title: miRNA array profiling of Lats2 deficient mouse embryonic fibroblasts

status: Public on Jul 26 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Chromatin modifying activities for construction of appropriate epigenetic landscapes by polycomb repressive complex 2 (PRC2) play an essential role in development and tumorigenesis. However, the spatiotemporal mechanisms by which PRC2 achieves diverse epigenomes for specific tissue or cellular contexts remain poorly understood. Here, we discovered that LATS2 knockout causes dysregulation of PRC2 and subsequent transcriptome changes for differentiation in both mouse and human cells. LATS2 depletion dependent dysregulation of PRC2 also effects H3K4me3 and forms negative feedback loop for maintenance of PRC2. Further analyses reveal that LATS2 on chromatin binds to EZH2 and LATS2 has ability to phosphorylate PRC2 in vitro. These LATS2 dependent H3K27me3 targets are highly induced during neurogenesis, and statistical analysis of glioblastoma multiforme reveals that LATS2-high cases show more dedifferentiated transcriptome and poor prognosis with silencing of H3K27me3 targets. These observations suggest that LATS2-mediated epigenome coordination is pivotal for development and disease, including cancer.

overall_design: The rabeled cRNAs from Lats2-/- mouse embryonic fibroblasts (MEFs) and litter wild type MEFs were subjected to Agilent Mouse miRNA Microarray 8 x 15K. Each sample was run in biological dupulicate (different PDL).

first: Kosuke

last: Torigata


title: Peripheral blood transcriptome profiles in adult male Japanese IT workers.

status: Public on Jul 25 2016

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

country: USA

institute: UCLA School of Medicine

summary: Analysis of transcript abundance estimates as a function generalized purpose in life and work-related dimensions of meaning.

overall_design: Gene expression profiling was conducted on peripheral blood samples collected from adult male employees of a Japanese technology firm.  In addition to health-relevant background characteristics (age, indcome, body mass index/BMI, smoking history, heavy alcohol consumption history), participants were also assessed for hedonic and eudaimonic dimensions of generalized well-being (assesed by the Short Flourishing Scale, Keyes, C (2006). The Mental Health Continuum-Short Form (MHC-SF) for adults) and work-specific variables including job evaluation (assessed by a12-item scale tapping both perceived significance of the firm’s work, through items such as “I am proud of my company” and “I think my company is really good,” as well as perceived significance of one’s own contribution to the firm's work, through items such as, “I think other employees within my company respect my work”), and workplace interdependence and independence of the self and coworkers (using the Singelis Self-Construal Scale, Singelis, T. M. (1994). The Measurement of Independent and Interdependent Self-Construals. Personality and Social Psychology Bulletin, 20(5), 580–591).  Higher values of each scale score indicate greater levels of well-being, job satisfaction, etc.  Dichotomous variables were coded 0=no/absent and 1=yes/present.  Valid gene expression data are available for 106 participants.


title: Controlled induction of 49 transcription factors in transgenic mouse ES cell lines

status: Public on Jul 21 2016

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary: Controlled induction of individual transcription factors (TFs) in embryonic stem cells (ESCs) with subsequent global gene expression profiling is a promising approach for identification of downstream genes regulated by these TFs in a relatively promiscuous epigenetic background. Here we generated and characterized mouse ESCs clones with 49 doxycycline-controllable TFs as a continuation of the NIA Mouse ESC Bank project. Together with the previous clone libraries, the project now comprises 186 TFs (ca. 10% of all TFs in the genome). Induction of individual TFs shifts the transcriptome towards specific differentiation fates (e.g., neural for Myt1, St18; fibroblasts and osteoblasts for Pitx1, Pitx2, Barhl2, and Lmx1a; thymocytes for Myb; lymph nodes and spleen for Etv2 and Plac1, and ovary for Pitx1, Pitx2, and Dmrtc2). Gene set enrichment analysis for expression profile change after induction of TFs provides additional information on the functions and phenotypes associated with these TFs. These data could facilitate methods for generating various types of cells in regenerative medicine as well as ameliorating pathogenic phenotypes in gene therapy.

overall_design: Dox- overexpressing transcription factor vs. Dox+ (control).

first: Kohei

last: Yamamizu

first: Alexei

middle: A

last: Sharov

first: Yulan

last: Piao

first: Misa

last: Amano

first: Hong

last: Yu

first: David

last: Schlessinger

middle: S


title: Protein expression related with cell cycle control phosphorylation between TCCSUP and KSHV-infected TCCSUP

status: Public on Jul 28 2016

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

country: South Korea

institute: Eulji University School of Medicine

summary: Protein expression profile was analyzed by antibody array for cell cycle control phosphorylation with 238 antibodies with bladder cancer cell line, TCCSUP, and KSHV-infected TCCSUP cells.

overall_design: Protein was extracted from uninfected bladder cancer cell line, TCCSUP, and KSHV-infected TCCSUP cells, and they were analyzed by antibody array for cell cycle control phosphorylation.

first: Myung

first: Jinsung

last: Park


title: Peripheral blood transcriptome profiles in Nepali child soldiers and civilians.

status: Public on Jul 27 2016

summary: Analysis of transcript abundance estimates as a function of child soldier status, PTSD symptoms, and psychological resilience.

overall_design: Gene expression profiling was conducted on dried blood spot (DBS) samples collected from community dwelling adolescents and young adults in Nepal.  Approximatley half of the sample were former child soldiers in the Nepal People's War and the other half were demographically similiar civilian non-combatants.  In addition to basic demographic characteristics (age, sex, ethnic minority status, social caste status, education level), participants were also assessed on syptoms of post-traumatic stress (PTS, assessed by a culturally adapted version of The Child PTSD Symptom Scale; Kohrt BA, et al. (2011) Validation of cross-cultural child mental health and psychosocial research instruments: adapting the Depression Self-Rating Scale and Child PTSD Symptom Scale in Nepal. BMC Psychiatry 11(1):e127, with higher values indicating greater PTSD symptoms) and psychological resilience (assessed by a culturally adapted version of the Resilience Scale; Wagnild GM & Young HM (1993) Development and psychometric evaluation of the Resilience Scale. Journal of Nursing Measurement, with higher values indicating greater resilience).  Dichotomous variables were coded 0=no/absent and 1=yes/present.  Valid gene expression data are available for 254 samples.


title: Analysis of representative organ specific genes and promoters of rice using 3’ ORF oriented long oligomer microarray

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

institute: GreenGene Biotech Inc.

type: Expression profiling by genome tiling array

summary:
The profiling was conducted with the Rice 3'-Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp).
In this research, an array of 27,448 rice genes was used to elucidate the transcriptome of 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination) using a rice 3′ ORF tilling microarray. The ratio of standard deviation to the mean of microarray intensities was used to distinguish between organ-specific and constitutively expressed genes. Accordingly, the genes are classified into highly variable, variable, and constitutive groups. To isolate the organ-specific promoters, several genes were selected and validated in planta using reporter gene analysis. We found that the Os01g0702500, Os11g0211800, and Os01g0257300 promoters were active in the calli, germinating seeds, and roots, respectively. The Os08g0135500 promoter was shown to drive transgene expression in various organs of the mature flowers, such as the anther, lemma, and palea, whereas the Os03g0369100 promoter was only active in the anther. Lastly, the Os09g0553100 promoter induced high levels of reporter gene expression in all organs. The gene expression data from representative organs could put a frame work for large dataset collections and then subsequent profiling by subdivision of organ/tissues might be more efficient to find appropriate promoters.

overall_design: A total of 14 chips were used for microarray. Total RNAs were extracted from rice 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination. Experiments were duplicated.

first: S

last: Chae

first: J

first: B

middle: H

last: Nahm

first: Y


title: Phenotypic, transcriptomic and genomic characterization of clonal plasma cells in light chain amyloidosis [Copy number analysis]

status: Public on Jul 22 2016

city: Pamplona

first: Bruno

last: Paiva

address: Av. Pio XII, 55

country: Spain

institute: Clinica Universidad de Navarra

summary: Immunoglobulin light-chain amyloidosis (AL) is a rare clonal plasma cell (PC) disorder that remains largely incurable. AL and multiple myeloma (MM) share the same cellular origin, but while knowledge about MM PC biology has improved significantly, the same does not apply for AL. Here, we undertook an integrative phenotypic, molecular, and genomic approach to study clonal PCs from 22 newly-diagnosed AL patients. Through principal-component-analysis, we demonstrated highly overlapping phenotypic profiles between AL and MGUS or MM patients. However, in contrast to MM, highly-purified FACSs-sorted clonal PCs in AL (n=9/22) show virtually normal transcriptomes with only 68 deregulated genes as compared to normal PCs, including a few tumor suppressor (CDH1, RCAN) and pro-apoptotic (GLIPR1, FAS) genes. Notwithstanding, clonal PCs in AL (n=11/22) were genomically unstable with a median of 9 copy-number-abnormities (CNAs) per case; many of which similar to those found in MM. Whole-exome sequencing (WES) was performed in three AL patients and revealed a median of 10 non-recurrent mutations per case. Altogether, we showed that although clonal PCs in AL display phenotypic and CNA profiles similar to MM, their transcriptome is remarkably similar to that of normal PCs. First-ever WES revealed the lack of a unifying mutation in AL

overall_design:
A total of 22 patients with confirmed diagnosis of AL based on the presence of amyloid-related systemic syndrome, positive amyloid tissue staining with Congo red, and evidence of PC clonality were studied. Samples were collected after informed consent was given, in accordance with local ethical committee guidelines and the Helsinki Declaration.
Genome-wide detection of CNAs and copy-number neutral loss-of-heterozygosity (LOH) were investigated using the Cytoscan 750K platform (Affymetrix) in 11/22 cases with adequate DNA extracted from FACS-sorted clonal PCs and paired T-lymphocytes. The AGCC and ChAS software programs (Affymetrix) were used for data analysis as described elsewhere. CNAs were reported when the three following criteria were met: ≥25 consecutive imbalanced markers per segment; ≥100Kb minimum genomic size and; <50% overlap with paired control DNA and/or genomic variants of Toronto DB (DGV). Only CNN-LOH larger that 5Mb, with ≥25 consecutive imbalanced markers per segment, and <50% overlap with patient-paired CNAs were considered.

first: Joaquin

last: Martinez-Lopez

first: Luis

last: Corchete

first: Noemi

last: Puig

first: Maria

last: Luz Sanchez

first: Paloma

last: Barcena

first: Diego

last: Alignani

first: Marta

last: Lasa

first: Alfonso

last: García de Coca

first: Emilia

last: Pardal

first: Fernando

last: Escalante

first: Tomás

middle: J

last: González-López

first: José

last: Alonso

first: Magdalena

last: Sierra

first: Abelardo

last: Bárez

last: Hernández

first: Josefina

last: Galende

first: Felipe

last: Prosper

first: Alberto

last: Orfao

first: Maria-Belen

last: Vidriales

first: Norma

middle: C

last: Gutierrez

first: María-Victoria

last: Mateos

first: Juan-Jose

last: Lahuerta

first: Jesús

middle: F

last: San Miguel


title: Functional maturation of rat beta cells

city: Distrito Federal

first: Carlos

middle: Alfonso

last: Larqué Velázquez

state: Distrito Federal

address: Circuito Exterior s/n Ciudad Universitaria. Del. Coyoacán. Mexico City

department: Neurodevelopment and Physiology

country: Mexico

institute: Instituto de Fisiología Celular UNAM

summary: The weaning period consist of a critical postnatal window for structural and physiologic maturation of rat beta cells. To investigate transcriptome changes involved in the maturation of beta cells neighboring this period we performed microarray analysis in FACS beta cell enriched populations to detail the global programme of gene expression to identify its changes during this process.

overall_design: Male Wistar rats were selected at the initial point of a postnatal critical period (postnatal 20d) for pancreatic maturation for RNA extraction and hybridization on Affymetrix microarrays. We obtained immature and mature beta cell-enriched populations from postnatal 20d and 2 months animals in order to compare  their expression profiles. To that end, we used primary cultured FACS-enriched beta cell populations according to their FSC, SSC and autoflourescence. We used three replicates for each condition.

last: Larqué

first: Myrian

last: Velasco

first: Francisco

last: Barajas

first: Neyvis

last: García-Delgado

first: Juan

middle: P

last: Chávez-Maldonado

first: Jazmín

last: García-Morales

first: Lorena

last: Orozco

first: Marcia

last: Hiriart


title: Expression data from antigen-specific CD4+T cells from peripheral blood of patietns with CD and healthy controls.

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

institute: IDIBAPS

summary:
Crohn's Disease (CD) is a chronic inflammatory disease of the intestinal tract.
We performed a whole-genome transcriptional analysis using sorted commensal antigen-specific CD4+T cells from peripheral blood of CD patients and from healthy controls.

overall_design: Peripheral blood sorted FlaX, Fla2 and YidX-specific CD4+T cells from Crohn's disease patients and from non-inflammatory controls were collected for RNA extraction and hybridization on Affymetrix microarrays. Inclusion criteria for CD patients were: age between 18 and 70, diagnosis of CD established at least 4 months before inclusion and exclusion of concomitant infection.

first: Elisabeth

last: Calderón-Gómez


title: Transcriptional profiling of orf19.5100/MLT1 ABC transporter  knockout in Candida albicans

city: New Delhi

first: Nitesh

middle: Kumar

last: Khandelwal

state: Delhi

address: Near Munirka

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

summary: Recent reports have been suggested involvement of ABC transporters in various physiological roles.To get better insight about possible involvement of vacuolar ABC  transporter MLT1/orf19.5100 in different physiological roles transcriptional profiling have been peformed and compared between WT(SC5314) Candida albicans cells vs  putative orf19.5100 knockout cells after 6hrs growth of culture.The assay as peformed in biological duplicate sample.

overall_design: Agilent one-color experiment,Organism: Candida albicans  ,Custom Agilent Candida albicans 8x15k Microarray Gene expression  (AMADID: 026377) designed by Genotypic Technology Private Limited  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

middle: K

first: Rajendra

last: Prasad


title: Copy Number Variation in Brca2 (G25R) variant mouse tumors

city: Frederick

first: Shyam

last: Sharan

address: 1050 Boyles St. Blg 560

department: Mouse Cancer Genetics Program

institute: National Cancer Institute

type: Genome variation profiling by genome tiling array

summary: To understand the overall amount of genomic instability seen in various genotypes of Brca2 (G25R) and to see where common gains and losses occur within a Trp53 heterozygous genetic background

overall_design: Comparing mouse tumor DNA with mouse genomic DNA

first: Suzanne

last: Hartford


title: In-Vivo Fusion of Human Cancer and Hamster Stromal Cells Permanently Transduces and Transcribes Human DNA

status: Public on Jul 29 2016

city: Morris Plains

first: David

middle: M

last: Goldenberg

state: NJ

address: 300 The American Road

department: Center for Molecular Medicine and Immunology

institute: Garden State Cancer Center

summary:
The heterotransplantation of human tumors to immune-deprived rodents has become an important preclinical tool for evaluating human tumor biology and responsiveness to therapeutic agents, based on the supposition that they reflect their original human origin. However, we demonstrate that such tumors can in fact change genetically, either by becoming tumors of the animal recipient or by becoming a hybrid of the human tumor and the animal host’s cells. Three human tumors transplanted to the cheek pouch of golden hamsters resulted in permanently transplantable tumors that metastasize in the hamsters. Based on diverse lines of evidence, these transplants from a human glioblastoma multiforme and two Hodgkin lymphomas were malignant hybrids, showing both human and hamster genes in the malignant tumor cells, while retaining the morphology of the original human tumors.
We demonstrate that even after being preserved for over 40 years in paraffin blocks, microarray analysis of RNA from these transplants disclosed over 3000 human genes derived from all 23 human chromosome pairs amongst these tumor transplants. A total of 3759 probe sets (ranging from 1040 to 1303 in each transplant) detected human gene transcripts in formalin-fixed, paraffin-embedded sections of the 3 hybrid tumors stored for over 40 years; the probe sets unambiguously map to 3107 unique Human Entrez Gene IDs and are representative of all human chromosomes, although, by karyology, one of the hybrid tumors (GB-749) had a total of 15 human chromosomes in its cells.  Among the genes mapped, 39 probe sets, representing transcripts from 33 human genes , were detected in all hybrid tumor samples. Five of these 33 genes encode transcription factors that regulate cell growth and differentiation, five encode cell adhesion and transmigration-associated proteins known to participate in oncogenesis and/or metastasis and invasion, and additional genes encode components of pathways involved with signal transduction,  regulation of apoptosis, DNA repair, and multidrug resistance. We posit that in-vivo fusion may disclose genes implicated in tumor progression, as well as gene families coding for the organoid phenotype. Thus, cancer cells can transduce adjacent stromal cells, with the resulting progeny having permanently transcribed genes with malignant and other functions of the donor DNA.

sample_organism:
Homo sapiens
Mesocricetus auratus

overall_design: Human gene expression profiles were determined by microarray analysis for 3 different Human-Hamster hybrid tumors, two Hodgkin lymphomas (GW-532, GW-584) and a glioblastoma multiforme (GB-749), that were first generated in the hamster cheek pouch after human tumor grafting and then propagated in hamsters and in cell cultures for years. Human gene expression was assessed using total RNA isolated from FFPE samples from GW-532 generations 2 and 34, GW-584 generation 28, and GB-749, in comparison to that for a Hamster control RNA sample isolated from a Hamster melanoma cell line (ATCC CCL-49).   Expressed human genes were identified using MAS 5.0  signal expression values and detection P-values in the following manner:  1) Unannotated probe sets, as well as probe sets with no signal value greater than the median signal for AFFX spike-in controls with all Absent Detection Calls, were omitted from further analysis;  2)  All remaining signal values for the hamster cell line sample were multiplied by the ratio of the median signal in all FFPE hybrid samples for AFFX spike-in control probe sets called present in all samples divided by the median signal for the same probe sets in the hamster CCL-49 sample;  3) Human transcripts were considered positive in a human-hamster hybrid FFPE sample if (a) a probe set signal exhibited a 2-fold or greater increase in any FFPE hybrid sample compared to the CCL-49 coontrol sample, (b) the fold change was greater than 2 standard deviations for that probe set across the FFPE samples, and (c) was called present (P) or marginal (M) for at least one or more FFPE samples.

first: Robert

last: Rooney

first: Meiyu

last: Loo

first: Chien-Hsing

last: Chang


title: Systems biology of tributyltin-induced pathogenesis in thicklip grey mullets (Chelon labrosus)

status: Public on Jul 31 2016

city: Leioa

first: Ibon

last: Cancio

address: B/sarriena s/n

institute: UPV/EHU

summary: Organotin compounds are highly persistent organic pollutants that bioaccumulate in marine biota, behaving as potent endocrine disruptors.  Tributyltin (TBT) has been described as an environmental obesogen, as it contributes in mammals to lipid accumulation in a mechanism mediated by PPARγ and RXR. With the aim of studying the molecular mechanisms that elicit TBT-induced pathogenesis in fish, thicklip grey mullets Chelon labrosus were exposed to low (10 ng/L) and high (500 ng/L) TBT concentrations for 1, 7 and 21 days, and gene transcription and metabolome profiles were studied. With this purpose, the multitissue transcriptome of mullet was sequenced by 454 pyrosequencing obtaining 126 Mb of sequence information. Assembly and annotation allowed spotting 8330 gene signatures on an oligonucleotide microarray that was used to identify hepatic gene transcription profiles specific to each TBT exposure set-up. Functional pathway analysis revealed that early profiles were characterized by genes related to response to organic substances and to oxidative stress and glucose metabolic processes. After 21 days of exposure, enriched GO terms in both concentrations were related to lipid homeostasis with a significant regulation of steroid metabolic and cholesterol biosynthetic processes. Also, the androgen receptor signalling pathway was regulated while PPAR signalling appeared as the most significantly regulated KEGG pathway. Neutral lipid accumulation measured by Oil-Red-O histochemistry did not show any treatment-related effect but hepatic and plasma NMR and GC-MS metabolomic analysis revealed distinctive metabolites. Aqueous profiles were characterised by lactate, glucose and alanine while GC-MS revealed a whole set of discriminating polyunsaturated fatty acids. Thus, TBT pathogenesis involves alterations of lipid metabolism through a mechanism that could involve PPARγ-regulated processes confirming the obesogen hypothesis for TBT in fish.

overall_design: Thicklip grey mullets were exposed to tributyltin (TBT). 3 treatments: control, TBT low dose (10ng/L), TBT high dose (500ng/L); 3 sampling times: 1 day, 1 week, 3 weeks. 6 mullets were dissected in each sampling point and group.

first: Oihane

last: Diaz de Cerio

first: Iratxe

last: Rojo

first: Jules

last: Griffin

first: Miren

last: Cajaraville


title: Induction of cells expressing markers of GABAergic neurons by transcription factors

first: Minoru

last: Ko

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

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

overall_design: Refer to individual Series


title: Prp8 Retinitis Pigmentosa Mutants Cause Defects in the Transition between the Catalytic Steps of Splicing

city: San Francisco

first: Megan

last: Mayerle

state: California

address: Genetech Hall Room N374, 600 16th St

department: Biochemistry and Biophysics

institute: University of California San Francisco

summary:
The essential process of pre-mRNA splicing must occur with high fidelity and efficiency for proper gene expression. The spliceosome employs DExD/H box helicases to promote on-pathway interactions while simultaneously minimizing errors. Prp8 and Snu114, an EF2-like GTPase, regulate the activity of the Brr2 helicase, promoting RNA unwinding by Brr2 at appro-priate points in the splicing cycle and repressing it at others. Mutations linked to Retinitis Pig-mentosa (RP), a disease that causes blindness in humans, map to the Brr2 regulatory region of Prp8. Previous In vitro studies of homologous mutations in Saccharomyces cerevisiae show that Prp8-RP mutants cause defects in spliceosome activation. Here we show a subset of RP muta-tions in Prp8 also cause defects in the transition between the 1st and 2nd catalytic steps of splic-ing. Though Prp8-RP mutants do not cause defects in splicing fidelity, they result in an overall decrease in splicing efficiency. Furthermore, genetic analyses link Snu114 GTP/GDP occupancy to Prp8-dependent regulation of Brr2. Our results implicate the transition between the 1st and 2nd catalytic steps as a critical place in the splicing cycle where Prp8-RP mutants influence splic-ing efficiency. The location of the Prp8-RP mutants, at the “hinge” that links the Prp8 Jab1-MPN regulatory “tail” to the globular portion of the domain, suggests that these Prp8-RP mutants inhibit regulated movement of the Prp8 Jab1/MPN domain into the Brr2 RNA binding channel to transiently inhibit Brr2 activity. Therefore, in Prp8-linked RP, disease likely results not only from defects in spliceosome assembly and activation, but also because of defects in splicing ca-talysis.
paper to be submitted

overall_design: Two channel microarrays were used. RNA isolated from wt yeast grown simultaneously to the mutant was used as a reference. This  reference was used in one of the channels for each hybridization and used in the statistical analysis to obtain an average expression-profile for each mutant relative to the wt. Three independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Strains, both WT and mutant, were grown at 37C until mid-log phase, OD600 of approximately 0.7. The mutated PRP8 gene is present on HIS marked CEN plasmid, and the corresponding genomic copy of PRP8 deleted. Strains labeled as wildtype also have the relevant genomic PRP8 deleted, but complemented with wildtype PRP8 on CEN plasmid.

first: Christine

last: Guthrie


title: Effects of Androstenedione, Ethinyl Estradiol, and Prednisone on Gene Expression in the Male Mouse Liver

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

summary: The goal of this study was to provide insights into the adverse outcome pathways that underlie the liver tumor effects of androstenedione in the mouse liver by comparing gene expression patterns to two liver noncarcinogens, ethinyl estradiol and prednisone.

overall_design: B6C3F1 male mice were exposed for 7 days to control diet or diet containing ethinyl estradiol (EE2) at 1, 2.5, 5, or  10 ppm or prednisone (PRED) at 1.25, 2.5, 5, 25 ppm.  Androstenedione (A4) was administered in 0.5% carboxymethyl cellulose by gavage at 2, 10, 20, and 50 mg/kg/day.  Separate groups of mice were exposed to 50 mg/kg/day A4, 10 ppm EE2 or 25 ppm PRED for 28 days.

first: Chris


title: Active biomonitoring of a polluted harbour using gene expression profiles in caged sentinel thicklip grey mullets (Chelon labrosus).

summary:
Thicklip grey mullet hepatic transcriptome comparission from PASAIA harbour, Basque Country
Active biomonitoring using sentinel species caged in differentially polluted aquatic environments is being implemented worldwide. To determine the biological effects of pollutants in a heavily polluted Basque harbour (Pasaia, 431700N 015500W), two cages specially designed to deploy thicklip grey mullets (Chelon labrosus) were placed in the inner- and outer-harbour. Cages were deployed for 5 and 21 days to determine possible differences between sites, linked to specific chemical burdens. Hepatic gene expression profiles were studied using Q-PCR and a toxicology tailored low density mullet microarray (160 genes). Chemical analysis showed high concentrations of metals, PAHs, PCBs, phthalates, and organometallic compounds at both sites, most chemicals showing slightly higher concentrations in the inner-harbour. Q-PCR expression studies confirmed chemical data as metallothionein and CYP1A showed significant expression upregulation at day 21 at both sites, but showed no differences between sites. The microarray showed gene expression profiles that were able to distinguish mullets according to the site they were deployed in and the day they were captured. Regarding sites, 39 genes showed significant differences at p<0.05 on the last sampling day. Two families of genes are to be highlighted. Phase I and II biotransformation genes CYP2, CYP3 and UGT were upregulated in the inner-harbour together with AhR2 and AhRR. Similarly, TBT binding protein and genes involved in lipid metabolism such us PPARa and CYP7 were upregulated. The latter two genes have also been reported to be regulated by TBT. In summary, the low density microarray designed for mullets proved to be useful to unveil even slight differences in pollutant burdens in field conditions.

overall_design: 24 samples:6 hepatic samples from Inner harbour after 3 days of exposure, 6 hepatic samples from outer harbour after 3 days of exposure, 6 hepatic samples from Inner harbour after 15 days of exposure and 6 hepatic samples from outer harbour after 15 days of exposure

first: Urtzi

last: Izagirre


title: Candidate driver genes in Sѐzary syndrome

city: London

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

country: United Kingdom

institute: Biomedical Research Centre

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

summary: Illumina human Omni5Exome arrays were used to investigate CNVs in Sѐzary syndrome tumours as part of a larger study involving whole exome sequencing of the same samples and targeted resequencing of a further cohort.

overall_design: 16 Samples underwent SNP array including 10 tumour/gDNA matched samples that also underwent whole exome sequencing, public databases were used as further control data for calling CNVs.

first: Wesley

last: Woollard

first: Ania

last: Lorenc

first: Varsha

last: Patel

first: Rosie

last: Butler

first: Anthony

last: Bayega

first: Nelema

last: Begum

first: Farrah

last: Bakr

first: Kiran

last: Dedhia

first: Joshua

last: Fisher

first: Silvia

last: Aguilar-Duran

first: Charlotte

last: Flanagan

first: Aria

last: Ghasemi

first: Ricarda

last: Hoffmann

first: Nubia

last: Castillo-Mosquera

first: Elisabeth

last: Nutall

first: Arisa

last: Paul

first: Ceri

last: Roberts

first: Emmanouil

middle: G

last: Solomonidis

first: Rebecca

last: Tarrant

first: Antoinette

last: Yoxall

first: Carl

middle: Z

last: Beyers

last: Ferreira

first: Isabella

last: Tosi

first: Michael

last: Simpson

first: Emanuele

last: de Rinaldis

first: Tracey

last: Mitchell

first: Sean

last: Whittaker


title: Transcriptomic and Epigenetic Signatures of Mouse Cardiac Progenitor Cells (CHARM)

status: Public on Jul 24 2016

city: Honolulu

first: Yiqiang

last: Zhang

state: HI

address: 651 Ilalo St BSB-311D

department: Anatomy, Biochemistry and Physiology

institute: University of Hawaii Manoa

type: Methylation profiling by genome tiling array

summary: Adult cardioyocytes undergo remarkable dedifferentiation and cell cycle reprogramming/reentery when cultured in mitogen-rich medium, continuously, and give rise to cardiac progenitor cells (CPCs). Using microfluidic device for single-cell capture and whole-transcriptomic amplification, we analyze the whole-genome transcriptomic profile in adult mouse cardiomyocytes (Ctl) and in their derived CPCs, and validate the gene expression by single-cell PCR and PCR array. Using two platforms for DNA methylation profiling: NimbleGen DNA methylation array and CHARM array, the whole-genome DNA methylation profile in myocytes (Ctl) and CPCs were compared and their regulations in relationship to the transcriptomics profile were analyzed. The results demonstrated remarkable molecular reprogramming pertaining to dedifferentiation, loss of cardiac contractile, structure, and function molecules, and reactivation of cell cycle and proliferation genes, significant changes in metabolisms. The reduction of cardiac function and structure genes are highly related to their hypermethylation of the promoter regions. GO and Pathway enrichment analysis revealed distinct coordianted transcriptomic and epigenetic regulation in the CPCs derived from cardiomyocytes.

overall_design: Genomic DNA isolated from adult mouse cardiomyocytes (Ctl) or cardiomyocyte-derived progenitor cells (CPCs) was subjected to digestion by methylcytosine-sensitive enzyme McrBC, and subsequently purification and amplification, labeling and hybridization according to NimbleGen protocol. Percentage methylation, hypermethylation or hypomethylation, and peak enrichment  were assessed using CHARM protocol.

first: Charles

last: Wang


title: Transcriptome profiles derived from parallel venipuncture, dried blood spot (DBS), and saliva samples

first: Steve

last: Cole

summary: Comparison of transcript abundance estimates derived from DBS vs saliva vs gold standard peripheral blood mononuclear cell (PBMC) samples.

overall_design: Gene expression profiling was conducted using parallel collection and assay of venipuncture blood samples (PBMC), DBS samples, and saliva. Data come from 58 community dwelling adults recruited from the Los Angeles metropolitan area.  Analyzed data include basic demographic characteristics (age, sex, race/ethnicity) and body mass index (BMI) as well as RNA indicators of major leukocyte subset prevalence (i.e., estimated abundance of mRNA for CD3, CD4, CD8, CD19, FCGR3A/CD16, NCAM1/CD56, and CD14; all provided here as log2-transformed values of normalized gene expression data).  Categorial variables were coded 0=no/absent and 1=yes/present.


title: Cis-encoded sRNAs repress expression of polysaccharide utilization loci in Bacteroides fragilis 638R

city: Greenville

middle: Jeffrey

last: Smith

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

type:
Expression profiling by array
Third-party reanalysis

summary: The phylum Bacteroidetes is a major component of the human gut microbiota which has a broad impact on the development and physiology of its host, and a potential role in a wide range of disease syndromes1-3. The predominance of Bacteroidetes and the genus Bacteroides in the distal gut is due in large part to the expansion of paralogous gene clusters, termed  Polysaccharide Utilization Loci (PULs), dedicated to the uptake and catabolism of host derived and dietary polysaccharides4,5. It is generally thought that the diversity of PULs is key to Bacteroides successful competition for nutrients in the gut environment6. The nutritive value of the available polysaccharides varies greatly and thus their utilization is hierarchical and strictly controlled. A typical PUL includes regulatory genes that control expression in response to the presence of specific glycan substrates. However the existence of additional regulatory mechanisms has been predicted to explain phenomena such as the hierarchical control, catabolite repression, and the fine tuning of gene expression to match catabolic activity7-9. Using Bacteroides fragilis as a model organism, this report describes a previously unknown layer of regulatory control in which cis-encoded antisense small RNAs (sRNA) act as repressors of the PULs’ catabolic genes. Nearly 30% of B. fragilis PULs are subject to this type of sRNA control and these PULs tend to be more closely linked to the utilization of host-derived glycans than dietary polysaccharides. The findings described here indicate the presence of a global  control mechanism that underlies the known regulatory circuits which modulate PUL expression in response to substrate availability, and hence provide novel insight into regulation of the gut Bacteroidetes physiology.

overall_design: This is a 4 chip study with 8 technical replicates on each chip.  This was an in vitro, exploratory study to determine if mutation or overexpression of a sRNA associated with the Don locus would affect gene expression. In vitro cultures were grown in defined media with mucin glycans as the sole carbon source.  The two chips representing growth of the wild type strain (638R) on mucin glycans were also used in a related study GSE53883 (GSM1303101 and GSM1303102).

first: C

first: Yanlu

last: Cao


title: Transcriptomic and Epigenetic Signatures of Mouse Cardiac Progenitor Cells (Methylation 3x720 CpG)

summary: Adult cardioyocytes undergo remarkable dedifferentiation and cell cycle reprogramming/reentery when cultured in mitogen-rich medium, continuously, and give rise to cardiac progenitor cells (CPCs). Using microfluidic device for single-cell capture and whole-transcriptomic amplification, we analyze the whole-genome transcriptomic profile in adult mouse cardiomyocytes (Ctl) and in their derived CPCs, and validate the gene expression by single-cell PCR and PCR array. Using two platforms for DNA methylation profiling: NimbleGen DNA methylation array and CHARM array, the whole-genome DNA methylation profile in myocytes (Ctl) and CPCs were compared and their regulations in relationship to the transcriptomics profile were analyzed. The results demonstrated remarkable molecular reprogramming pertaining to dedifferentiation, loss of cardiac contractile, structure, and fucntion molecules, and reactivation of cell cycle and proliferation genes, significant changes in metabolisms. The reduction of cardiac function and structure genes are highly related to their hypermethylation of the promoter regions. GO and Pathway enrichment analysis revealed distinct coordianted transcriptomic and epigenetic regulation in the CPCs derived from cardiomyocytes.

overall_design: Genomic DNA isolated from adult mouse cardiomyocytes (Ctl) or cardiomyocyte-derived progenitor cells (CPCs) was subjected to digestion by methylcytosine-sensitive enzyme McrBC, and subsequently purification and amplification, labeling and hybridization to the NimbleGen 3x720K DNA methylation Promoter array, according to NimbleGen protocol. Percentage methylation, hypermethylation or hypomethylation, and peak enrichment were assessed using CHARM protocol.


title: RT quantitative PCR analysis of Rosveratrol plus N-acetylcysteine of oxidative stress and inflammation genes in rat choclea.

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

summary: Two month-old male Wistar rats received either resveratrol (10 mg/kg) plus N-acetylcysteine (400 mg/kg) or vehicle during 5 consecutive days. The second day of treatment, a concentrated solution of kanamycin and furosemide was placed on the round window of the right ears of rats receiving treatment or vehicle. Hearing was assessed by recording auditory brainstem responses before and 5, 16 and 23 days after starting the treatment with resveratrol and N-acetylcysteine. Cochlear samples were taken at the end of the treatment (5 days) and once the treatment had been suspended (23 days) to study cochlear cytoarchitecture and the evolution of the expression of oxidative stress, antioxidant defense and inflammation genes by using PCR arrays and RT-qPCR.

overall_design: qPCR gene expression profiling. Cochlea samples from 3-6 animals per group were analised.  The expression of genes related to oxidative stress, antioxidant defense, and inflammation was studied at 5 and 23 days after the initiation of the 5 days treatment with resveratrol plus NAC.

first: Sara

last: Pulido


title: Mycobacterium avium subsp. paratuberculosis (MAP) during bovine monocyte-derived macrophage infection: untreated vs. bafilomcyin A1 treatment

city: Saint Paul

first: Elise

last: Lamont

state: MN

address: 1971 Commonwealth Avenue, Veterinary Science, Room 205

institute: University of Minnesota

summary: Transcriptional profiling of M. avium subsp. paratuberculosis inside bovine monocyte-derived macrophages (MDMs; in vitro infection) during phagosome acidification at 30 min post-infection. M. avium subsp. paratuberculosis profiles from bafilomcyin A1 (acidification inhibitor) treated and untreated monocyte-derived macrophages were compared.

sample_organism: Mycobacterium avium subsp. paratuberculosis K-10

overall_design: Two-condition experiment; 3 control (bafilomcyin treated) and 3 test, independently conducted. 1 control, 1 test per microarray.

first: Sreevatsan

last: Srinand

first: Kugadas

last: Abirami


title: Claudin-based barrier differentiation in the colonic epithelial crypt niche involves Hopx/Klf4 and Tcf7l2/Hnf4-alpha cascades

status: Public on Jul 23 2016

city: New York

first: Loukia

last: Lili

state: NY

address: 770 Lexington Ave, 14-07 14th floor

department: Icahn School of Medicine at Mount Sinai

institute: The Institute for Next Generation Healthcare

summary: Analysis of the complex expression of claudin genes and transcription factors during intestinal epithelial cell differentiation across the crypt-to-surface colonic axis. Characterization of the complex expression gradients of transcription factors Hopx, Hnf4a, Klf4 and Tcfl2 and 12 claudin genes. In vitro confirmatory methods identified two pathways that stimulate claudin expression; Hopx/Klf4 activation of Cldn4, 7 and 15, and Tcf7l2/Hnf4a upregulation of Cldn23. Chromatin Immunoprecipitation confirmed a Tcf7l2/Hnf4a/Claudin23 cascade. Hnf4a conditional knockout mice fail to induce Cldn23 during colonocyte differentiation.

overall_design: The distal colon tissue was obtained from 4 male, 10-12 week old, C57BL/6 (WT) mice. The Arcturus Laser Capture Microdissection (LCM) system (Applied Biosystems/Life Technologies) was used to isolate crypt-base and surface cell populations providing two samples per mouse (crypt-base and surface). This resulted in 8 total samples for microarray analysis.

first: Christopher

middle: T

last: Capaldo


title: Drosophila Oga deletion perturbs O-GlcNAcylation of chromatin factors

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Drosophila development is a complex and dynamic process regulated, in part, by members of the Polycomb (Pc), Trithorax (Trx) and Compass chromatin modifier complexes.  O-GlcNAc Transferase (OGT/SXC) is essential for Pc repression suggesting that the O-GlcNAcylation of proteins plays a key role in regulating development. OGT transfers N-acetyl-D-glucosamine (GlcNAc) onto hydroxyl groups of serine or threonine residues of key transcriptional regulators using the nutrient-derived UDP-GlcNAc as a substrate, which is dynamically removed by O-GlcNAcase (OGA).  We performed ChIP-chip and microarray analysis after OGT or OGA RNAi knockdown in Drosophila S2 cells and found that O-GlcNAc was elevated genome wide particularly at genes related to mitosis and cell cycle in OGA RNAi cells, but not at sites co-occupied by Pc member Pleiohomeotic (Pho), such as the Hox and NK homeobox gene clusters. Microarray analysis suggested that altered O-GlcNAc cycling perturbed the expression of genes associated with morphogenesis and cell cycle regulation. To examine the in vivo consequences of disturbed O-GlcNAc cycling in the whole animal, we produced a null allele of oga (ogadel.1) in Drosophila. Epigenetic activators including Trx group members Trithorax (Trx), Absent small or homeotic discs 1 (Ash1) and Compass member Set1 histone methyltransferases are O-GlcNAc modified in ogadel.1 mutants. ogadel.1 mutants displayed altered expression of a distinct set of cell cycle related genes in ovaries. Our results suggest that the loss of OGA could affect epigenetic machinery by accumulating O-GlcNAc on numerous chromatin factors including Trx, Ash1 and Set1 in Drosophila.

overall_design:
We performed affymetrix tilingarray  analysis after OGT or OGA RNAi knockdown in Drosophila S2 cells to find if that O-GlcNAc was elevated genome wide particularly at genes related to mitosis and cell cycle in OGA RNAi cells, but not at sites co-occupied by Pc member Pleiohomeotic (Pho),
-------------------------------
This represents the gene expression component only

first: Ilhan

last: Akan

first: Dona

last: Love

first: Katryn

last: Harwood

first: Michelle

middle: R

last: Bond

first: J

middle: L

last: Brown

first: Judith

last: Kassis

first: John

last: Hanover


title: Transcriptome analysis of mononuclear cells derived from bone marrow of pediatric patients with acute myeloid leucosis, acute lymphoid leucosis and from heathy donors peripheral blood

status: Public on Jul 20 2016

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: The aim of this research was to explore activation/deactivation of signaling pathways in mononuclear cells from pediatric patients with acute myeloid leucosis and acute lymphoid leucosis.

overall_design: Mononuclear cells were separated shortly after bone marrow or blood samples collection. Cells were obtained by a density gradient centrifugation method using Ficoll. Cells were dissolved in RNALater solution, aliquoted and stored at -20°C till RNA extraction and microarray hybridisation.

first: Olga

last: Mutororva

first: Elena

last: Ilnitskaya

first: Ivan

last: Petrov

first: Maksim

last: Sorokin

first: Anton

last: Buzdin


title: Comparison of testis transcriptome changes resulting from mutations in dany and representative meiotic arrest genes

city: Zurich

first: Christian

middle: F.

last: Lehner

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

summary: The Drosophila gene dany is expressed specifically in spermatocytes and encodes a nuclear protein with similarity to the products of the genes distal antenna (dan) and distal antenna-related (danr). Loss of dany function results in male sterility. Mutant spermatocytes fail to differentiate similar as previously observed in mutants lacking tTAF and tMAC function. Microarray analyses were performed to characterize the effects of loss of dany function on gene expression in testis and for a comparison of the effects with those caused by mutations in the tTAF gene spermatocyte arrest (sa) and the tMAC genes always early (aly) and  matotopetli (topi)

overall_design: RNA was isolated after testis dissection from adult males and used for the production of probes for microarray hybridization. Five different genotypes were used for testis dissection: control, dany mutant, sa mutant, aly mutant, topi mutant. The number of biological replicates per genotypes was between two and four.

first: Stefano

last: Leo

first: Ariane

last: Blattner


title: TOXICOLOGY TAILORED LOW DENSITY MICROARRAY FOR THE THICKLIP GREY MULLET Chelon labrosus DEVELOPMENT, PRODUCTION AND VALIDATION

first: Ibon

last: Cancio

summary: The widely distributed thicklip grey mullet (Chelon labrosus) has been proposed as a suitable sentinel of pollution since it is able to survive heavily polluted marine/estuarine waters. Previous studies applying molecular to histological level biomarkers have indicated that mullets respond to exposure to chemical compounds. Microarrays are used to identify gene pathways responsive to specific chemical exposures. In this context, fragments of 129 genes relevant in peroxisome proliferation, detoxification, lipid metabolism, inflammatory/immune response, metal sequestration, oxidative and general stress, cell cycle regulation and proliferation, apoptosis, protein synthesis/degradation, and endocrine disruption were cloned through homological cloning using degenerate primers for microchip creation. Additional 31 sequences available in databases belonging to mugilid fishes were included in the final Agilent custom-microchip design. Female multitissue transcritome analysis was performed in mullets from Ondarrua. 108 genes showed differential expression when comparing female brain, gonad, gill and liver. Typical brain transcripts such as aromatase or dopamine receptor were expressed preferentially in the brain, whereas liver specific genes were detected in the liver; choriogenin-L, vitellogenins, fibrinogens or hepatocyte growth-factor. Genes related to peroxisome proliferation were systematically overrepresented in gonads.

overall_design:
Female thicklip grey mullet tissue transcriptome comparission from Ondarrua, Basque Country
GSM861357-GSM861379: 23 samples: 5 female samples from Gonad: female-Ondarru (F-L); 6 female samples from gonad: female-Ondarru (F-GO); 6 female samples from gill: female-Ondarru (F-GI); 6 female samples from brain: female-Ondarru (F-B);
GSM886139-GSM886153: 15 samples:  2 intersex samples from Ondarru (I-L); 2 intersex gonad samples: intersex-Ondarru (I-GO); 6 female hepatic samples: female-Arriluze (F-A); 5 male  hepatic samples: male-Arriluze (M-A)

Immature Thicklip grey mullets were exposed to accetone, cadmium, benzo(a)pyrene and to nonylphenol and hepatic transcriptome was compared
GSM886154-GSM886183: 30 samples: immature thicklip grey mullets hepatic samples 6 control seawater exposed samples, 6 acetone exposed samples; 6 cadmium exposed samples, 6 benzo(a)pyrene exposed samples (BAP) and 6 nonylphenol (NP) exposed samples.

first: Oihane

last: Diaz de Cerio

first: Eider

last: Bilbao

first: Urtzi

last: Izagirre

first: Miren

last: Cajaraville


title: Transcriptome analysis of tomato introgression line during fruit development.

city: Sendai

first: Yoshinori

last: Kanayama

state: Miyagi

address: 1-1, Tsutsumidori-amamiyamachi, Aobaku

department: Graduate School of Agricultural Science

institute: Tohoku University

summary: We performed transcriptome analyses throughout fruit development using the tomato cultivar M82 and its near-isogenic line IL8-3, with interesting and useful traits such as a high content of soluble solids. To identify genes that show differential expression between M82 and IL8-3 fruits, we used a custom microarray containing 43,803 tomato probes. Some genes, such as cell wall invertase and sucrose synthase genes, which are encoded by LIN6 (Solyc10g083290) and TOMSSF (Solyc12g009300) respectively, are well known to play a key role in the sink function of fruit. In this study, the levels of LIN6 and TOMSSF transcripts were higher in IL8-3 than in M82 fruit at 20 and 30 DAF, which are developmental stages for starch accumulation and increased hexose content, respectively, in IL8-3 fruit (Ikeda et al. 2013), and decreased to the level of M82 at ripening stage. Similar patterns were observed in many metabolites of glycolysis and the pentose phosphate pathway as well as metabolites in starch and sucrose metabolism.

overall_design: Gene expressions during fruit development were analyzed. Three biological replicates were prepared for each stage, and a total of 24 samples were analyzed.

first: Hiroki

last: Ikeda

first: Tomoki

last: Shibuya

first: Shunsuke

last: Imanishi

first: Hisashi

last: Aso

first: Manabu

last: Nishiyama


title: Transcriptome analisys of bone marrow mononuclear cells derived from pediatric patients with acute myeloid leucosis

first: Maria

last: Suntsova

overall_design: Mononuclear cells were separated shortly after bone marrow samples collection. Cells were obtained by a density gradient centrifugation method using Ficoll.  Cells were dissolved in RNALater solution, aliquoted and stored at -20°C till RNA extraction and microarray hybridisation.

first: Olga

last: Mutororva

first: Elena

last: Ilnitskaya

first: Ivan

last: Petrov


title: mRNA microarray analysis on young adults C.elegans exposed to GO and rGO

status: Public on Jul 19 2016

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

institute: University of Seoul

summary:
In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to GO and rGO on nematode, Caenorhabditis elegans. We performed whole genome DNA microarray experiments using age synchronized young adult C. elegans population exposed to GO and rGO for 24h.
We used whole genome microarrays to screen for global changed in C. elegans transcription profiles and with subsequent quantitative analysis conducted on selected genes.

overall_design: Young adults of C.elegans were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Jinhee

last: Choi

first: Nivedita

last: Chatterjee


title: Coordinate Regulation of Metabolites Glycosylation and Stress Hormones Biosynthesis by TT8 in Arabidopsis

city: Singapore

first: Sanjay

last: Swarup

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

summary: Secondary metabolites play a key role in coordinating ecology and defense strategies of plants. Diversity of these metabolites arise by conjugation of core structures with diverse chemical moieties, such as sugars in glycosylation. Active pools of phytohormones, including those involved in plant stress response are also regulated by glycosylation. While, much is known about the enzymes involved in glycosylation, we know little about their regulation or coordination with other processes. We characterized the flavonoid pathway transcription factor, TRANSPARENT TESTA 8 (TT8) in Arabidopsis thaliana, using an integrative omics strategy. This approach provides a systems level understanding of the cellular machinery that is used to generate metabolite diversity by glycosylation. Metabolomics analysis of TT8 loss-of-function and inducible overexpression lines showed that TT8 coordinates glycosylation of not only flavonoids, but also nucleotides, thus, implicating TT8 in regulating pools of activated nucleotide sugars. Transcriptome and promoter network analyses revealed that TT8 regulome included sugar transporters, proteins involved in sugar binding and sequestration, and a number of carbohydrate active enzymes. Importantly, TT8 affects stress response, along with brassinosteroid and jasmonic acid biosynthesis, by directly binding to the promoters of key genes of these processes. This combined effect on metabolites glycosylation and stress hormones by TT8 inducible overexpression led to significant increase in tolerance towards multiple abiotic and biotic stresses. Conversely, loss of TT8 leads to increased sensitivity to these stresses. Thus, the transcription factor TT8 is an integrator of secondary metabolism and stress response. These findings provide novel approaches to improve broad-spectrum stress tolerance.

overall_design:
Gene expression analysis for 6-day old Arabidopsis thaliana seedling were performed for TT8 loss-of-function line, tt8-3 (in Ws background), and its wild type background control, Ws.
Two independent biological replicates for each line were hybridized onto two slides of Agilent SurePrint G2 Agilent Arabidopsis V4 (4x44K), with each slide having two technical replicates for each line.
Contributors: Amit Rai, Shivshankar Umashankar, Megha, Lim Boon Kiat, Johanan Aow Shao Bing, Sanjay Swarup.

first: Amit

last: Rai

first: Shivshankar

last: Umashankar

first: Megha

first: Lim

middle: B

last: Kiat

first: Johanan

last: Aow Shao Bing


title: Regulation of Fetal Liver Growth in a Model of Diet Restriction in the Pregnant Rat

status: Public on Jul 18 2016

city: Providence

first: Joan

last: Boylan

state: RI

address: 593 Eddy Street

department: Pediatrics

institute: Rhode Island Hospital

summary: The present study was designed to test the hypothesis that limited growth of the fetal liver in the model of maternal fasting is independent of well-characterized signaling mechanisms that are known to regulate somatic growth in adult animals.

overall_design: We profiled the fetal hepatic transcriptome and translatome in control (n=3) and IUGR (n=3) fetuses. To induce IUGR, pregnant dams were fasted for 48hr starting on E17, term being 21 days. Fetal rats were delivered by C-section and livers were removed. All livers were flash frozen in liquid nitrogen. RNA was extracted from polysomes that were generated using sucrose density fraction, as well as total liver. RNA was hybridized to Affymetrix GeneChip Rat Gene 1.0 ST Arrays.

first: Philip

middle: A

last: Gruppuso

first: Jennifer

last: Sanders


title: Identification of genes and proteins associated with anagen wool growth

city: Qingdao

first: Hegang

last: Li

state: Shandong

address: 149 Xiazhuang Road, Licang District

department: Animal Reproduction and Breeding

country: China

institute: Qingdao Institute of Animal Science and Veterinary Medicine

summary: Sheep provide considerable materials for the animal fibre industry. Identifying genes of major effect for wool growth would offer strategies for improving the quality and increasing the yield of fine wool. In this study, we employed Agilent Sheep Gene Expression Microarray and proteomic technology to investigate the gene expression patterns of body side skin (more wool growing) in Aohan fine wool sheep (a Chinese indigenous breed) in comparison with groin skin (no wool growing) at the anagen stage of wool follicle. Microarray study revealed that 4772 probes were differentially expressed, including 2071 upregulated and 2701 downregulated probes in the comparisons of body side skin versus groin skin (S/G). The microarray results were verified by means of quantitative PCR. 1099 probes were assigned to unique genes/transcripts. The number of distinct genes/transcripts (annotated) was 926, of which 352 were up-regulated and 574 were down-regulated. In S/G, 13 genes were up-regulated by more than 10-fold, while 60 genes were down-regulated by more than 10-fold.  Further analysis revealed that the majority of the genes possibly related to the wool growth could be assigned into the categories including regulation of cell division, intermediate filament, cytoskeletal part and growth factor activity. Several potential gene families might participate in hair growth regulation, including fibroblast growth factors, transforming growth factor-β, WNTs, insulin-like growth factor, vascular endothelial growth factors and so on. Proteomic analysis also got 196 differentially expressed protein points, of which 121 were identified as single protein points. Furthermore, according to the results at both mRNA and protein levels, similar regulation mechanism of gene activity might be engaged during skin development and embryo development.

overall_design: One ram and two ewes of 12-month-old Aohan fine wool sheep were used in the microarray study. These animals were half sibs (sharing the same father). In August 2010, two areas of full-thickness skin were sampled from the same animal under local anaesthesia: body side skin (wool bearing) and groin skin (non-wool bearing) for microarray and proteomic experiments. The area of each sample was about 1 cm2. All samples were immediately put into collection tubes and stored in liquid nitrogen for RNA and protein extraction. A total of 15, 208 probes were spotted on this Agilent Sheep Gene Expression Microarray (Santa Clara, CA, USA).

first: Jinshan

last: Zhao

last: Liu

first: Kaidong

first: Jianning

last: He

first: Juanjuan

last: Yu

first: Ran

last: Bu

first: Ming

last: Cheng

first: Wei

last: De

first: Jifeng


title: mRNA microarray analysis on young adults C.elegans exposed to UV, TiO2 and UV+TiO2

status: Public on Jul 16 2016

first: jinhee

last: choi

summary:
In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to UV, TiO2 and UV+TiO2 on nematode, Caenorhabditis elegans. We performed whole genome DNA microarray experiments using age synchronized young adult C. elegans population exposed to UV, TiO2 and UV+TiO2 for 24h.
We used whole genome microarrays to screen for global changed in C. elegans transcription profiles and with subsequent quantitative analysis conducted on selected genes.

overall_design: Young adults C. elegans were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Jinhee

last: Choi

first: Nivedita

last: Chatterjee


title: Comparison of the Global Gene Expression Profiles in the IFNT treatment bovine cells

city: Sapporo

first: Noriyuki

last: Toji

state: Hokkaido

address: North10-West8, Kita-ku,

institute: Hokkaido university

summary: To examine the difference of the bovine cells between PBS and IFNT treatment, gene expression profiles were compared. The expressions of 902 genes were significantly higher in granulocytes with IFNT treament than those PBS treatment, whereas 1810 genes were lower (Fold change<1, P=0.05 or lower). The expressions of 555 genes were significantly higher in Bovine Endometrial Stromal cells (BES) with IFNT treatment than those PBS treatment, whereas 874 genes were lower (Fold change<1, P=0.05 or Low)

overall_design: Bovine granulocytes and BES were treated with PBS or IFNT

first: Keiichiro

last: Kizaki


title: miRNA expression in moncytes in response to estradiol

status: Public on Jul 12 2016

city: Dublin

first: Paul

middle: Joseph

last: McKiernan

address: Beaumont Hospital - ERC

department: Medicine

country: Ireland

institute: RCSI

summary:
This profiling experiment evaluates the global changes in miRNA expression in monocytic cells in response to 10 nM Estradiol treatment.
Levels of circulating 17β-estradiol (E2) may influence the progression of many human diseases. We hypothesize that E2 modulates the inflammatory response of circulating innate immune cells through microRNA (miRNA)-based modulation of secretory leucoprotease inhibitor (SLPI), a multifunctional antiprotease with immunomodulatory functions. Monocytes were treated with E2 or control, and differentially expressed miRNAs in monocytes were identified using PCR profiling. Cells were transfected with miRNA mimics or antimiRs and SLPI mRNA and protein levels were quantified by qPCR and ELISA, respectively. Luciferase activity assay was performed using SLPI-3’UTR reporter constructs. ChIP was carried out on monocytes treated with E2. SLPI expression is downregulated, and miR-19 is upregulated in response to E2 in monocytes, via increased MIR17HG promoter activity mediated by c-MYC. Transfection of monocytic cells with premiR-19b reduced SLPI expression. This was abrogated using antimiRs against miR-19b. miR-19b directly binds the SLPI 3’UTR as determined by luciferase activity assay. The data show that E2 decreases expression of SLPI in human monocytic cells, via changes in miRNA expression and further highlights the potential for E2 to modulate key components of innate immunity. Modulation of these miRNAs may offer a new therapeutic approach in the treatment of chronic inflammatory diseases.

middle: J


title: Ascl2 acts as an R-spondin/Wnt responsive switch to control stemness in intestinal crypts [ChIP-seq]

status: Public on Jul 15 2016

city: Utrecht

first: Jurian

last: Schuijers

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Insitute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Wnt signals control three functions of intestinal crypts: maintenance of Lgr5 stem cells, proliferation of transit-amplifying daughters and formation of Paneth cells. Here, we study how the Wnt effector β-catenin/Tcf4 cooperates with the Wnt-activated transcription factor Ascl2 to control a stem cell transcription program. DNA elements that are co-occupied and synergistically regulated by Ascl2 and Tcf4 specifically map to stem cell genes. In vitro, Tcf4-/- mini-guts are rescued by Ascl2 expression, while Ascl2-/- organoids are rescued by Wnt signaling. A direct auto-activatory loop leads to an on/off expression pattern of Ascl2 with a threshold that depends on the previous state. Wnt/R-spondin1 activates this loop. This mechanism interprets Wnt levels in crypts and translates this continuous signal into a discrete Ascl2 “on” or “off” decision. In turn Ascl2, together with β-catenin/Tcf, activates stem cell genes. Thus, Ascl2 forms a transcriptional 'stemness switch' that is both Wnt-responsive and Wnt-dependent

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Examination of Tcf4, B-catenin and Ascl2 DNA occupancy in murine intestinal organoids and human colorectal cancer cell lines
*** Original raw files unavailable due to loss during backup ***

first: J

first: H

last: Clevers


title: Expression data from uterus tissue of sheep

city: Beijing

first: Xihui

last: Sheng

address: No.7 Beinong Road, Huilongguan Town, Changping District

institute: Beijing university of agriculture

summary:
Embryo implantation is an essential step for the establishment of pregnancy and is crucial for the successful embryo transplantation of in vitro fertilization embryos. The successful implantation of an embryo depends upon cellular and molecular dialog between the uterus and the embryo.
We used microarrays to detail the key regulated genes underlying embryo implantation process in sheep.

overall_design: In this study, all ewes were assigned to two experimental groups randomly as follows: in vivo embryo (IVV) group (n = 12) and in vitro embryo (IVT) group (n = 9). The ewes of IVV group were mated with fertile rams of the same strain to induce pregnancy respectively. In addition, the ewes of IVT group were transplanted 3 in vitro fertilization (IVF) embryos at 4 ~ 8 cell stage respectively after synchronization of estrus. Uterus tissue at implantation and inter-implantation sites of both groups were collected at successive stages of implantation period and used for microarray analysis.

first: Yong

last: Guo

first: Hemin

last: Ni


title: Gene expresssion changes associated to diet induced fatty liver in hamster

status: Public on Jul 14 2016

city: Reus

first: Josep

middle: Maria

last: del Bas

state: Tarragona

address: Avd Universitat 1

institute: Centre tecnològic de Nutrició i Salut

summary: Our aim was to study the gene expression changes associated to the development of non hepatic steatohepatitis from simple steatosis in a model of diet induced obesity in hamster (mesocricetus auratus)

overall_design: 10 golden hamsters (mesocricetus auratus) were fed a standard diet (STD) and 10 more a high fat diet (HFD). For gene expresion analysis, RNA from STD were pooled and gene expression changes of each HFD was evaluated againts the STD pool.

last: delBas


title: DNA methylation proﬁling in GC-2 cells following  2×10-5M diethylstilbestrol exposure

status: Public on Jul 08 2016

city: ChongqingPR China

first: Li

last: Yin

address: 69 Hongguang Road Huaxi Street, Banan District

department: College of Pharmacy and Biological Engineering

institute: Chongqing University of Technology

summary:
Aberrant DNA methylation expression has been related to diethylstilbestrol exposure, but little is known about effect of diethylstilbestrol exposure on DNA methylation in male reproductive system.
To identify DNA methylation varied in GC2 cells treated with DMSO and diethylstilbestrol, we performed Gene promoter methylation using an Affymetrix Mouse Promoter 1.0R Array to analysis different DNA methylation pattern.

overall_design: Mouse spermatocyte-derived GC-2 cells were treated with 2×10-5M diethylstilbestrol for 72h, and DMSO was added to control cells. DNA methylation expression was profiled using Affymetrix GeneChip Mouse Promoter 1.0R Array.

first: Jin-yi

last: Liu


title: Genomic profiling of murine mammary tumors identifies potential personalized drug targets for p53-deficient mammary cancers

city: Chapel Hill

first: Charles

middle: M.

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Breast cancer is the second leading cause of cancer related death in American women. Patient care is complicated by inherent tumor heterogeneity that can be classified into at least six intrinsic subtypes. While targeted treatments are standard of care for most subtypes, there remains a clinical need for targeted therapies against basal-like tumors that are typically ‘triple negative breast cancers’. As such, the molecular mechanisms underlying basal-like tumors are under intense investigation to identify genetic drivers and possible drug targets of this subtype. Somatic p53 mutations are one of the most common genetic events in basal-like breast tumors. This genetic foundation primes cells to accumulate secondary genetic aberrations, a subset of which is predicted to promote tumorigenesis. To identify additional drivers of basal-like tumors, a comparative study between human and murine tumors was performed utilizing a p53null mammary transplant murine model. The p53null mammary transplant murine model produced a genomically diverse set of tumors, a subset of which we show resemble the human basal-like subtype. Microarray and sequencing technologies were used to interrogate the secondary genetic aberrations of these murine tumors which were then compared to human basal-like tumors to highlight conserved features. Of the ‘omic’ datasets analyzed, DNA copy number variation produced the largest number of conserved candidate driver genes. These candidate gene lists were further filtered using a DNA-RNA Pearson correlation cutoff of 0.5 and a requirement that the gene was deemed essential in at least one human basal-like cell line from a genome-wide RNA-mediated interference screen database. These steps highlighted seven potential driver genes that are at amplified loci in both murine and human basal-like tumors: Atp11a, Col4a2, Cul4a, Lamp1, Met, Pnpla6, and Tubgcp3. Inhibition of Met using Crizotinib caused Met amplified tumors to regress, confirming that this genetic event is a driver in a subset of p53null transplant mammary tumors. This study identifies MET as a driver of basal-like murine tumors, thus identifying a shared potential driver of human basal-like breast cancer. Our results also highlight the importance of comparative genomic studies for discovering drug targets and for providing models to study whether patient populations are likely to respond to selective targeted treatments.

overall_design: Agilent CGH microarrays were performed comparing DNA from BALB/c p53null mammary transplant tumors to DNA from FVB wild-type mice

first: Adam

middle: D

last: Pfefferle

first: Yash

middle: N

last: Agrawal

first: Jason

middle: I

last: Herschkowitz

first: Dan

middle: C

last: Koboldt

first: Krishna

last: Kanchi

first: Elaine

last: Mardis

first: Jeffrey

last: Rosen


title: Real-time quantitative PCR analysis of long non-codign RNAs transcripts in non-end stage heart failure patients

status: Public on Jul 11 2016

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

summary: Left ventricle (LV) cardiac biopsies from patients affected by non-end-stage dilated hypokinetic ischemic cardiomyopathy (HF) where collected during Surgical Ventricular Restoration procedure.

overall_design: Total RNA from tissues was extracted using TRIzol (Life Technologies, Thermo Fisher Scientific Inc.) and long noncoding RNA (lncRNAs) expression profiles were measured using primers from the Disease-related human lncRNA Profiler (System Biosciences) in 13 HF patients and in 12 age- and sex-matched controls, not affected from CVDs .1 µg total RNA was retro-transcribed using the SuperScript III Reverse Transcriptase kit (Life Technologies, Thermo Fisher Scientific Inc.) according to the manufacturer’s instructions. cDNAs were analyzed using the SYBR-GREEN qPCR method (Life Technologies, Thermo Fisher Scientific Inc.) according to the manufacturer’s instructions.

first: Simona

last: Greco

first: Lorenzo

last: Menicanti

first: Serenella

last: Castelvecchio


title: microRNA expression in the megabladder mouse model of CKD and CON

city: Columbus

first: Susan

last: Ingraham

address: 700 Childrens Drive

institute: Nationwide Children's Hospital

summary: Congenital obstructive nephropathy (CON) is the leading cause of chronic kidney disease (CKD) in children. CON is a complex disease process involving pathological changes in kidney development and function that occur as a result of obstructed antegrade urine flow beginning in utero. The megabladder (mgb-/-) mouse is an animal model of CON that develops kidney disease secondary to a bladder-specific defect in smooth muscle development. Expression levels of specific microRNAs were compared by microarray analysis on the Agilent platform and by quantitative PCR (qPCR) of kidney samples from wild type and mgb-/- mice.

overall_design: MicroRNA expression was measured in control and megabladder mouse kidneys. A total of 4 control kidneys were compared to 4 mutant kidneys from age-matched male animals.

first: Michael

middle: E

last: Wilhide

first: Ahmad

middle: Z

last: Mohamed

first: Brian

last: Becknell

first: Ashley

last: Jackson

first: Kirk

middle: M

last: McHugh


title: ChIP-on-chip from MDA-MB-231 cells with PHF1, CUL4B and PRMT5

status: Public on Jul 07 2016

city: Tianjin

first: Yan

last: Wang

address: #22 Qixiangtai Road

department: Department of Biochemistry and Molecular Biology

institute: Tianjin Medical University

type: Genome binding/occupancy profiling by genome tiling array

summary:
It has been reported that PHF1, CUL4B and PRMT5 all play important roles in epigenetic regulation. We reported that PHF1, CRL4B and PRMT5 may act as a complex in transcriptional regulation and have a vital effect in breast cancer progression. So we performed ChIP-on-chip assays to find unique promoters co-targeted by PHF1, CUL4B and PRMT5.
PHF1, CUL4B and PRMT5 have a predominant cooperation, at least in MDA-MB-231 cells.

overall_design: comparison of PHF1, CUL4B and PRMT5 target genes


title: Small Traditional Human Communities Sustain Genomic Diversity Over Microgeographic Scales Despite Linguistic Isolation

city: Tucson

first: Tatiana

last: Karafet

state: AZ

address: BSW #246, 1041 E Lowell Str.

department: ARL

institute: University of Arizona

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

summary: Illumina single nucleotide polymorphism (SNP) array data were generated to study genome-wide patterns of genomic variation on Sumba and Timor, two small islands in eastern Indonesia. Both islands have a complex history from their initial settlement ~50,000 years ago, to admixture with Austronesian-speaking groups during the Neolithic farming expansion, and more recent intra-island gene flow and community interactions. As part of this detailed microgeographic study, we also collected associated cultural and linguistic information. The primary study location was Sumba, for which we genotyped SNPs in 235 individuals from eight communities that span the island, including groups that speak most of Sumba’s nine languages. Particular attention was paid to genomic data that are informative for recent aspects of population history, including reconstructions of past gene flow, socio-genetic interactions and possible signals of selection.

overall_design: 240 samples from 10 populations have been genotyped using the Illumina platform GPL19699

first: J

middle: S

last: Lansing

first: Murray

middle: P

last: Cox

first: Herawati

last: Sudoyo

first: Olga

middle: V

last: Savina


title: Antifungal effect of Sesamol (Ses) on C. albicans SC5314

city: Gurgaon

first: Saif

last: Hameed

state: Haryana

address: Amity Education Valley

institute: Amity University Haryana

summary: Transcriptional profiling of Candida cells comparing the control vs Ses treated cells

overall_design: Organism : Candida albicans, Agilent custom C.albicans Gene Expression  8x15k Array (AMADID: 026377) designed by Genotypic Technology Private Limited

first: Moiz

last: Ansari

first: Zeeshan

last: Fatima


title: High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2 [tiling array]

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary: Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally-encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures and exposing the interplay of plasmid and chromosomal functions. All xyl sequences were transcribed in response to aromatic substrates and the 3'-termini of both upper and lower mRNA operons extended beyond the ir coding regions, i.e., the 3'-end of the lower operon mRNA penetrated into the convergent xylS regulatory gene. Furthermore, xylR mRNA for the master m-xylene responsive regulator of the system was decreased by aromatic substrates, while the cognate upper operon mRNA was evenly stable throughout its full length. RNA-seq confirmed these data at a single-nucleotide level and refined the formerly misannotated xylL sequence. The chromosomal ortho route for degradation of benzoate (the ben, cat clusters and some pca genes) was activated by this aromatic, but not by the TOL substrates, toluene or m-xylene. We advocate this scenario as a testbed of natural 16 retroactivity between a pre-existing metabolic network and a new biochemical pathway implanted through gene transfer.

overall_design: Custom Agilent tiling microarrays containing relevant regions of pWW0 plasmid were hybridized with two RNA samples each: altered and control (two channel-format). Four biological replicates were hybridized independently for each comparison.

first: Juhyun

last: Kim

first: Danilo

last: Pérez-Pantoja

first: Rafael

last: Silva-Rocha

first: Victor

last: de Lorenzo


title: Early life adversity alters normal sex-dependent developmental dynamics of DNA methylation in rhesus monkeys

status: Public on Jul 06 2016

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

summary: This study mapped the genome wide DNA methylation changes in CD3+ T lymphocytes from rhesus monkeys from postnatal day 14 through two years of age in both males and females and determined the impact of maternal deprivation on the DNA methylation profile. We show here that DNA methylation profiles evolve from birth to adolescence and are sex dependent. DNA methylation changes accompany imposed weaning, attenuating the difference between males and females.

overall_design: Altogether 71 T cell DNA samples were used in 4 different groups (male control, male stress, female control, female stress) at 4 different developmental stage (1 month, before weaning at 6-7 months, after weaning at 9-10 months, and after 2 years at 26-30 months) having 3-6 samples per each group. The DNA samples were pooled in each group and then subjected to Whole Genome Amplification in triplicates.

first: Renaud

last: Massart

first: Matthew

last: Suderman

first: Stephen

last: Suomi


title: CCL19 as a Chemokine Risk Factor for Posttreatment Lyme Disease

city: Stanford

first: William

last: Robinson

state: CA

address: 269 Campus Dr

institute: Stanford University

summary: Approximately 10% to 20% of patients optimally treated for early Lyme disease develop persistent symptoms of unknown pathophysiology termed posttreatment Lyme disease syndrome (PTLDS). The objective of this study was to investigate associations between PTLDS and immune mediator levels during acute illness and at several time points following treatment. Seventy-six participants with physician-documented erythema migrans and 26 healthy controls with no history of Lyme disease were enrolled. Sixty-four cytokines, chemokines, and inflammatory markers were measured at each visit for a total of 6 visits over 1 year. An operationalized definition of PTLDS incorporating symptoms and functional impact was applied at 6 months and 1 year following treatment completion, and clinical outcome groups were defined as the return-to-health, symptoms-only, and PTLDS groups. Significance analysis of microarrays identified 7 of the 64 immune mediators to be differentially regulated by group. Generalized logit regressions controlling for potential confounders identified posttreatment levels of the T-cell chemokine CCL19 to be independently associated with clinical outcome group. Receiver operating characteristic analysis identified a CCL19 cutoff of >111.67 pg/ml at 1 month following treatment completion to be 82% sensitive and 83% specific for later PTLDS. We speculate that persistently elevated CCL19 levels among participants with PTLDS may reflect ongoing, immune-driven reactions at sites distal to secondary lymphoid tissue. Our findings suggest the relevance of CCL19 both during acute infection and as an immunologic risk factor for PTLDS during the posttreatment phase. Identification of a potential biomarker predictor for PTLDS provides the opportunity to better understand its pathophysiology and to develop early interventions in the context of appropriate and specific clinical information.

overall_design: A total of 65 immune and inflammatory mediators were profiled in serum samples derived from early Lyme disease patients and age- and sex-matched controls. These samples have been generated as part of a prospective cohort study that includes a well-defined cohort of patients with acute Lyme disease enrolled from a Lyme endemic area of the mid-Atlantic United States. Only patients with untreated, confirmed early Lyme disease manifesting an active EM skin lesion at the time of enrollment, as defined by CDC case criteria are eligible. Patients with a history of prior Lyme disease or the presence of confounding preexisting medical conditions associated with prolonged fatigue, pain or neurocognitive symptoms are excluded. Controls are nonhospitalized age- and sex-matched and have no prior history of Lyme disease or any exclusionary medical conditions including lack of inflammatory disorders.

first: John

last: Aucott

first: Mark

last: Soloski

first: Alison

last: Rebman

first: Lauren

last: Crowder

last: Lahey

first: Catriona

last: Wagner

first: Nithya

last: Lingampalli

middle: H

first: Kathleen

middle: T

last: Bechtold


title: DNA methylation in CD34 positive cells derived from cord blood at birth following prenatal stress

summary: DNA methylation profiling of CD34 positive cells derived from cord blood at birth following prenatal stress

overall_design: The groups consist of 8 individuals with low levels of prenatal stress (control) and 10 individuals with high levels of prenatal stress (stress)

first: Vanessa

last: Nieratschker


title: Gene expression profile for SvGRP-transformant and WT Arabidopsis seedlings under salt stress

city: Hachioji

first: Yuichi

last: Tada

state: Tokyo

address: 1404-1 Katakura

institute: Tokyo University of Technology

summary: Sprobolus virginicus is a halophytic C4 grass found in worldwide from tropical to warm temperate regions. A Japanese genotype showed a salinity tolerance up to 1,500 mM NaCl, a three-fold higher concentration than seawater salinity. To identify key genes involved in the regulation of salt tolerance in S. virginicus, random cDNA libraries were constructed from salt-treated leaves, and were introduced into Arabidopsis for salt tolerant plant screening. Eight independent transgenic lines were found to be more salt tolerant than wild type from the screen of 3011 lines on the medium containing 175 mM NaCl. Among the selected lines, two contained cDNAs encoding glycine-rich RNA-binding proteins (GRPs). To identify transcriptomic change in the GRP-transgenic line, we performed microarray analysis of the transgenic line and WTunder salt stress.

overall_design: Gene expression in transgenic Arabidopsis expressing a gene for glycine-rich RNA-binding protein from S. virginics was analysed. Five-day old transgenic and WT (Col-0) seedlings were transplanted to medium supplemented with 0 or 150 mM NaCl, harvested  at 24 h after transplanting, and used for RNA extraction. n=3

first: Tada

last: Yuichi

first: Katsuhara

last: Maki


title: Whole brain gene expression study of dominant, subordinate and brooding females of the African cichlid fish A. burtoni

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

summary:
Comparison of social dominance phenotypes induced in the cichlid A. burtoni females with the goal of comparing to other gene expression profiles of social dominance Used platform GPL928
In many species, under varying ecological conditions, social interactions among individuals result in the formation dominance hierarchies. Despite general similarities, there are substantial differences across species, populations, environments, life stages, sexes, and individuals. Understanding the proximate mechanisms of this variation is an important step toward understanding the evolution of social behavior. However, physiological changes associated with dominance such as gonadal maturation and somatic growth, often complicate efforts to identify the specific underlying mechanisms. We demonstrate complementary analysis tools to allow a comparative approach to high-throughput expression profiling that allow us to both test a priori hypotheses and generate new hypotheses about the mechanisms and evolution of social dominance. Using experimental manipulation to produce female dominance hierarchies in the cichlid A. burtoni, heralded as a genomic model of social dominance, we generate gene lists, and assess molecular gene modules.  We demonstrate a general pattern of “masculinization” of the female neural gene expression profile and compare expression biases between male and female dominance hierarchies. Using a threshold-free approach to identify correlation throughout gene ranked lists, we query previously published datasets from maternal behavior, alternative reproductive tactics, cooperative breeding and sex-role reversal to describe correlations among neural gene expression profiles. These complementary approaches capitalize on the high-throughput gene expression profiling from similar behavioral phenotypes in order to address the mechanism associated with social dominance behavioral phenotypes.

overall_design: This is a  loop design experiment with n=5/phenotype, each labeled 4 times (twice in each color), and competitively hybridized against 2 individuals of the other phenotypes. Duplicate arrays were run for each hybridization A & B

first: Hans

last: Hofmann


title: Epigenome analysis of Peripheral Blood samples from 53 pediatric ASD patients and 10 pediatric controls

city: Barcelona

first: Ivon

last: Cuscó

address: C/Dr Aiguader, 88

department: Departament de Ciències Experimentals i de la Salut

institute: Universitat Pompeu Fabra

summary: Genome wide DNA methylation profiling of blood samples from patients with ASD and controls. The IlluminaInfinium HumanMethylation450 BeadChip  was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Samples included 53 individuals with idiopathic ASD (aged 2 to 14) and 10 age-matched controls.

overall_design: Bisulphite converted DNA from the 63 samples were hybridized to the  IlluminaInfinium HumanMethylation450 BeadChip

first: Luis

middle: A

last: Pérez Jurado


title: DNA methylation signatures of parental deprivation in peripheral tissues of male rhesus macaques

first: Moshe

last: Szyf

summary: This study mapped the genome wide DNA methylation changes in whole blood and buccal swab samples of 2 year old male rhesus monkeys subjected to parental deprivation in their first months of life (surrogate peer-reared condition).

overall_design: Equal numbers of control mother-reared (MR) and surrogate peer-reared (SPR) male monkeys whole blood (5 vs 5) and buccal swab samples (3 vs 3) were analyzed by methylated DNA immunoprecipitation (MeDIP) coupled with promoter tiling arrays.

first: Renaud

last: Massart

first: Matthew

middle: J

last: Suderman

first: Zsofia

last: Nemoda

first: Angela

last: Ruggiero

first: Stephen

last: Suomi


title: Differentially expressed Transcribed ultraconserved regions (T-UCRs) in Crohn's disease (CD) comparing to normal controls (NC)

status: Public on Jul 05 2016

city: Shanghai

first: Xiaoxian

last: Qian

address: No. 160 Pu Jian Ave, Shanghai 200127, China.

department: Gastroenterology and Hepatology

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: To date, 481 transcribed ultraconserved regions (T-UCRs) have been discovered in human genome. We aimed to investigate their characteristics in Crohn’s disease (CD) with conparison to healthy normal controls, to reveal differentially expressed T-UCRs.

overall_design: 3 CD patients and 3 NC volunteers were recruited in this study. With colonoscopy, colon mocosa  pinch biopsy samles were got at  inflammed site in CD patients and normal sites in  NC volunteers respectively.

first: Jun

last: Shen

first: Zhihua

last: Ran


title: Male Rat DNA methylation in the Prefrontal Cortex at postnatal day 62 following prenatal restraint stress

summary: DNA methylation profiling of Prefrontal Cortex of male rats at postnatal day 62 whose mothers were exposed to restraint stress from gestation day 14 until delivery

overall_design: The groups consist of 1. Control rats (Ctrl) 2. Prenatally stressed rats (PNS)

first: Marco

last: Riva

first: Alessia

last: Luoni


title: High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the assembly-versus-assembly method

city: Chengdu

first: Mingzhou

last: Li

state: Sichuan

address: No.211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

summary: Porcine 60K BeadChip genotyping arrays (Illumina)  are increasingly being applied in pig genomics to validate SNPs identified by re-sequencing or assembly-versus-assembly method. Here we report that more than 98% SNPs identified from the porcine 60K BeadChip genotyping array (Illumina) were consistent with the SNPs identified from the assembly-based method. This result demonstrates that whole-genome de novo assembly is a reliable approach to deriving accurate maps of SNPs.

overall_design: To compare SNPs identified by genotyping arrays and de novo assembly method, we genotyped 10 pig breeds by porcine 60K BeadChip genotyping array (Illumina), including 1 berkshire pig, 1 hampshire pig, 1 landrace pig, 1 large white pig,1 piétrain pig, 1 bamei pig,1 jinhua pig, 1 meishan pig, 1  rongchang pig and 1 Tibetan wild boar.

first: Li

last: Mingzhou

first: Tang

last: Qianzi


title: Ankyrin-3 as a Molecular Marker of Early Life Stress and Vulnerability to Psychiatric Disorders

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

sample_organism:
Macaca mulatta
Homo sapiens
Rattus norvegicus

overall_design: Refer to individual Series


title: Gene expression profiles of PML knockdown or WDR4 overexpression in A549 cells

status: Public on Jul 04 2016

city: Taipei

first: Ya-Ting

last: Wang

address: 6F.-602, IBC, No.128, Sec. 2, Academia Rd., Nangang Dist.

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: Lung cancer cell line, A549 cells, was transfected with siPML or siCtrl for 48hr to knockdown PML expression. WDR4 or vector was overexpressed in A549 cells for 48hr. These four sets of cells were then subjected to microarray profiling using the Human OneArray microarray (version HOA6.1, GEO Platform GPL19137) from Phalanx Biotech Group.

overall_design: Comparison of transcriptomes from siPML/siCtrl and W4/vec in A549 cells

first: Y

first: R

last: Chen


title: Carcinoma of the colon and rectum with deregulation of insulin-like growth factor 2 signaling: clinical and molecular implications

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: We here show that loss of imprinting (LOI) of IGF2 is a frequent and early event in the development of colon cancer and occurs throughout the large intestine. LOI leads to AKT1-dependent activation and suppression of a defined set of genes, many of which are cell cycle related. Our results further showed that IGF2 induces non-canonical wnt signaling. We hypothesize that IGF2 and Wnt5a cooperate in cancer progression. LOI is an attractive target for tumor prevention or targeted therapy.

overall_design: This is a comparison of colon cancer samples with (LOI) and without (ROI) loss of imprining of IGF2. All cases were from the sigmoid colon and were in UICC tumor stage pT2 N0 M0.

first: Philipp

last: Ströbel


title: Methylation profiling of 3T3-L1 Cells: Control vs slincRAD-shRNA8 stable transfected

status: Public on Jul 01 2016

city: Beijing

first: fan

last: yi

address: Xue Yuan Road 38

department: Peking University

institute: State Key Laboratory of Natural and Biomimetic Drugs

type: Methylation profiling by high throughput sequencing

summary: Genome-wide methylation profiling of mouse 3T3-L1 Cells comparing control wildtypes with cells stable transfected with slincRAD shRNA8 (sh8).

overall_design: Two-condition experiment, 3T3-L1 wildtype vs. slincRAD-shRNA8 stable transfected cells before and after Adipogenesis. One replicate per array.

first: Fan

last: Yi


title: Recruitment of Saccharomyces cerevisiae Cmr1/Ydl156w to coding regions promotes transcription genome wide

city: Rochester

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

institute: Oakland University

type: Genome binding/occupancy profiling by array

summary:
Cmr1 (changed mutation rate 1) is a largely uncharacterized nuclear protein that has recently emerged in several global genetic interaction and protein localization studies. It clusters with proteins involved in DNA damage and replication stress response, suggesting a role in maintaining genome integrity. Under conditions of proteasome inhibition or replication stress, this protein localizes to distinct sub-nuclear foci termed as intranuclear quality control (INQ) compartments, which sequester proteins for their subsequent degradation. Interestingly, it also interacts with histones, chromatin remodelers and modifiers, as well as with proteins involved in transcription including subunits of RNA Pol I and Pol III, but not with those of Pol II. It is not known whether Cmr1 plays a role in regulating transcription of Pol II target genes. Here, we show that Cmr1 is recruited to the coding regions of transcribed genes of S. cerevisiae. Cmr1 occupancy correlates with the Pol II occupancy genome-wide, indicating that it is recruited to coding sequences in a transcription-dependent manner. Cmr1-enriched genes include Gcn4 targets and ribosomal protein genes. Furthermore, our results show that Cmr1 recruitment to coding sequences is stimulated by Pol II CTD kinase, Kin28, and the histone deacetylases, Rpd3 and Hos2. Finally, our genome-wide analyses implicate Cmr1 in regulating Pol II occupancy at transcribed coding sequences. However, it is dispensable for maintaining co-transcriptional histone occupancy and histone modification (acetylation and methylation). Collectively, our results show that Cmr1 facilitates transcription by directly engaging with transcribed coding regions.
ChIp-chip experiments were perfomed to determine genome-wide distribution of Cmr1 in WT and gcn4Δ cells (S. cerevisiae). Rpb3 occupancy in WT and cmr1Δ cells was also determined to reveal the changes in Pol II occupancy in the absence of Cmr1.

overall_design: The WT and mutant strains were grown in Synthetic complete and cells were indcued for Gcn4 by treating with Sulfometuron methyl for 30 minutes and processed for chromatin immunoprecipitation using antibodies against Myc and Rpb3 (subunit of Pol II).

middle: K