated and have tight corresponding regulation with respect to one another. We show that limiting manganese concentrations elicit similar growth and biofilm phenotypes to those seen under iron-limiting conditions. Microarray analysis comparing gene expression in manganese-replete versus manganese-limiting conditions identified a small number of differentially regulated transcripts. These results indicate that the redox-active manganous and ferrous ions are required for wild-type levels of growth and biofilm formation, and that the manganese-dependent response is primarily post-transcriptional and complementary to, but not redundant with, the iron-dependent response.

overall_design: Four biological replicates, independent RNA preparations, two dye swaps.


title: Expression profiling of peripheral blood gene expression of women with hereditary breast cancer and controls

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

overall_design: Refer to individual Series


title: The endometrial gene expression signature of recurrent implantation failure after IVF

status: Public on Jun 01 2015

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

institute: AUMC

summary: Transcriptomic studies have identified gene expression profiles characteristic of the window of implantation and preliminary studies have indicated that these may be disrupted in some women with recurrent implantation failure (RIF). The aims of this study were to elucidate how the endometrial gene expression profile differs between women with RIF and controls, and to investigate whether a predictor set of genes could be identified able to distinguish between these women.

overall_design: Between 2006 and 2013, mid-luteal phase endometrial biopsies were taken in the natural cycle from two serial cohorts, each consisting of women with RIF, defined as ≥3 failed IVF/ICSI treatments or replacement ≥10 embryos without the occurrence of a pregnancy (n=22 and n=21), and controls (n=23 and n=49). All subjects had undergone IVF/ICSI treatment in two tertiary hospitals. The control group had all conceived within the first two cycles of ICSI (n=49) or first three cycles of IVF treatment (n=23), and were therefore considered unlikely to have an endometrial factor. Microarray profiling and subsequent analysis sought to identify a gene expression signature predictive of RIF.

middle: R

first: Yvonne

last: Koot

first: Carolien

last: Boomsma

first: Dik

last: van Leenen

first: Marian

middle: J

last: Groot Koerkamp

first: Mariëtte

last: Goddijn

first: Marinus

last: Eijkemans

first: Bart

middle: C

last: Fauser

first: Frank

last: Holstege

first: Nick

last: Macklon


title: Expression profiling of peripheral blood gene expression of women with hereditary breast cancer and controls (set 2)

first: Andrea

last: Bild

overall_design:
For the Utah cohort, there are 124 samples total: 16 who had a family history of breast cancer and carried a BRCA mutation and had developed breast cancer, 23 with a family history of breast cancer but did not carry a BRCA1/2 mutation and had developed breast cancer, 22 with a family history of breast cancer and carried a BRCA1/2 mutation but had not developed breast cancer, 22 with a family history of breast cancer but did not carry a BRCA1/2 mutation and had not developed breast cancer, 22 with no family history of breast cancer and had developed breast cancer, and 19 with no family history of breast cancer and had not developed breast cancer. The Ontario cohort included 73 samples: 11 who had a family history of breast cancer and carried a BRCA mutation and had developed breast cancer, 17 with a family history of breast cancer but did not carry a BRCA1/2 mutation and had developed breast cancer, 14 with a family history of breast cancer and carried a BRCA1/2 mutation but had not developed breast cancer, 18 with a family history of breast cancer but did not carry a BRCA1/2 mutation and had not developed breast cancer, 8 with no family history of breast cancer and had developed breast cancer, and 5 with no family history of breast cancer and had not developed breast cancer. 36 of the Ontario samples were scanned and processed at Duke University; the remaining 37 samples were handled at Boston University.

The batch-adjustment process was repeated twice independently: [1] all 124 Utah samples were adjusted jointly with the 36 Ontario samples that had been processed at Duke University (set 1) and [2] all 124 Utah samples were adjusted jointly with the 37 Ontario samples that had been processed at Boston University (set 2).
This dataset represents set 2.

middle: H

first: Stephen

last: Piccolo


title: Comparative analysis of extremely thermophilic Caldicellulosiruptor species reveals common and differentiating cellular strategies for plant biomass utilization

status: Public on Jul 31 2015

city: Raleigh

first: Jeffrey

last: Zurawski

state: NC

address: 840 Main Campus Drive Room 3309

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70°C to simple sugars, acetate, lactate, CO2 and H2.  C. bescii, C. kronotskyensis and C. saccharolyticus solubilized 38%, 36% and 29% (by weight) of unpretreated switchgrass (5 g/l), repectively, which was about half of the concentration of crystalline cellulose (Avicel, 5 g/l) that was solubilized under the same conditions. The lower yields with C. saccharolyticus were unexpected, given that its genome encodes the same GH9-GH48 multi-domain cellulase (CelA) found in the other two species. However, the genome of C. saccharolyticus lacks two other cellulases with GH48 domains, which could be responsible for its lower levels of solubilization. Transcriptomes for growth of each species comparing Cellulose to switchgrass showed that many carbohydrate ABC transporters and multi-domain extracellular glycoside hydrolases were differentially regulated, reflecting the heterogeneity of lignocellulose. However, significant differences in transcription levels for conserved genes among the three species were noted, indicating unexpectedly diverse regulatory strategies for deconstruction for these closely related bacteria. Genes encoding the Che-type chemotaxis system and flagella biosynthesis were up-regulated in C. kronotskyensis and C. bescii during growth on cellulose, implicating motility in substrate utilization. The results here show that capacity for plant biomass deconstruction varies across Caldicellulosiruptor species and depends in a complex way on GH genome inventory, substrate composition, and gene regulation.

sample_organism:
Caldicellulosiruptor bescii
Caldicellulosiruptor saccharolyticus
Caldicellulosiruptor kronotskyensis

overall_design: A dye swap was completed with each of three Caldicellulosiruptor species: C. bescii, C. kronotskyensis and C. saccharolyticus growing on cellulose and switchgrass. Half of the RNA sample for one condition was labeled with Cy3 and the other half Cy5. The two differentially labeled samples were run on two different slides and analyzed to investigate differences in transcription during growth on cellulose and switchgrass.

first: J

middle: V

last: Conway

first: L

middle: L

last: Lee

first: H

last: Simpson

middle: A

last: Izquierdo

first: S

last: Blumer-Schuette

first: I

last: Nookaew

first: M

middle: W

last: Adams

first: R

last: Kelly


title: Accumulated α-synuclein affects the progression of GM2 gangliosidoses

status: Public on May 12 2015

city: Setagaya

first: Seiichi

last: Kanzaki

institute: NCCHD

summary:
The accumulation of α-synuclein (ASyn) has been observed in several lysosomal storage diseases (LSD), but it remains unclear if the accumulation of ASyn contributes to the pathology.
The mitochondria degeneration, reduced expression of manganese superoxide dismutase 2, and reactive oxygen species-mediated oxidative damage were observed in the neurons of Hexb-/- mice.

overall_design: Gene expression in the brain of 14-week-old Hexb-/- ASyn+/+, Hexb-/- Asyn-Tg, and Hexb-/- ASyn-/- mice were analyzed.

first: Akira

last: Yamaguchi

first: Kyoko

last: Suzuki

first: Shoji

last: Yamanaka

first: Masato

last: Kawashima

first: Takashi

last: Togo

first: Omi

last: Katsuse

first: Noriko

last: Koumitsu

first: Naoya

last: Aoki

first: Eizo

last: Iseki

first: Kenji

last: Kosaka

first: Kayoko

first: Makoto

last: Hashimoto

first: Ichiro

first: Yoshio

last: Hirayasu


title: Contribution of cell-bound and cell-free cellulosomal versus non-cellulosomal systems in deconstruction of cellulosic biomass by Clostridium thermocellum

status: Public on Feb 28 2015

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

summary: The  high cellulose digestion capability of the anaerobic thermophilic bacterium, Clostridium thermocellum, can be attributed to its efficient glycoside hydrolase system, consisting of both a free-enzyme system and a cellulosomal system, wherein carbohydrate active enzymes (CAZymes) are organized by primary and secondary scaffoldin proteins into large protein complexes bound to the bacterial cell wall.  Using an integrated series of experiments encompassing polysaccharide depolymerization assays, direct biochemical analyses and transcriptomics, we show herein that, in addition to cell-bound cellulosomes and “free” enzymes, C. thermocellum naturally employs a system of cell-free cellulosomes that are not designed to be tethered to the cell and can diffuse away to attack polysaccharide substrates at some distance from the cell.  By characterizing the cells and the secretomes of a series of mutants in which genes for either individual scaffoldins or combinations thereof are deleted, we demonstrate that the cellulosome is far more important in cellulose degradation than are the free enzymes, and that the primary scaffoldin CipA is much more important for the action of the cellulosomes than is the collective contribution of the secondary scaffoldins.  Extensive transcriptomics analyses confirm the above results and extend the study to the effects of scaffoldin deletions on the organism as a whole.

overall_design: To gain insights into the transcriptome profiles of C. thermocellum strains when various cellulosomal scaffoldin genes were deleted.  High quality RNA was extracted from C. thermocellum grown on cellulose. Transcriptome profiles were obtained at one time point during actively growing fermentations, mid exponential phase when 50% of the substrate had been consumed.

first: Qi

last: Xu

first: Kara

last: Podkaminer

first: Shihui

last: Yang

first: Michael

middle: G

last: Resch

first: Dawn

middle: M

last: Klingeman

first: Bryon

middle: S

last: Donohoe

first: Daniel

last: Olson

first: John

middle: O

last: Baker

first: Steve

last: Decker

first: Richard

last: Giannone

first: Robert

last: Hettich

first: Steven

last: Brown

first: Lee

last: Lynd

first: Edward

last: Bayer

last: Himmel

first: Yannick

last: Bomble


title: Affymetrix Oncoscan array data for aggressive variant prostate cancer (AVPC) samples

status: Public on Oct 10 2015

city: Houston

first: LI

last: SHEN

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

summary: Prostate cancers with clinical features of small cell prostate carcinomas (SCPC) but diverse morphologies share chemotherapy responsiveness with SCPC. We prospectively collected tumor tissues from clinically defined, morphologically diverse, aggressive variant prostate cancers (AVPCa) to determine if they also share molecular features with SCPC

overall_design: 59 prostate cancer samples from 40 men (10 with SCPC) registered to clinical trial NCT00514540, and 8 PDX from 6 of them, were stained for RB, p53, AR, NKX3-1, ASCL1, AURKA, UBE2C and Ki67. We determined copy number alterations (CNA) by Oncoscan® using DNA from 36 of the 59 samples and 8 PDX lines.

first: Ana

last: Aparicio

first: Sankar

middle: N

last: Maity


title: Advanced Age is Associated with Worsened Outcomes and a Unique Genomic Response in Severely Injured Patients with Hemorrhagic Shock

status: Public on Jan 06 2015

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: We performed epidemiological, cytokine, and transcriptomic analyses on a prospective, multi-center cohort of 1,928 severely injured patients.

overall_design: We wished to characterize the relationship of advanced age to clinical outcomes and to transcriptomic responses after severe blunt traumatic injury with hemorrhagic shock.

first: Erin

last: Vanzant

first: Rachael

last: Hilton

first: Cecilia

first: Jianyi

last: Zhang

first: Ricardo

middle: F

last: Ungaro

first: Lori

last: Gentile

first: Benjamin

last: Szpila

first: Ronald

last: Maier

first: Joseph

last: Cuschieri

first: Azra

last: Bihorac

first: Christiaan

last: Leeuwenburgh

first: Frederick

last: Moore

first: Henry

first: Lyle

last: Moldawer

first: Scott

last: Brakenridge

first: Philip

last: Efron


title: miRNA regulated by Notch signaling in macrophage

status: Public on Mar 28 2015

city: Xi’an

first: Junlong

last: Zhao

state: Shaanxi

address: Chang-Le Xi Street #17

department: Department of Medical Genetics and Developmental Biology

country: China

institute: Fourth Military Medical University

summary: This two-color miRNA chip was perfored to identify the downstream miRNAs regulated by Notch signaling in macrophage polarization.

overall_design: To identify the downstream miRNAs mediated by Notch signaling during macrophage polarization regulating, RNA was isolated from bone marrow drived macrophages (BMDMs) of Notch signaling deletion and wild type mice as experiment samples. Three control (+/-) and three experiment (-/-) samples were detected.

first: Fei

last: He


title: Comparative genomic, microRNA, and tissue analyses reveal subtle differences between non-diabetic and diabetic foot skin [microRNA PCR panel]

status: Public on May 01 2015

city: Miami

first: Horacio

middle: Adrian

last: Ramirez

state: Florida

address: 1600 NW10th Avenue RMSB room 2029A

department: Dermatology

country: USA

institute: University of Miami

summary: Diabetes Mellitus (DM) is a chronic, severe disease rapidly increasing in incidence and prevalence and is associated with numerous complications. Patients with DM are at high risk of developing diabetic foot ulcers (DFU) that often lead to lower limb amputations, long term disability, and a shortened lifespan. Despite this, the effects of DM on human foot skin biology are largely unknown. Thus, the focus of this study was to determine whether DM changes foot skin biology predisposing it for healing impairment and development of DFU. Foot skin samples were collected from 20 patients receiving corrective foot surgery and, using a combination of multiple molecular and cellular approaches we performed comparative analyses of non-ulcerated non-neuropathic diabetic foot skin (DFS) and healthy non-diabetic foot skin (NFS). MicroRNA (miR) profiling of laser captured epidermis and primary dermal fibroblasts from both DFS and NFS samples identified 5 miRs de-regulated in the epidermis of DFS though none reached statistical significance. MiR-31-5p and miR-31-3p were most profoundly induced. Although none were significantly regulated in diabetic fibroblasts, miR-29c-3p showed a trend of up-regulation, which was confirmed by qPCR in a prospective set of 20 skin samples. Gene expression profiling of full thickness biopsies identified 36 de-regulated genes in DFS (>2 fold-change, unadjusted p-value ≤ 0.05). Of this group, three out of seven tested genes were confirmed by qPCR: SERPINB3 was up-regulated whereas OR2A4 and LGR5 were down-regulated in DFS. However no morphological differences in histology, collagen deposition, and number of blood vessels or lymphocytes were found. No difference in proliferative capacity was observed by quantification of Ki67 positive cells in epidermis. These findings suggest DM causes only subtle changes to foot skin. Since morphology, mRNA and miR levels were not affected in a major way, additional factors, such as neuropathy, vascular complications, or duration of DM, may further compromise tissue’s healing ability leading to development of DFUs.

overall_design: samples were fixed in formalin and paraffin embedded. Between 16 and 20 8-10µm sections were cut from the formalin-fixed paraffin embedded tissue blocks of non-diabetic and diabetic foot skin, placed on Arcturus PEN-membrane glass slides (Life Technologies, Carlsbad, CA, USA) and dried at 37°C for 1-2 hours. LCM was carried out on a Arcturus Veritas laser capture microdissection instrument and the epidermis was collected on CapSure® Macro LCM Caps (Life Technologies). The caps were transferred to a tube containing 60µl of deparaffinization buffer (QIAGEN Inc., Valencia, CA, USA) and total RNA, including the microRNA fraction, was extracted using the FFPE miRNeasy kit (QIAGEN Inc.) according to the manufacturer’s instructions.  Total RNA concentration of the samples was quantified using NanoDrop 2000 (NanoDrop products, Wilmington, DE) and the RNA quality of these samples was determined by RT-qPCR of SNORD48 and miR-21 using the commercially available platforms miRCURY LNA™ (Exiqon, Woburn, MA, USA) or Quanta qScript™ microRNA Quantification System (Quanta BioSciences, Inc., Gaithersburg, MD, USA). The miR profiles for the epidermis of 3 NFS and 3 DFS, were generated using the miR Ready-to-Use PCR panels V3 (Exiqon) following the manufacturer’s specifications. The Ct values were normalized to the stably expressed reference gene SNORD49 using the Exiqon GenEX software and the expression levels in the NFS and DFS were compared.

first: Lisa

last: Liang

first: Irena

last: Pastar

first: Ashley

last: Rosa

first: Olivera

last: Stojadinovic

first: Thomas

last: Zwick

first: Robert

last: Kirsner

first: Anna

last: Maione

first: Jonathan

last: Garlick

first: Marjana

last: Tomic-Canic


title: Plasma profiling of miRNAs in human specimens from osteosarcoma patients.

status: Public on Jan 17 2015

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Osteosarcoma (OS) is the primary bone tumor in children and young adults.  Currently, there are no reliable, non-invasive biological markers to detect the presence or progression of disease, assess therapy response, or provide upfront prognostic insights. Using a qPCR-based platform that analyzes more than 750 miRNAs, we analyzed control and diseased-associated plasma from human cases of OS to identify a profile of differentially expressed miRNAs.

overall_design: Comprehensive miRNA expression profiling was completed using the Exiqon miRNome platform (human panels I+II, V3) on 20 disease samples (10 localized, 10 metastatic) and 15 healthy controls.

first: Jason

last: Yustein

first: Wendy

last: Allen-Rhoades