title: Genome-wide analysis of primary plasma cell leukemia identifies recurrent imbalances associated with transcriptional Profile alterations (Expression)

summary: Primary plasma cell leukaemia (pPCL) is a rare, yet aggressive form of de novo plasma cell tumor, distinguished from secondary PCL (sPCL) which represents a leukemic transformation of pre-existing multiple myeloma (MM). Here, we performed a comprehensive molecular analysis of a prospective series of pPCLs by means of FISH, single nucleotide polymorphism (SNP) array and gene expression profiling (GEP). IGH@ translocations were identified in 87% of pPCL cases, with prevalence of t(11;14) (40%) and t(14;16) (30.5%), whereas the most frequently altered regions were located at 1p (38%), 1q (48%), 6q (29%), 8p (42%), 13q (74%), 14q (71%), 16q (53%) and 17p (35%). A relevant finding of our study was the identification of a minimal biallelical deletion (1.5 Mb) in 8p21.2 encompassing the putative tumor suppressor gene PPP2R2A that was significantly down-regulated in deleted cases. Mutations of TP53 were identified in 4 cases all but one associated with a monoallelic deletion of the gene, whereas activating mutations of BRAF occurred in one case and were absent for N- and K-RAS. To evaluate the influence of allelic imbalances in transcriptional expression we performed an integrated genomic analysis with GEP data, showing a significant dosage effect of genes involved in transcription, translation, methyltransferases activity, apoptosis as well as Wnt and NF-kB signaling pathways. Overall, we provide a compendium of genomic alterations in a prospective series of pPCLs which may contribute to our understanding of this particular form of plasma cell dyscrasia and to better elucidate the mechanisms of tumor progression in MM.

overall_design:
This series of microarray experiments contains the gene expression profiles of purified plasma cells (PCs) obtained from 21 primary plasma cell leukemia (pPCL) at diagnosis. PCs were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases. 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual). The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol. Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G). Log2-transformed expression values were extracted from CEL files and normalized using NetAffx Transcript Cluster Annotations, Release 31 and robust multi-array average (RMA) procedure in Expression Console software (Affymetrix Inc.). The expression values of transcript cluster ID specific for loci representing naturally occurring read-through transcriptions or mapped to more than one chromosomal location were summarized as median value for each sample.
gene expression analysis of 21 primary Plasma Cell Leukemia

first: Laura

last: Mosca

first: Pellegrino

last: Musto

first: Katia

last: Todoerti

first: Marzia

last: Barbieri

first: Sonia

last: Fabris

first: Giacomo

last: Tuana

first: Marta

last: Lionetti

first: Eleonora

last: Bonaparte

first: Silvia

last: Sirchia

first: Vitina

last: Grieco

first: Gabriella

last: Bianchino

first: Fiorella

last: D'Auria

first: Teodora

last: Statuto

first: Carmela

last: Mazzoccoli

first: Luciana

last: De Luca

first: Maria

middle: T

last: Petrucci

first: Fortunato

last: Morabito

first: Massimo

last: Offidani

first: Francesco

last: Di Raimondo

first: Antonietta

last: Falcone

first: Paola

last: Omede'

first: Mario

last: Boccadoro

first: Antonio

last: Palumbo

first: Antonino

last: Neri


title: Microarray gene expression profiling of zebrafish embryos after 3-hour 0.1% DMSO or 25 µM Beclomethasone treatment

status: Public on Oct 30 2012

city: Halifax

first: Sergey

last: Prykhozhij

state: Nova Scotia

address: 5850/5980 University Avenue

department: Pediatrics

country: Canada

institute: IWK Health Centre

summary: To uncover the genes regulated by pharmacological activation of the Glucocorticoid Receptor, we performed microarray-based expression profiling of whole zebrafish embryos at 24 and 72 hours post fertilization (hpf) after 3-hour treatment with 25 µM of Beclomethasone, a potent glucocorticoid previously tested in zebrafish or with 0.1 % DMSO as control.

overall_design: Embryos at 24 and 72 hpf stages were treated with either 0.1 % DMSO or 25 µM Beclomethasone for 3 hours in triplicate experiments and then frozen for RNA extraction.

first: Sebastiaan

middle: H

last: Meijsing


title: Transcriptome responses to heat stress in hypothalamus of a meat-type chicken

status: Public on Oct 01 2012

city: Beijing

first: hongyan

last: sun

address: Poultry genetic group, College of Animal Science and Technology, China Agricultural Univeristy, Yuanmingyuan West Rd. No. 2, Haidian District, Beijing, China

country: China

institute: Iowa State University

summary: By using a 44k chicken Agilent microarray, we systematically analyzed the chicken hypothalamus transcriptome response to thermal stress. Twelve hypothalamus samples were chosen from three groups (four samples per group) to be used in chicken genome microarray to examine differential gene expression.We compared the expression profiles between each pairs of the three groups using the microarray data. Totally, 2474 genes were found to be differentially expressed in the three comparisons with p＜0.05 and fold change (FC) higher than 1.5 and the genes were mainly involved in self-regulation and compensation required to maintain homeostasis, including heat shock protein family, enzyme and the hormone, neurotransmitter, cell-cell signaling, metabolism and cytokines. The transcripts of heat shock protein including Hsp 40 and Hsp 90 were significantly changed respond to thermal stress and genes involved in regulation of cell morphogenesis were significantly upregulated in heat stressed group with comparison to control and temperature recovery group. Additionally, the down-regulated genes in both heat stress and temperature recovery groups compared to control group were enriched in muscle organ development, striated muscle tissue development, cardiac muscle tissue development and muscle tissue development, which indicates that muscle development was inhibited during and in short-term after heat treatment.  Most of genes dysregulated in heat stress group were found to be recovered in temperature recovery group, which confirmed their roles they could play in coping with heat stress. The present study provides a broader understanding of molecular mechanisms underlying the stress response in chicken and discovery of novel genes that are regulated in a thermal stress specific manner.

overall_design: Hypothalamus samples were collected from non-heat treated group (reared at 25C, used as control), 24h 34C treated group (heat stress treated group) and temperature recovery group (25C for 24h followed heat stress).

first: Hongyan

last: Sun

first: Lujiang

last: Qu

first: Runshen

last: Jiang

first: Shengyou

last: Xu

first: Guiyun

first: Jiangxia

last: Zheng

first: Ning

last: Yang


title: Transcripts and metabolites of grape ripening and aroma development

city: Lisboa

first: Ana

middle: Margarida

last: Fortes

address: Campus da FCUL

department: Plant Biology

country: Portugal

summary: Grapes (Vitis species) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening in berries as well as how aroma is developed are aspects not fully understood.   In an attempt to identify the common mechanisms associated with the onset of ripening independently of the cultivar, grapes of Portuguese elite cultivars, Trincadeira, Aragonês, and Touriga Nacional, were studied. The mRNA expression profiles corresponding to veraison (EL35) and to mature berries (EL36) were compared. Across the three varieties, 9,8% (2255) probesets corresponding to 1915 unigenes were robustly differentially expressed at EL 36 compared to EL 35. Eleven functional categories were represented in this differential gene set: primary metabolism, “secondary metabolism”, cellular metabolism”, development”, “cellular process”, “diverse functions”, “regulation overview”, response to stimulus, stress”, “signaling”, “transport overview”, and “xenoprotein, transposable element” besides 32.24% genes of “unknown” function. Information on gene expression related to primary and secondary metabolism was verified by RT-qPCR analysis of selected candidate genes at four developmental stages (EL32, EL35, EL36 and EL 38). Gene expression data were integrated with metabolic profiling data from GC-EI-TOF/ MS and headspace GC-EI-MS platforms.   Molecular and metabolic markers of grape ripening related to primary and secondary metabolism were established and revealed a substantial developmental reprogramming of cellular metabolism. Altogether the results provide valuable new information on the main metabolic events leading to grape ripening. Furthermore, we provide first hints about how the development of a cultivar specific aroma is controlled at the transcriptional level.

overall_design: 2 time points in 2008 season. 3 biological replicates. 3 cultivars

middle: M

first: Maria

middle: S

last: Pais


title: A phase II study of adding the multikinase inhibitor sorafenib to endocrine therapy in patients with metastatic ER-positive breast cancer.

status: Public on Sep 13 2012

city: Lexington

first: Suleiman

last: Massarweh

state: KY

address: 800 Rose St., Cc452

country: USA

institute: University of Kentucky and Markey Cancer Center

summary: Growth factor signaling and angiogenesis may promote endocrine-resistance in breast cancer and blocking these pathways can overcome resistance in preclinical models.  We conducted a phase-II study of adding the VEGFR/Ras/Raf/MAPK inhibitor sorafenib to endocrine therapy in metastatic ER-positive breast cancer, either upon progression or after maximal response with measurable residual disease. Tumor biopsies and serum were collected on days 1 and 28. Primary endpoint was response by RECIST after 3 months and secondary endpoints included safety, time to progression (TTP), and biomarker assessment. Planned sample size was 43 patients but the study closed after 11 patients because of slow accrual. 8 patients had progressive disease (PD) on entry and 3 had stable disease (SD). One patient with SD discontinued sorafenib after 2-weeks because of grade 3 rash. Of the 10 remaining patients after adding sorafenib, 7 had SD (70%), 3 had PD (30%) and median TTP was 6.1-months. Of the 8 patients who entered the study with PD on endocrine therapy, 5 converted to SD (62%) with a median TTP of 6.4-months. Notably, patients on tamoxifen had a median TTP of 8.4-months. The most common adverse events were hypophosphatemia, hypokalemia, and rash, and the majority were grade 1&2 with no grade 4 toxicities. There was a significant reduction in serum VEGFR2 and PDGFR-α on day-28 (p-values 0.0035 and 0.017, respectively). Both serum VEGF and sVEGFR-1 were increased on day-28, but the differences were not statistically significant (p-values 0.3223 and 0.084, respectively). Microarray analysis identified 32 suppressed genes with an FDR of <0.20 and at least a 2-fold change with no induced genes and 29 KEGG pathways were enriched on day-28.  Our study suggests that sorafenib can restore endocrine sensitivity, particularly tamoxifen, and this strategy of adding novel agents in patients progressing on endocrine therapy should be examined in future trials.

overall_design: This was a single-institution, phase II study of adding sorafenib to existing endocrine therapy.  On study entry, eligible patients underwent serum sample collection and core biopsy of accessible disease (if applicable) on endocrine therapy and prior to starting sorafenib.  Serum and a second biopsy were then collected on day 28. Sorafenib dose was 400mg orally twice daily along with continuing the same endocrine agent.  Patients were followed monthly for clinical and toxicity evaluation. Disease response by RECIST criteria was assessed after 3 months by appropriate scans and these were obtained every 2 months thereafter until progression. Sorafenib and the endocrine agent were continued until disease progression or unacceptable toxicity

first: Jessica

last: Moss

first: Chi

last: Wang

first: Edward

last: Romond

first: Stacey

last: Slone

first: Heidi

last: Weiss

first: Rouzan

middle: G

last: Karabakhtsian

first: Dana

last: Napier

first: Esther

middle: P

last: Black


title: Follicular Lymphoma Array CGH

status: Public on Sep 20 2012

city: New York

first: Elisa

last: Oricchio

address: 1275 York Avenue

institute: MSKCC

type: Genome variation profiling by genome tiling array

summary: We run aCGH of 64 FL samples and we looked for recurrent chromosomal alterations.

overall_design: we analyzed 64 FL samples by aCGH

first: Hans-Guido

last: Wendel


title: Genome-wide analysis of primary plasma cell leukemia identifies recurrent imbalances associated with transcriptional Profile alterations (Copy number)

status: Public on Oct 12 2012

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

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

overall_design:
This series of microarray experiments contains the genome-wide profiles of 17 primary Plasma Cell Leukemia. 250 nanograms of genomic DNA was processed and, in accordance with the manufacturer's protocols, 90 micrograms of fragmented biotin-labeled DNA were hybridized on GeneChip Human Mapping 250K NspI Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. The raw data for individual SNPs were extracted from CEL files and converted into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares using the Hidden Markov Model algorithm with a genomic smoothing window set to 0. After the pre-processing, piecewise constant estimates of the underlying local DNA copy number (CN) variation was calculated using the DNAcopy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS).
genotyping analysis of 17 primary Plasma Cell Leukemia

first: Laura

last: Mosca

first: Pellegrino

last: Musto

first: Katia

last: Todoerti

first: Marzia

last: Barbieri

first: Sonia

last: Fabris

first: Giacomo

last: Tuana

first: Marta

last: Lionetti

first: Eleonora

last: Bonaparte

first: Silvia

last: Sirchia

first: Vitina

last: Grieco

first: Gabriella

last: Bianchino

first: Fiorella

last: D'Auria

last: Petrucci

first: Fortunato

last: Morabito

first: Massimo

last: Offidani

first: Francesco

last: Di Raimondo

first: Antonietta

last: Falcone

first: Paola

last: Omede'

first: Mario

last: Boccadoro

first: Antonio

last: Palumbo

first: Antonino

last: Neri


title: Aging effects on DNA methylation modules in blood tissue

status: Public on Sep 21 2012

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary: Genome wide DNA methylation profiling of whole blood in schizophrenia patients and healthy subjects. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Raw data included 325 schizophrenia patients (2) and 394 controls (1) from Dutch descent. One sample was excluded since it was a bipolar patient, indicated by 3 in diseaseStatus column. The column used_in_analysis shows the samples that were used in our study. The excluded samples failed quality control. Normalized data are also included in the non_normalized.txt (i.e. AVG_Beta column).

overall_design: Bisulphite converted DNA from 720 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip [Publication: Horvath et al., Genome Biology, Special Edition]

first: Roel

last: Ophoff


title: Transcriptional profiling of swine lung and hilar node after experimental infection with Actinobacillus pleuropneumoniae

status: Public on Nov 16 2012

city: ya'an

first: zhicai

last: ZUO

state: sichuan

address: xinkang road

department: College of Veterinary Medicine

institute: Sichuan Agricultural University

summary: This study aimed at: (1) Establishing the pleuropneumoniae pathological model of artificial infection; (2) Using the Agilent swine genome-wide microarray containing 43,603 probes to detect the changes in gene expression of infected pigs’ lungs and hilar nodes.

overall_design: Infection induced gene expression in swine lung and hilar node were measured at 48 hours after being inoculated with 1 mL containing 3.8 × 10^7 cfu/mL pleuropneumoniae serotype I by atomizing inhalation in each nostril.

first: Zhicai

last: Zuo

first: Hengmin

last: Cui


title: Expression analysis of Phytophthora infestans isolates 06_3928A and NL07434 during potato infection 2-4 days post-inoculation

status: Public on Sep 01 2012

city: Norwich

first: Liliana

middle: Maria

last: Cano

state: Norfolk

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

summary: The expression of genes in P. infestans isolates 06_3928A and NL07434 was monitored from 2 to 4 days time course of a potato infection. Genes encoding known and putative effector proteins were found induced at two and/or three days post-inoculation.

platform_organism:
Solanum lycopersicum
Phytophthora infestans

overall_design: We used a custom chip GPL8093 from Roche Nimblegen’s proprietary Maskless Array Synthesis (MAS) technology uses digital light processing and rapid, high-yield photochemistry to synthesize long oligo, high-density DNA microarrays with extreme flexibility. Each GPL8093 chip measures the expression level of 18155 genes from Phytophthora infestans with 60-mer probe pairs (PM/MM) per gene. Total RNA samples recovered from mycelia in two medias (rye sucrose agar and V8 agar) and infected potato leaves from a time couse infection (2, 3 and 4 days post incoulation). Experiments included two biological repllicates from each sample. We carried out total RNA extractions (mycelia and potato infected material) for two P. infestans isolates 06_3928A and NL07434. cDNA synthesis was performed Nimblegen.

first: Sophien

last: Kamoun


title: The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program

status: Public on Sep 10 2012

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

summary: The first genome-wide transcriptomic atlas of grapevine (Vitis vinifera) is based on 54 diverse samples expressing ~93% of predicted grapevine genes. Pollen and senescent leaves have unique transcriptomes but microarray analysis grouped all other samples into vegetative/green or mature/woody categories based on maturity rather than organ identity. This fundamental transcriptome reprograming during maturation was highlighted by three distinct statistical approaches supported by gene coexpression analysis. The shift to the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of  neighboring genes and global regulation based on codon preference.

overall_design: A total of 54 grapevine samples, covering most of the Grape organs at different stages, were collected. Three biological replicates were taken for each sample, resulting in a total of 162 observations. The collected plant organs were: bud, inflorescence, tendril, leaf, stem, root, developing berry, withering berry, seed, rachis, anther, carpel, petal, pollen, and seedling.

first: Marianna

last: Fasoli

first: Silvia

last: Dal Santo

first: Sara

last: Zenoni

first: Giovanni

middle: B

last: Tornielli

first: Lorenzo

last: Farina

first: Anita

last: Zamboni

first: Andrea

last: Porceddu

first: Luca

last: Venturini

first: Manuele

last: Bicego

first: Vittorio

last: Murino

last: Delledonne

last: Pezzotti


title: Expression data from aquatic axolotl full thickness epithelial flank wounds, innervated limbs, and denervated limbs collected over seven days

status: Public on Sep 17 2012

city: Gainesville

first: James

middle: R

last: Monaghan

state: FL

address: 2033 Mowry Road

department: Biology

institute: University of Florida

summary: Salamander limb regeneration is dependent upon tissue interactions that are local to the amputation site. Communication among limb epidermis, peripheral nerves, and mesenchyme coordinate cell migration, cell proliferation, and tissue patterning to generate a blastema, a mass of progenitor cells that forms missing limb structures. An outstanding question is how molecular cross-talk between these tissues gives rise to the regeneration blastema. To identify genes associated with epidermis-nerve-mesenchymal interactions during limb regeneration, we examined histological and transcriptional changes during the first week following injury in the wound epidermis and subjacent cells between three injury types; 1) a flank wound on the side of the animal that will not regenerate a limb, 2) a denervated limb that will not regenerate a limb, and 3) an innervated limb that will regenerate a limb. Early, histological and transcriptional changes were highly similar between the three injury types, presumably because a common wound-healing program is employed across anatomical locations. However, we identified transcripts that were enriched in the limb compared to the flank and are associated with vertebrate limb development. Many of these genes were activated before blastema outgrowth and in situ hybridization showed that some of these genes were expressed in specific tissue types including the epidermis, peripheral nerve, and mesenchyme. We also identified a relatively small group of transcripts that were more highly expressed in innervated limbs versus denervated limbs. These transcripts encode for proteins that are associated with myelination of peripheral nerves, epidermal maintenance, and cell proliferation, suggesting that denervation affects myelinating Schwann cells, epidermal cell function, and proliferation of mesenchymal cells. Overall, our study identifies limb-specific and nerve-dependent genes that are upstream of regenerative growth, and thus promising candidates for the regulation of blastema formation.

overall_design: We used microarray analysis to determine the gene expression changes that take place during limb regeneration, flank wound healing, and an denervated amputated limb.  Epidermal tissue and cells adhered to the epidermis were collected as samples.  Two harvested samples was pooled for each animal.  Four biological replicates were collected from uninjured epidermis (D0) and at 1, 3, and 7 days post injury.

first: Antony

last: Athippozhy

first: Ashley

middle: W

last: Seifert

first: Srikrishna

last: Putta

first: Arnold

middle: J

last: Stromberg

first: Malcolm

last: Maden

first: David

last: Gardiner

first: S

last: Voss


title: Prospective transcriptomic identification and validation of a circulating biomarker panel for human lymphatic vascular insufficiency

status: Public on Aug 01 2012

city: Stanford

first: Stanley

middle: G.

last: Rockson

address: 300 Pasteur Dr.

department: Cardiovascular Medicine

institute: Stanford University

summary: Transcriptional profiling of human skin biopsies to determine differential gene expression between normal tissue from an unaffected limb and lymphedema tissue from an affected limb.

overall_design: Single condition experiment, paired normal and diseased skin biopsies from each study subject were tested for differential gene expression

first: Shin

last: Lin

first: Jeanna

last: Kim

first: Xuhuai

last: Ji


title: Mu killer-mediated and spontaneous silencing of Zea mays Mutator family transposable elements define distinctive paths of epigenetic inactivation

status: Public on Jul 28 2012

first: John

middle: F

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

summary: Mu killer contains a partial inverted duplication of the mudrA transposase gene and two copies of the terminal inverted repeat A region of MuDR. Mu killer can effectively silence single copy MuDR/Mu lines but failed to silence about 25% of the time in multiple copy lines. Mu killer was partially sequenced and shown to be collinear with mudrA. Mu killer individuals that silenced MuDR contained two short antisense transcripts, while individuals that failed to silence MuDR contained multiple sense transcripts but no antisense transcripts. Transcriptomes from Mu killer-silenced individuals were compared to epigenetically silenced lines; the 2 silencing mechanisms were shown to affect different pathways.

overall_design: 4 replicates of the Mu-active and Mu-inactive lines at 2 anther stages (1.0mm, 2.00mm) with a balanced dye-swap design. Normalized intensities for each channel are provided.

last: Skibbe

first: Virginia

last: Walbot


title: PACAP and TNF regulate discrete population of genes in bovine chromaffin cells

city: Bethesda

first: Babru

middle: Bahan

last: Samal

state: MD

address: 9000 Rockville Pike

department: LCMR

institute: NIMH

summary: The bovine chromaffin cell (BCC) is a unique model—a highly homogeneous and accessible neuroendocrine cell—in which to study gene regulation through first messenger-initiated signaling pathways that are specific to post-mitotic cells. BCCs were treated with tumor necrosis factor (TNF) or pituitary adenylate cyclase activating polypeptide (PACAP), two critical regulators of neural cell transcriptional programming during inflammation that act on TNFR2 and PAC1 receptors, respectively, in post-mitotic neuroendocrine cells. Transcripts which were significantly up regulated by either or both first messenger were identified from microarray analysis using two bovine oligonucleotide arrays (Affymetrix and Agilent) followed by statistical analysis with Partek Genomic suite. Microarray data were combined from the two arrays using qRT-PCR sampling validation, and the first-messenger transcriptome derived from TNF and PACAP signaling were compared. More than 90 percent of the genes up regulated either by TNF or PACAP were specific to a single first messenger. BioBase suite, DIRE and Opossum were used to identify common promoter/enhancer response elements that control the expression of TNF- or PACAP-stimulated genes. Bioinformatic analysis revealed that distinct groups of transcription factors control the expression of genes up regulated by either TNF or PACAP . Most of the genes up regulated by TNF contained response elements for members of the Rel transcription factor family, suggesting TNF-TNFR2 signaling mainly through the NF-kB signaling pathway. On the other hand, the PACAP regulated genes showed no enrichment for any single response element, containing instead response elements for combinations of transcription factors allowing activation through multiple signaling pathways, including cAMP, calcium and ERK, in neuroendocrine cells. Pharmacological strategies for mimicking neuroprotection by either PACAP or TNF in the context of CNS injury or degeneration in disease might focus on individual downstream gene activation pathways to achieve greater specificity in vivo.

overall_design: For our analysis we have used both Affymetrix and Agilent arrays to identify the genes that are regulated up or down by neuropeptide PACAP and TNF-alpha. On Affyemetrix platform we performed technical repeats with 3 arrays with untreated samples, 3 arrays with samples from PACAP treatment, and 3 array with samples from TNF-alpha treatment. On the Agilent platform we performed technical repeats with 3 arrays for each treatment hybridizing Cy3-labelled RNA from untreated samples and Cy5-labelled RNA from either TNF-alpha or PACAP treated samples.


title: Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

status: Public on Jul 12 2012

city: South San Francisco

first: Brad

middle: A

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

type: Expression profiling by high throughput sequencing

summary: Differentiated cells acquire unique structural and functional traits through coordinated expression of lineage-specific genes. An extensive battery of genes encoding components of the synaptic transmission machinery and specialized cytoskeletal proteins is activated during neurogenesis, but the underlying regulation is not well understood. Here we show that genes encoding critical presynaptic proteins are transcribed at a detectable level in both neurons and non-neuronal cells. However, in non-neuronal cells, the splicing of 3’-terminal introns within these genes is repressed by polypyrimidine tract-binding protein (Ptbp1). This inhibits the export of incompletely spliced mRNAs to the cytoplasm and triggers their nuclear degradation. Clearance of these intron-containing transcripts occurs independently of the nonsense-mediated decay (NMD) pathway but requires components of the nuclear RNA surveillance machinery including the nuclear pore-associated protein Tpr and components of the exosome complex. When Ptbp1 expression decreases during neuronal differentiation, the regulated introns are spliced out thus allowing the accumulation of translation-competent mRNAs in the cytoplasm. We propose that this mechanism counters ectopic and precocious expression of functionally linked neuron-specific genes and ensures their coherent activation in the appropriate developmental context.

overall_design: PTBP1 siRNA, PTBP1+PTBP2 siRNA, or control siRNA

first: Karen

last: Yap

first: Zhao

middle: Q

last: Lim

first: Piyush

last: Khandelia

first: Eugene

middle: V

last: Makeyev


title: Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin hubs

status: Public on Jul 01 2012

first: Xun

last: Lan

address: 318 Campus Dr. Room S240

department: Genetics

summary: We have analyzed publicly available K562 Hi-C data, which enables genome-wide unbiased capturing of chromatin interactions, using a Mixture Poisson Regression Model to define a highly specific set of interacting genomic regions. We integrated multiple ENCODE Consortium resources with the Hi-C data, using DNase-seq data and ChIP-seq data for 46 transcription factors and 8 histone modifications. We classified 12 different sets (clusters) of interacting loci that can be distinguished by their chromatin modifications and which can be categorized into three types of chromatin hubs. The different clusters of loci display very different relationships with transcription factor binding sites. As expected, many of the transcription factors show binding patterns specific to clusters composed of interacting loci that encompass promoters or enhancers. However, cluster 6, which is distinguished by marks of open chromatin but not by marks of active enhancers or promoters, was not bound by most transcription factors but was highly enriched for 3 transcription factors (GATA1, GATA2, and c-Jun) and 3 chromatin modifiers (BRG1, INI1, and SIRT6). To validate the identification of the clusters and to dissect the impact of chromatin organization on gene regulation, we performed RNA-seq analyses before and after knockdown of GATA1 or GATA2. We found that knockdown of the GATA factors greatly alters the expression of genes within cluster 6. Our work, in combination with previous studies linking regulation by GATA factors with c-Jun and BRG1, provide genome-wide evidence that Hi-C data identifies sets of biologically relevant interacting loci.

overall_design: RNA-seq of control, siGATA1 and siGATA2 K562 cells

first: Peggy

last: Farnham

first: Victor

middle: X

last: Jin

first: Emery

middle: H

last: Bresnick


title: PAHM4 vs PAO1 37C LB

city: Atlanta

last: Varga

state: GA

address: 1510 Clifton Road

institute: Emory University

summary: Pseudomonas aeruginosa strains PAHM4 and PAO1 were grown at 37C on LB and RNA was hybridized on the Affymetrix P. aeruginosa chip to compare transcript differences from a BQ isolate to a well characterized wound isolate.

sample_organism:
Pseudomonas aeruginosa PAO1
Pseudomonas aeruginosa PAHM4

overall_design: Strains PAHM4 and PAO1 were grown in triplicate.  Total RNA from each sample was pooled and amplified then assayed in triplicate resulting in 6 total samples.  PAO1 is the control strain while PAHM4 is the experimental strain.

first: Mariette

last: Barbier

first: Piotr

last: Bielecki

first: Jacek

last: Puchałka

first: Vitor

middle: M

last: Dos Santos

first: Roberts

last: Geffers

first: Sebastian

last: Alberti

first: Joanna

last: Goldberg


title: Genome-wide baseline microRNA expression quantification in HapMap phase I CEU and YRI samples

status: Public on Jul 29 2012

city: Chicago

first: R. Stephanie

last: Huang

state: IL

address: 900 E 57th street

institute: University of Chicago

summary: Baseline microRNA (miRNA) expression was evaluated in 107 HapMap lymphoblastoid cell lines (LCLs; 53 CEU and 54 YRI) using Exiqon miRCURY LNA arrays v10.0 (Exiqon array).

overall_design: Total RNA from each of the 107 HapMap sample was labeled and hybridized onto an Exiqon array

first: R

middle: S

first: M

middle: E

last: Dolan


title: Comparison of vineyard, enological and laboratory yeast transcriptomes at different steps of the fermentation curve

status: Public on Mar 31 2014

city: Padova

first: Stefano

last: Campanaro

address: Via Ugo Bassi 58/b

institute: University of Padua

summary: Here we report the massively parallel cDNA sequencing (RNA-seq) analysis performed using high throughput sequencing of four vineyard yeast strains collected from the vineyards of the “Prosecco di Conegliano-Valdobbiadene” (P283 and P301 strains) and Piave AO (Appellation of origin) (R008 and R103 strains) regions in North East of Italy. Results were compared with RNA-seq performed on a commercial yeast strain (EC1118) and a laboratory strain (S288c). Yeast cells were collected at two different steps of the fermentation curve: at the beginning of the process, when the CO2 produced by the cells was 6 g/l (middle exponential growth phase), and in the middle of fermentation, at 45 g/l (early stationary phase). Three biological replicates of the fermentations were performed for each strain and samples for RNA-seq were gathered at the beginning of the process. The aim of this experiment was the comparison of the transcriptomes of the six yeast strains to identify the genes characterizing wild type yeast isolates, "commercial" and laboratory strains.

overall_design: Twelve samples were analyzed: S288c strain at middle exponential growth phase (6 g/l CO2 produced), S288c strain in the middle of fermentation (45 g/l CO2 produced), EC1118 strain at middle exponential growth phase (6 g/l CO2 produced), EC1118 strain in the middle of fermentation (45 g/l CO2 produced), P283 strain at middle exponential growth phase (6 g/l CO2 produced), P283 strain in the middle of fermentation (45 g/l CO2 produced), R008 strain at middle exponential growth phase (6 g/l CO2 produced), R008 strain in the middle of fermentation (45 g/l CO2 produced), R103 strain at middle exponential growth phase (6 g/l CO2 produced), R103 strain in the middle of fermentation (45 g/l CO2 produced), P301 strain at middle exponential growth phase (6 g/l CO2 produced), P301 strain in the middle of fermentation (45 g/l CO2 produced).

first: Laura

last: Treu

first: Giorgio

last: Valle

first: Viviana

last: Corich

first: Alessio

last: Giacomini

first: Chiara

last: Toniolo

first: Michela

last: D'Angelo


title: Expression data from vaginal tissue from estrogen-treated WT and Fbln5-/- mice

status: Public on Aug 22 2012

city: Dallas

first: Ruth

last: Word

state: TX

address: 5323 Harry Hines Blvd

department: Ob-Gyn

institute: Univ TX Southwestern Med Ctr

summary: We used microarrays to detail the global program of gene expression changes in wild type and Fbln5-/-  adult mice.  Estrogen status was controlled

overall_design: Wt and Fblin5 KO mice of same strain (C57Bl6) were ovariectomized at 2 wks and then treated with estradio (50 µg/kg/d) x 3 d

first: Hiromi

last: Yanagisawa


title: Deep sequencing of microRNAs in multiple tissues of Scylla paramamosain under Vibrio parahaemolyticus infection

status: Public on Aug 07 2012

city: Shantou

first: Zhu

last: Shuo

state: Guangdong

address: Daxue Road

department: Science

institute: Shantou University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: The Scylla paramamosain is a very important aquaculture crustacean species in the southeast coastal areas of China including Shantou. For the past few years, mud crab cultured in Niutianyang of Shantou suffered from serious diseases, especially the bacterial diseases (such as Vibrio parahaemolyticus). In eukaryotes, small RNAs can regulate gene expression in post-transcription to act on host-pathogen interaction system.
Aims: V.parahaemolyticus isolated from Shantou Niutianyang crab culture area was injected to S.paramamosains to carry out an essential analysis on global miRNA expression in diverse tissues between two groups by the Illumina Solex deep sequencing technology.
Methodology:To examine the relationship between mud crab miRNA expression and the bacterial pathogen, we collected mixed two pools of equal amounts of RNA from 7 different mud crab tissues (mesenteron, heart, liver, gill, brain, muscle and blood) and sequencing by Illumine/Solexa deep sequencing technology under normal conditions and during infection with V.parahaemolyticus. The high throughput sequencing resulted in 19,144,358 and 18,559,070 raw reads corresponding to 17,496,577 and 16,888,096 high-quality mappable reads for the normal and infected mixed pools, respectively. Stem-loop RT-qPCRs were used to confirm the microRNAs expression in different tissues of two pools. The results show that miRNAs might play a key role in regulating gene expression during mud crab S.paramamosain infection with V.parahaemolyticus.
Conclusions: We identified a large number of miRNAs during the mud crab Scylla paramamosain infection with V.parahaemolyticus, some of which are differentially expressed between the treatments and the controls. The study provides an opportunity for further understanding of small RNA function in the regulation of molecular response and gives us clues for further studies of the mechanisms of V.parahaemolyticus infection in mud crab.

overall_design: Examination of miRNA expression in normal Scylla paramamosain group and the Scylla paramamosain infected with Vibrio parahaemolyticus

first: S

middle: K

last: Li

last: Zhu


title: microRNA expression data from human corneal epithelial cells exposed to media, human tear, media + P. aeruginosa antigens, tear + P. aeruginosa antigens

status: Public on Jul 14 2012

city: Berkeley

first: James

last: Mun

address: 688 Minor Hall

department: Vision Science

institute: UC Berkeley

summary: Exposure to tear fluid can enhance corneal epithelial cells' ability to resist bacterial virulence mechanisms by upregulating epithelial-derived innate defense genes. The aim of this study was to further elucidate the mechanisms by which tear fluid modulates epithelial cell susceptibility to P. aeruginosa internalization and the relationship to known to be upregulated genes with tear fluid exposure. The hypothesis tested was that tear fluid effects on epithelial cells involve the induction of microRNA expression to modify innate defense gene responses to bacterial challenge.

overall_design: Human corneal epithelial cells were incubated in either 40 ul of fresh human tear fluid or high calcium KGM without antibiotics for 16 hours before extraction or before incubation with P. aeruginosa antigens for 3 h then extraction.

first: Connie

last: Tam

first: Justin

last: Choi

first: Evans

last: David

first: Fleiszig

last: Suzanne


title: Expression profiling of tomato pre-abscission pedicels

status: Public on Jul 20 2012

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

country: Japan

institute: National Food Research Institute

summary:
Organ abscission is a general activity found in plants and its regulation is an important agronomical concern because the trait directly affects the harvesting efficiency of fruits or grains and the yields. Generally, abscission takes place at a specialized cell layer, which is called abscission zones (AZs). So far, investigations on organ abscission have been focused mainly on the cell activities during organ detachment. By contrast, little attention has been paid to the properties of AZ cells at the pre-abscission stage. The pre-abscission cells are at a turning point for initiating abscission; until an abscission initiating signal is provided, the AZ cells keep their physiological state, while once the signal occurs, the cells immediately change their state into the onset of abscission.
In this study, to screen the genes involved in the regulation of abscission at the pre-abscission state, we investigated the gene expression profiles of tomato flower pedicels at anthesis. The screening revealed many genes that characterize cell identities in each pedicel region.

overall_design: We harvested tomato flower pedicels at the anthesis stage and divided them into three parts: the abscission zone (AZ) and the flanking proximal- (Prox) and distal- (Dis) regions.  RNA was isolated and subjected to DNA microarray analyses. Experiments were performed three times with independently prepared samples.

first: Toshitsugu

last: Nakano

first: Masaki

last: Fujisawa

first: Yoko

last: Shima


title: Deciphering Gene Expression Program of MAP3K1 in Mouse Eyelid Morphogenesis

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary:
Embryonic eyelid closure is a critical step of mammalian ocular surface development involving the forward movement and ultimate fusion of the upper and lower eyelids. Although its underlying mechanism of action is not fully understood, a functional mitogen-activated protein kinase kinase kinase 1 (MAP3K1) is essentially required for eyelid closure.
We used microarray to characterize the central role that MAP3K1 plays in embryonic eyelid closure.

overall_design: We used Laser Capture Microdissection (LCM) to obtain highly enriched eyelid leading edge and inner eyelid cells from E15.5 wild type and MAP3K1-deficient fetuses and analyze genome-wide expression profiles.

first: Chang

last: Jin

first: Jing

last: Chen

first: Qinghuan

last: Meng

first: Vinicius

last: Carreira

first: Neville

first: Esmond

last: Geh

first: Saikumar

last: Karyala

first: Shuk-mei

last: Ho

first: Xiangtian

last: Zhou

first: Ying

last: Xia


title: Response to drought stress at reproductive stage

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

institute: NARO/HARC

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

overall_design: Refer to individual Series


title: Immune Clearance of Attenuated Rabies Virus Results in Neuronal Survival with Altered Gene Expression

status: Public on Jun 28 2012

city: Philadelphia

first: Emily

middle: Ann

last: Gomme

state: PA

address: 233 S. 10th Street, Room 531

department: Microbology & Immunology

institute: Thomas Jefferson University

summary: Rabies virus (RABV) is a highly neurotropic pathogen that typically leads to mortality of infected animals and humans. The precise etiology of rabies neuropathogenesis is unknown, though it is hypothesized to be due either to neuronal death or dysfunction. Our approach to study the survival and integrity of RABV-infected neurons was to infect Cre reporter mice with recombinant RABV expressing Cre-recombinase (RABV-Cre) to switch neurons constitutively expressing tdTomato (red) to expression of a Cre-inducible EGFP (green), permanently marking neurons that had been infected in vivo. We were able to isolate these previously infected neurons (“infected”) by flow cytometry and assayed their gene expression profiles compared to uninfected cells (“uninfected”) from the same mice.

overall_design: Two cre reporter mice were infected intranasally with RABV-Cre, allowed to resolve the acute infection, and then sacrificed at 3 months post-infection. EGFP+ cells from the brains of these mice were collected by FACS and represent those infected with RABV (“Infected-1” and “Infected-2”); tdTomato+ cells collected from these same mice represent uninfected cells (“Uninfected-1” and “Uninfected-2”). RNA was collected from these samples for microarray analysis.

first: Christoph

last: Wirblich

first: Sankar

last: Addya

first: Glenn

last: Rall

first: Matthias

last: Schnell


title: Discovery and validation of gene classifiers for endocrine disrupting chemicals in Zebrafish (Danio rerio)

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

institute: US EPA

summary:
Background: Development and application of transcriptomics-based gene classifiers for ecotoxicological applications lag far behind those of human biomedical science.  Many such classifiers discovered thus far lack vigorous statistical and experimental validations, with their stability and reliability unknown. A combination of genetic algorithm/support vector machines and genetic algorithm/K nearest neighbors were used in this study to search for classifiers of endocrine disrupting chemicals (EDCs) in zebrafish.  Searches were conducted on both tissue-specific and all tissue combined datasets, either across the entire transcriptome or within individual transcription factor (TF) networks previously linked to EDC effects. Candidate classifiers were evaluated by gene set enrichment analysis (GSEA) on both the original training data and a dedicated validation dataset.

Results: Multi-tissue dataset yielded no classifiers.  Among the 19 chemical-tissue conditions evaluated, the transcriptome-wide searches yielded classifiers for six of them, each having approximately 20 to 30 gene features unique to a condition.  Searches within individual TF networks produced classifiers for 15 chemical-tissue conditions, each containing 100 or fewer top-ranked gene features pooled from those of multiple TF networks and also unique to each condition.  For the training dataset, 10 out of 11 classifiers successfully identified the gene expression profiles (GEPs) of their intended chemical-tissue conditions by GSEA.  For the validation dataset, classifiers for prochloraz-ovary and flutamide-ovary also correctly identified the GEPs of corresponding conditions while no classifier could predict the GEP from prochloraz-brain.

Conclusions:  The discrepancies in the performance of these classifiers were attributed in part to varying data complexity among the conditions, as measured to some degree by Fisher’s discriminant ratio statistic.  This variation in data complexity could likely be compensated by adjusting sample size for individual chemical-tissue conditions, thus suggesting a need for a preliminary survey of transcriptomic responses before launching a full scale classifier discovery effort.  While GSEA appeared to provide a flexible and effective tool for application of gene classifiers, a similar but more refined algorithm, connectivity mapping, should also be explored for ecotoxicological applications.  The distribution characteristics of classifiers across tissues, chemicals, and TF networks suggested a differential biological impact among the EDCs on zebrafish transcriptome involving some basic cellular functions.

chemical abbreviations: EE2, 17α-ethynyl estradiol; FAD, fadrozole; TRB, 17 -trenbolone; FIP, fipronil; PRO, prochloraz; FLU, flutamide; MUS, muscimol; KET, ketoconazole; TRI, trilostane; VIN, vinclozolin

overall_design: Since this study was conducted in several phases, three different version of Agilent zebrafish two color microarrays were used based on their availability at the time.  These include G2518A (designID 013223) and G2519F (designID 015064, 019161). There were a total of 58 treatment conditions with various combinations of chemical, tissue type, exposure time, and gender.  Each condition contained eight to 12 independent samples, half from chemical-treated fish and half from water- control fish.

first: David

last: Bencic

first: Adam

last: Biales

first: Robert

last: Flick

first: Jim

last: Lazorchak

first: Daniel

last: Villeneuve

first: Gerald

middle: T

last: Ankley


title: The transcriptome of ejaculates used for successful/failed in vitro-fertilization

city: 20246 Hamburg

first: Andrej-Nikolai

last: Spiess

address: Martinistr. 52

department: Andrology

country: Germany

institute: University Hospital Hamburg-Eppendorf

summary: We investigated the transcriptome obtained from microarray analysis of human ejaculates used in an IVF programme. The gene expression profiles are to be correlated with successful/failed induction of oocyte fertilisation and/or pregnancy. Since human ejaculates are often contaminated with so-called 'round cells' (mostly somatic cells such as leukocytes and macrophages, but also immature germ cells), a considerable part of the gene expression pertains not to spermatozoa. Rigorous statistical analysis of the data is to be used to extract genes that correlate with fertilization success.

overall_design: A set of 25 human ejaculates (12 pregnancy; 3 biochemical pregnancy; 7 oocyte fertilization; 3 no oocyte fertilization) from an IVF procedure were used for RNA extraction and microarray hybridization.

first: Heike

last: Cappallo-Obermann

first: Vera

last: Baukloh

first: Wolfgang

last: Schulze


title: Cell cannibalism, a cell-death process driven by the Transforming Growth Factor-β and the Nuclear Protein 1, opposes to metastasis in pancreatic cancer

status: Public on Jun 18 2012

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

summary: Pancreatic adenocarcinoma (PDAC) is an extremely deadly disease for which all treatments available have failed to improve life expectancy significantly. This may be explained by the high metastatic potential of PDAC cells, which results from their physiological dedifferentiation towards a mesenchymal phenotype. Some PDAC present cell-in-cell structures but their origin and significance is currently unknown. We show here that cell-incells form after cell cannibalism. We found PDAC patients whose tumors display cell cannibalism develop less metastasis than those without. In vitro, cell cannibalism was enhanced by the TGFβ and repressed by the Nuclear protein (Nupr)1, and was coupled to a defective epithelial-to-mesenchymal transition of PDAC cells. Cannibalism ends with death of PDAC cells, consistent with a metastasis suppressor role for this phenomenon. Hence, our data indicates a protective role for cell cannibalism in PDAC and identifies Nupr1 and TGFβ as molecular regulators of this process.

overall_design: Cell culture and culture reagents. Panc-1 cells were cultured in Glutamax-containing DMEM(Invitrogen) and BxPC3 in RPMI (Invitrogen), both supplemented with 10% FBS (PAA Laboratories). All cells were maintained at 37°C, 5% CO2, H2O saturated. TGFβ1 (Peprotech) was used at 10 ng/ml .siRNA-mediated gene silencing. Panc-1 cells were seeded in 6-wells plates to reach 30% to 50% confluence. Twenty-four hours later, a mix containing 2.2 pmoles of siRNA and 8 μl of the transfection reagent INTERFERIN (Polyplus Transfection) was added to the culture medium according to manufacturer’s instructions. Panc-1 Nupr1-depleted cells (sip8), and controls cells (siCtrl) were further incubated for 7 or 24 hrs before TGFβ1 treatment without change of medium.

first: Carla

last: Cano

first: María

last: Sandí

first: Tewfik

last: Hamidi

first: Olivier

last: Turrini

first: Laurent

last: Bartholin

first: Céline

last: Loncle

first: Véronique

last: Secq

first: Stéphane

last: Garcia

first: Gwen

last: Lomberk

first: Guido

last: Kroemer

first: Raul

last: Urrutia

first: Juan

last: Iovanna


title: Gene expression comparison of L. reuteri ATCC PTA 6475 and tetrahydrofolate synthase 1 mutant

status: Public on Jun 11 2012

city: Houston

first: Toni-Ann

last: Mistretta

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

summary: Gene expression comparison of L. reuteri ATCC PTA 6475 and tetrahydrofolate synthase 1 in MRS medium in anaerobic conditions at 37C.

overall_design: Includes 3 biological replicates and dye-swaps, with one additional replicate  for ATCC PTA 6475 versus tetrahydrofolate synthase 1 mutant. Reference time point is L. reuteri ATCC PTA 6475.

first: Carissa

last: Thomas


title: Comparative analyses of transcriptome during skeletal muscle development between pig breeds differing in muscle growth rate by deep-sequencing

city: College Station

first: Jason

last: Karpac

state: Texas

address: Reynolds Medical Building

department: Molecular and Cellular Medicine

institute: Texas A&M University Health Sciences Center

summary: Obese and lean pig show breed-specific traits in muscle growth and meat quality. However, the mechanisms underlying remains unclear. Here, we reported the first genome-wide muscle development research from embryonic to 6 months old between Lantang (obese) and Landrace (lean) using Solexa/Illumina’s Genome Analyzer. We obtained 4.22±0.9×107 total reads per sample with approximately 5×106 distinct tags. Filtered adaptor tags, empty reads, low quality tags and tags of copy number =1, we obtained 3.84±0.9×107 clean total tags with 1.5±0.5×106 clean distinct tags.

overall_design: 20 libraries of longissimus muscle samples were sequenced in Lantang and Landrace at days 35, 49, 63, 77, 91 prenatal and 2, 28, 90, 120, 180 postnatal days.

first: Xiao

last: Zhao

first: Dolin

last: Mo

first: Anning

last: Li

first: Wen

last: Gong

first: Yue

last: Zhang

first: Shuqi

last: Xiao

first: Yaosheng

last: Chen


title: The role of SOX10 in human melanoma

status: Public on Jul 03 2012

city: Zurich

first: Michal

last: Okoniewski

state: Zurich

address: Binzmühlestrasse 130

country: Switzerland

institute: ETH Zurich

summary: We have shown that Sox10 plays a crucial role in the initiation and maintenance of giant congenital nevi and melanoma in a mouse model of melanoma.To dissect the molecular mechanisms and analyze the role of SOX10 in the maintenance of human melanoma, we have performed microarray study.

overall_design: Human melanoma cell line M010817 was transfected with either control shRNA or SOX10 shRNA.  RNA was isolated at 48 hours and 96 hours after transfection and subjected to hybridization on Affymetrix microarrays.

first: Olga

last: Shakhova

first: Lukas

last: Sommer


title: ChIP-Seq for NIPBL for SMC1 in human lymphoblastoid cells (hLCLs)

status: Public on Jun 01 2012

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The gene expression program is regulated by a cell-type specific chromosome architecture. The connection between enhancer and promoter regions is dependent on a protein complex containing Nipbl, Mediator and Cohesin. To gain insights into the chromosome architecture of human differentiated cells, we profiled NIPBL and SMC1 in lymphoblastoid cells (LCLs).

overall_design: DNA was enriched from hLCLs and chromatin immunoprecipitations (ChIPs) were analyzed by Solexa sequencing. ChIPs were performed using an antibody against NIPBL and SMC1. Whole cell extract is provided for background.

first: Steve

last: Bilodeau


title: Differentially regulted genes in neural stem cells treated by oleanolic acid

status: Public on Jun 02 2012

city: Shanghai

first: Huang

last: Jianhua

address: Wulumuqi Middle Road

institute: Institute of Integrated Chinese and Western Medicine, Huashan Hospital, Fudan University

summary: Oleanolic acid significantly inhibited neurosphere formation in a dose-dependent manner, and achieved a maximum effect at 10 nM. OA also reduced the 5-ethynyl-2’-deoxyuridine (EdU) incorporation into NSCs, indicating an inhibition on proliferation of NSCs. Next, in western blotting analysis, the protein expression of neuron-specific marker tubulin-βⅢ (TuJ1) and Mash1 was increased, while the astrocyte-specific marker glial fibrillary acidic protein (GFAP) decreased. In immunofluorescence analysis, OA significantly elevated the percentage of TuJ1-positive cells and reduced GFAP-positive cells. Using DNA microarrays, 183 genes were found to be differentially regulated by OA.

overall_design: Neural stem cells derived form mouse embrynic brains were treated with Oleanolic acid or not. Each group had 4 biological relicates each from a mouse.

first: Jianhua

last: Huang

first: Ziyin

last: Shen


title: MicroRNA expression data from leukemia and breast cancer cell lines with/without treatment with microparticles

status: Public on Jun 09 2012

city: Sydney

first: Ritu

last: Jaiswal

address: 92 - 94 Parramatta Rd

country: Australia

institute: The University of Sydney

summary:
Microparticles (MPs) comprise the major source of systemic RNA including microRNA (miRNA), the aberrant expression of which appears to be associated with stage, progression and spread of many cancers. We have shown MPs to transfer multidrug resistance proteins accross both haematological and and non-haematological cancers.
using microarray miRNA profiling analysis we now analyze changes in miRNA profiles of both cancer types following microparticle transfer. We identified certain upregulated miRNAs in both cancer types.

overall_design: Total RNA was extracted and pooled from duplicate experiments for hybridization on Affymetrix microarrays from (i) the parental drug sensitive leukaemia (CEM) or breast cancer (MCF-7) cells, (ii) their Multidrug Resistant strains leukaemia (VLB100) or breast cancer ( DX cells), (iii) the microparticles isolated from the resistant cells: VLBMP or DXMP, and (iv) the cocultured samples: sensitive cell co-incubated with MPs from their resistant cells ( leukaemia: CEM+VLBMP) or(breast cancer:  MCF-7+DXMP). We sought to examine the miRNA profiles of the drug sensitve cells after MP transfer from drug resistant cells across leukaemia nd breact cancer cell lines.

first: Joyce

first: Frederick

last: Luk

first: Mary

last: Bebawy


first: Toni-Ann

last: Mistretta

summary: Gene expression comparison of L. reuteri ATCC PTA 6475 and tetrahydrofolate synthase 2 mutant in MRS medium in anaerobic conditions at 37C.

overall_design: Includes 3 biological replicates and dye-swaps for ATCC PTA 6475 versus tetrahydrofolate synthase 2 mutant. Reference time point is L. reuteri ATCC PTA 6475.

first: Carissa

last: Thomas


title: Comparative transcript profiling of gene expression between seedless Ponkan mandarin (Citrus reticulata Blanco) and its seedy wild type during floral organ development

status: Public on May 22 2012

city: wuhan

first: Qiu

last: wen-ming

state: hubei

address: shizishan street

institute: Key Laboratory of Horticultural Plant Biology (Ministry of Education)

summary: Seedlessness is an important agronomic trait for citrus, and male sterility (MS) is one main cause of seedless citrus fruit. However, the molecular mechanism of citrus seedlessness remained not well explored. An integrative strategy combining SSH (suppression subtractive hybridization) library with cDNA microarray was employed to study the underlying mechanism of seedlessness of a Ponkan mandarin seedless mutant (Citrus reticulate Blanco). Screening with custom microarray, a total of 279 differentially expressed clones were identified, and 133 unigenes (43 contigs and 90 singletons) were obtained after sequencing. Gene Ontology (GO) distribution showed that the majority of differential genes involved in metabolic process, responded to stimulus and functioned as DNA/RNA binding, catalytic activity and oxidoreductase activity. Expression dynamics of some candidate clones revealed a gene encoding male sterility protein 2 was highly up-regulated, while several transcription factors (TFs) such as AP2/EREBP, MYB, WRKY, NAC and C2C2-GATA zinc-finger domain TFs were specifically down-regulated in the seedless mutant compared with the wild type. Our research highlighted some candidate pathways that participated in the citrus male gametophyte development and could be beneficial for seedless citrus breeding in the future.

overall_design: Flower buds from the seedless citrus mutant and its wild type were collected at four developmental stages: quaring stage (SF, about 20 DBF), medium bud stage (MF, about 10 DBF), flowers at full bloom stage (BF) and young ovaries of 2-3 days after flowering (OV). Total RNA extracted from the mutant and the wild type was hybridized to the array. The hybridization was performed in duplicate by dye swap.

last: Wen-Ming

first: Zhu

last: An-Dan

first: Wang

last: Yao

first: Chai

last: Li-Jun

first: Ge

last: Xiao-Xia

first: Deng

last: Xiu-Xin

first: Guo

last: Wen-Wu


title: Methodoligies for identifying lead toxicity

city: Chicago

first: Zarema

last: Arbieva

address: 835 S. Wolcott A301

department: RRC

institute: UIC

summary: Quantifying impact of lead on cytokine production and gene expression in PBMCs

overall_design: Cells were treated with 10mkM lead acetate for one day, washed and grown in RPMI for the second day. Lead acetate was not added to matching control cells.

first: Igor

last: Gavin

first: Bruce

last: Gillis


title: microRNA-143 downregulates Hexokinase 2 in colon cancer cells

status: Public on May 02 2012

city: Berlin

first: Lea

middle: Haarup

last: Gregersen

address: Robert-Rössle-Str. 10

institute: Max-Delbrück-Centrum für Molekulare Medizin (MDC)

summary: MicroRNAs (miRNAs) have emerged as important gene regulators and are recognized as key players in tumorigenesis. miR-143 is reported to be down-regulated in several cancers, but knowledge of its targets in colon cancer remains limited. To investigate the role of miR-143 in colon cancer, we have employed a microarray based approach to identify miR-143 targets. Based on seed site enrichment analyses and unbiased word analyses, we found a significant enrichment of miRNA binding sites in the 3’-untranslated regions (UTRs) of transcripts down-regulated upon miRNA overexpression. Here we identify Hexokinase 2 (HK2) as a direct target of miR-143 and show that re-introduction of miR-143 in the colon cancer cell line DLD-1 results in a decreased lactate secretion, indicating that miR-143 down-regulation of HK2 affects glucose metabolism in colon cancer cells.

overall_design: DLD-1 cells were transfected with 50 nM miR-143 duplex or mock transfected. Total RNA was harvested 24 hours post-transfection and analyzed on Affymetrix HG-U133 Plus 2.0 human arrays.

first: L

first: A

last: Jacobsen

middle: B

last: Frankel

first: J

last: Wen

last: Krogh

last: Lund


title: Impact of oxidative stress on ascorbate biosynthesis in Chlamydomonas via regulation of the VTC2 gene encoding a GDP-l-galactose phosphorylase

status: Public on May 03 2012

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

summary: The l-galactose (Smirnoff-Wheeler) pathway represents the major route to l-ascorbic acid (vitamin C) biosynthesis in plants. Arabidopsis thaliana VTC2 and its paralogue VTC5 function as GDP-l-galactose phosphorylases converting GDP-l-galactose to l-galactose-1-P, thus catalyzing the first committed step in the biosynthesis of l-ascorbate. Here we report that the l-galactose pathway of ascorbate biosynthesis described in higher plants is conserved in green algae. The Chlamydomonas reinhardtii genome encodes all the enzymes required for vitamin C biosynthesis via the Smirnoff-Wheeler pathway. We have characterized recombinant C. reinhardtii VTC2 as an active GDP-l-galactose phosphorylase. C. reinhardtii cells exposed to oxidative stress show increased VTC2 mRNA and l-ascorbate levels. We have also shown that enzymatic components of the ascorbate-glutathione system (e.g. ascorbate peroxidase, Mn superoxide dismutase, dehydroascorbate reductase) are up-regulated in response to increased oxidative stress. These results indicate that C. reinhardtii VTC2, like its plant homologs, is a key enzyme in ascorbate biosynthesis in green algae and together with components of the ascorbate recycling system represents the major route in providing  protective levels of ascorbate in oxidatively stressed algal cells.  Our results suggest that C. reinhardtii cells exposed to oxidative stress conditions produce more ascorbate both by de novo synthesis (Smirnoff-Wheeler pathway) and by recycling via the ascorbate-glutathione cycle.

overall_design: Sampling of Chlamydomonas 2137 exposed to hydrogen peroxide

first: Eugen

middle: I

last: Urzica

first: Lital

middle: N

last: Adler

first: Dudley

last: Page

first: Carole

last: Linster

first: Mark

last: Arbing

first: David

last: Casero

first: Matteo

last: Pellegrini

first: Steven

middle: G

last: Clarke


title: cDNA Microarray 1: Compression Xylem vs. Opposite Xylem

status: Public on May 06 2012

city: Malaga

first: Rocio

last: Bautista

address: Edificio de Bioinnovación, C/ Severo Ochoa, 34

country: Spain

institute: Plataforma Andaluza de Bioinformatica, Universidad de Malaga

summary: The within-tree variation in wood properties constitutes an exceptional model to study the mechanisms that adjust the different biosynthetic pathways providing substrates with the massive and variable demands of different biosynthetic reactions of cell wall polymers. Although a few genes have been reported as differentially expressed in differentiating compression wood compared to normal or opposite wood, the expression of a larger set of genes is expected to change due the broad range of features that distinguish this reaction wood. By combining the construction of different cDNA libraries with microarray analyses, using samples from different Pinus pinaster provenances collected in different years and geographic locations, we have identified a total of 496 genes that change their expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Consistent with the well-known structural and chemical characteristics of compression wood, a large number of genes involved in the biosynthesis of cell wall components were shown to be up-regulated during compression wood differentiation, including genes involved in synthesis of cellulose, hemicellulose, lignin and lignans. In particular, further analysis of a set of these genes involved in providing S-adenosylmethionine, ammonium recycling, lignin and lignans biosynthesis showed parallel expression profiles to levels of lignin accumulation in cells undergoing xylogenesis in vivo and in vitro. The comparative transcriptomic analysis of compression and opposite wood formation in this work have revealed a broad spectrum of coordinated transcriptional modulation of biosynthetic reactions for different cell wall polymers associated to within-tree variations in softwood structure and composition. In particular, it suggest the occurrence of a mechanism that modulates at transcriptional level genes encoding enzymes involved in S-adenosylmethionine synthesis and ammonium assimilation with coniferyl alcohol demand for lignin and lignan synthesis, as a key metabolic requirement in cells undergoing lignification.

overall_design: Two-condition experiment including dye-swap experiments, Compression Differentiating Xylem vs. Opposite Differentiating Xylem. Biological replicates: 4 compression xylem, 4 opposite xylew, harvested from four different individual pine trees. Two replicates per array.

middle: P

last: Villalobos

first: Sara

last: Diaz-Moreno

first: Manuel

last: Claros

first: Francisco

middle: R

last: Canton


title: Compression Xylem vs. Opposite Xylem

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

overall_design: Refer to individual Series


title: Changes in rice NILs shoot expression profile in response to drought stress at reproductive stage

status: Public on Jul 01 2012

first: Kouji

last: Satoh

summary: The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background (Donar parent: Aday Sel, Recurrent parent: IR64),  but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. We obtained gene expression profile in shoots of rice NILs under different levels of drought stress help to identify genes and mechanisms involved in drought stress.

overall_design: Comparison between drought and well-watered shoot.   Biological replicates: 3 (0.2FTSW (Fraction of transpirable soil water)-treated: 3, 0.5FTSW-treated: 3, 1.0FTSW-treated (control): 3).  Independently grown and harvested.  Genotypes: 5 (Drought resistant: IR77298-14-1-2-B-10, IR77298-5-6-B-18, Drought susceptive: IR77298-14-1-2-B-13, IR77298-5-6-B-11, IR64)  1 samples derived from 5 plants grown under same conditons.  Total 45 samples, 30 data

first: Ali

last: Moumeni

first: Ramaiah

last: Venuprasad

first: Somayanda

last: Impa

first: Rachid

last: Serraj

first: Arvind

last: Kumar

first: Hei

last: Leung

first: Shoshi

last: Kikuchi


title: Gene Expression Analysis of Thymic Neoplasms

city: Indianapolis

first: Sunil

last: Badve

state: IN

address: 350 West 11th street

institute: Indiana University

summary: Histologic classification of thymomas has significant limitations since complete surgical excision can be curative. In order to better understand the biology of the disease processes, we performed whole genome gene expression analysis. RNA was extracted from fresh frozen tumors from 36 patients with thymomas and follow-up data was available. Gene expression data was correlated with clinicopathological data. Using the Illumina BeadStudio® platform and Human Ref-8 Beadchip, gene expression data was analyzed by Partek®, and Ingenuity Pathways Analysis (IPA). Validation of the chosen genes was performed using quantitative real-time RT-PCR (qRT-PCR). Unsupervised clustering resulted in identification of four clusters of tumors (C1-C4). Using IPA, the top significant biological functions and pathways displayed cell cycle related category and genes in C1 and C2. Carbohydrate metabolism and cellular growth and proliferation were among the most significant for C3 and C4, respectively. On the other hand, cancer and metabolism related functions and pathways were prominent in clinical outcome including metastasis and stage. Our gene expression analysis representing one of the largest series in literature, revealed at least four distinct clusters of thymic tumors. The study identified number of metastasis-associated genes that are potential candidates for therapeutics

overall_design: 41 Samples, 3 Cell Line samples with 1 duplicate (total = 4). 37 Patient samples including 1 duplicate (total = 37).

first: Yesim

last: Polar

first: Chirayu

last: Goswami


title: microRNA expression in epicardial mesothelial cells undergoing Epithelial-to-Mesenchymal Transition

status: Public on Apr 27 2012

city: Odense

first: Hasse

middle: B.

last: Jensen

address: Winsløwparken 21, 3.

country: Denmark

institute: University of Southern Denmark

summary:
Cardiac fibrosis is a detrimental pathophysiological state involved in a number of cardiovascular diseases. Myofibroblasts mediate fibrosis by excessive remodeling of the extracellular matrix, which ultimately leads to tissue stiffness and impaired heart performance. Recently, it was shown that a substantial fraction of cardiac myofibroblasts may originate from the epicardium through Epithelial-to-Mesenchymal Transition (EMT).
We have developed a cellular model of EMT in which adult murine epicardium-derived cells are differentiated into myofibroblast-like cells in the presence of Interleukin-1beta, Tumor Necrosis Factor-alpha, or Transforming Growth Factor-beta. Using this model of EMT, the microRNAome was assessed by microRNA (miRNA) arrays. Subsequently, expression levels of differentially expressed miRNAs were validated by qPCR. These miRNAs were targeted by transfecting epicardium-derived cells with anti- or pre-miRs prior to EMT initiation. The ability of the anti- or pre-miRs to inhibit EMT was assessed on a number of phenotypic markers.
In this study we have identified a number of miRNAs that potentially play an intrinsic role in cardiac EMT. We speculate that by targeting those miRNA, the onset and long-term progression of cardiac fibrosis can be substantially reduced.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design:
Epicardial mesothelial cells were isolated and expanded from the epicardium of adult rats (8-10 weeks). Epithelial-to-mesenchymal Transition was induced by 10 ng/mL Interleukin-1beta, Tumor Necrosis Factor-alpha, or Transforming Growth Factor-beta1 for 48h. The assocciated differential microRNA expressions relative to a control treatment was computed by microRNA arrays.
The experiment was conducted on biological quadruplicates for the control treatment and biological triplicates for cytokine treatments.

last: Brønnum

first: Ditte

middle: C

last: Andersen

first: Mikael

last: Schneider

first: Maria

last: Boysen


title: cDNA Microarray 2: Compression Xylem vs. Opposite Xylem

first: Rocio

last: Bautista

first: David

last: Villalobos

first: Sara

last: Diaz-Moreno

first: Manuel

last: Claros

last: Canton


title: Transcriptional response of FZF1 alleles from S. cerevisiae and S. paradoxus to the addition of sulfite

status: Public on May 01 2012

city: Saint Louis

first: Justin

last: Fay

state: Missouri

address: Center for Genome Sciences Rm 5526, 4444 Forest Park Pkwy

institute: Washington University

summary: Transcriptional profiling of four different yeast FZF1 alleles: S. cerevisiae, S. paradoxus and two reciprocal chimeras with the coding and 5' noncoding region from opposite species of S. cerevisiae and S. paradoxus, both before and 15 minutes after sulfite addition.  FZF1 is a transcription factor that is known to be turned on in response to sulfite.  Here we determine whether the FZF1 allele from two species leads to different transcriptional responses and the effect of the individual noncoding and coding regions on the transcriptional response.

overall_design: Two-color experiment,  4 Strains x 2 Timepoints each compared to a reference pool made up of all samples.  3 Biologic replicates. With dye-swaps

first: Elizabeth

last: Engle


title: Whole Transcriptome RNA Sequencing Detects Multiple 1a,25-Dihydroxyvitamin D3-Sensitive Metabolic Pathways in Zebrafish Embryos

status: Public on Jun 29 2012

city: Baltimore

first: Yuji

last: Zhang

state: MD

address: 660 W. Redwood Street

institute: University of Maryland

summary: Vitamin D receptors (VDR) are abundantly expressed in developing zebrafish as early as 48 hours post-fertilization, and prior to the development of a mineralized skeleton, and mature intestine and kidney.  We probed the role of VDR in zebrafish biology by examining changes in expression of RNA by whole transcriptome shotgun sequencing (RNA-seq) in fish treated with picomolar concentrations of the VDR ligand and hormonal form of vitamin D3, 1a,25-dihydroxyvitamin D3 (1a,25(OH)2D3).  We observed significant changes in RNAs encoding proteins of fatty acid, amino acid, and xenobiotic metabolism pathways, and RNAs of transcription factors, leptin, peptide hormones, receptor-activator of NFkB ligand (RANKL), and calcitonin-like ligand receptor pathways.  Early small, and subsequent massive changes in >10% of expressed cellular RNAs were observed.  At day 2 (24h 1a,25(OH)2D3-treatment), only 5 RNAs were differentially expressed (hormone vs. vehicle).  On day 4 (72h-treatment), 78 RNAs; on day 6 (120h-treatment) 1040 RNAs; and on day 7 (144h-treatment), 1755 RNAs were differentially expressed in response to 1a,25(OH)2D3.  Fewer RNAs (n = 482) were altered in day 7 embryos treated for 24h with 1a,25(OH)2D3 vs. those treated with hormone for 144h.   At 7 days, in 1a,25(OH)2D3-treated embryos, pharyngeal cartilage was larger and mineralization was greater.  Changes in expression of RNAs for transcription factors, peptide hormones, and RNAs encoding proteins integral to fatty acid, amino acid, leptin, calcitonin-like ligand receptor, RANKL and xenobiotic metabolism pathways, demonstrate heretofore unrecognized mechanisms by which 1a,25(OH)2D3 functions in vivo in developing eukaryotes.

overall_design: Zebrafish embryos were obtained from mating of Segrest wild-type (SWT) parents under controlled barrier conditions, in the Mayo Clinic Zebrafish Core Facility, in Instant Ocean media .  Zebrafish embryos (25-30) were placed in 20 mL embryo medium (pH 7.2) containing 1-phenyl-2-thiourea (PTU) (0.003% (w/v) and were maintained at 28-30 oC.  At 24 hpf (1 day post fertilization, dpf), 10 microliters of 1a,25(OH)2D3  in ethanol was added to embryos maintained in 20 mL fresh embryo medium with PTU.  The final concentration of 1a,25(OH)2D3 was 300 pM.  Control zebrafish were treated with 10 microliters ethanol alone (vehicle controls).  The medium containing either 300 pM 1a,25(OH)2D3 or vehicle was changed every 24 h .   In experiment 1, at 2, 4, 6 and 7 dpf embryos/larvae were removed and immediately frozen at -80 0C for later RNA preparations.  25-30 embryos per set were used for preparation on RNA.  At the same times, 7-12 embryos were fixed in 4% paraformaldehyde in 0.75 X Dulbecco’s phosphate buffered saline (DPBS).  In experiment 2, 6 dpf larvae were treated with 1a,25(OH)2D3 (300 pM) or vehicle for 24 h.  RNA was prepared from three sets of larvae.

first: Rajiv

last: Kumar


title: Basal expression in daDREAM transgenic mouse hippocampus

status: Public on Apr 25 2012

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary: Changes in nuclear Ca2+ homeostasis activate specific gene expression programs and are central to the acquisition and the plastic storage of memories. DREAM /KChIP proteins form heterotetramers that bind DNA and repress transcription in a Ca2+-dependent manner. Single ablation of one member of the DREAM/KChIP family may result in a mild or the absence of phenotype due to partial gene compensation. To study the function of DREAM/KChIP proteins in the brain, we used transgenic mice expressing a Ca2+-insensitive/CREB-independent dominant active mutant DREAM (daDREAM). We show that daDREAM controls the expression of several activity-dependent transcription factors including Npas4, Nr4a1, Mef2C, JunB and c-Fos, as well as the chromatin modifying enzyme Mbd4 and proteins related to actin polymerization like Arc and gelsolin. Thus, directly or through these targets, expression of daDREAM in the forebrain resulted in a complex phenotype characterized by i) impaired learning and memory, ii) loss of recurrent inhibition and enhanced LTP in the dentate gyrus without affecting Kv4-mediated potassium currents, and iii) modified spine density in DG granule neurons. Our results propose DREAM as a master-switch transcription factor regulating several activity-dependent gene expression programs to control synaptic plasticity, learning and memory.

overall_design: We used Affymetrix microarrays (GeneChip Mouse Genome 430 2.0) to compare global gene expression in wild type (WT) versus transgenic hippocampi (L26 mice). For ech type of sample three hybridizations were carried-out (independent biological replicates).

first: Britt

last: Mellström

first: Shira

last: Knafo

first: Ignasi

last: Sahún

first: Ana

last: Ruiz-Nuño

first: Patricia

last: Murtra

first: Alejandro

last: Higueras

first: Xiangyao

last: Li

first: Rosa

last: Gomez-Villafuerte

first: Asta

last: Kastanauskaite

first: Magali

last: Savignac

first: Michael

last: Errington

first: Rafael

last: Maldonado

first: Min

last: Zhuo

first: John

last: Jefferys

first: Javier

last: DeFelipe

first: Mara

last: Dierssen

first: Tim

middle: V

last: Bliss

first: Jose

last: Naranjo


title: Expression analysis of Trichoderma reesei QM9414 and delta-blr1, delta-blr2 and delta-env1 in light and darkness

status: Public on Apr 01 2012

city: Vienna

first: Doris

last: Tisch

state: Vienna

address: Gumpendorferstraße 1a

department: Chemical Engineering

country: Austria

institute: Technical University of Vienna

summary:
Investigation of whole genome gene expression level changes in response to different light conditions of the T. reesei QM9414 deletion strains delta-blr1, delta-blr2 and delta env1 cultivated on 1% microcrystalline cellulose.

Perception and proper interpretation of environmental signals is crucial for survival in any natural habitat. Although the biotechnological workhorse Trichoderma reesei (Hypocrea jecorina) is predominantly known for its capability of efficient plant cell wall degradation, recent studies show that it has not lost its evolutionary heritage. Transmission of nutrient signals via the heterotrimeric G protein pathway has been shown to be influenced by light. We show that this interconnection is mainly established by the light regulatory protein ENV1 and the phosducin-like protein PhLP1 via mutual transcriptional regulation and influence on GNB1 (G protein beta subunit) function. ENV1 thereby exerts a more severe effect on gene transcription than BLR1 or BLR2. Lack of either one of the photoreceptors or PhLP1, GNB1 or GNG1 leads to a partial shutdown of processes upregulated in light, indicating that heterotrimeric G protein signalling exerts its major function in light and is a target of the light response machinery. Consequently, signals transmitted via the G protein pathway are of different relevance in light and darkness. Investigation of regulation of glycoside hydrolases as one of the major output pathways of this mechanism revealed that 79% of all genes belonging to this group, representing all GH-families available in T. reesei, are potentially responsive to light. We conclude that ENV1 is a key factor in connecting nutrient signalling with light response and establishes a signalling output pathway independent of BLR1 and BLR2.

overall_design: We used two biological replicates of three T. reesei strains (delta-blr1, delta-blr2 and delta-env1), cultivated in constant light (LL, 1800 lux) or constant darkness (DD) on microcrystalline cellulose. The strains used in this study were cultivated, hybridized and analyzed together with strains and samples from GSE27581; the corresponding wild-type strain QM9414 samples have accession numbers GSM683732, GSM683733, GSM683734 and GSM683735.

first: Monika

last: Schmoll


title: ICGC Pancreas: Genomic analysis reveals roles for chromatin modification and axonguidance in pancreatic cancer

status: Public on Mar 31 2012

first: Jianmin

last: Wu

state: NSW

address: 370 Victoria Street Darlinghurst

department: Cancer Division

institute: Garvan Institute of Medical Research

summary:
Pancreatic cancer (PC) is the fourth leading cause of cancer death with an overall 5-year survival rate of < 5%, a statistic that has changed little in almost 50 years. A deeper understanding of the underlying molecular pathophysiology is expected to advance the urgent need to develop novel therapeutic and early detection strategies for this disease. Genomic characterisation of PC has previously relied on targeted PCR based exome sequencing of small cohorts of mixed primary and metastatic lesions propagated as xenografts or cell lines (Jones et al, Science 321:1801-1806), leaving the true mutational spectrum of the clinical disease largely unresolved. Here we use exome sequencing (https://www.ebi.ac.uk/ega/studies/EGAS00001000154) and copy number analysis (not submitted) to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (Stage I and II) pancreatic adenocarcinoma. Detailed analysis of 99 informative tumours identified 1982 non-silent mutations and 1628 significant CNV events, and defined 439 significantly mutated genes based on stringent Significant Mutated Gene or GISTIC analysis. Integration with functional data from in vitro shRNA and in vivo Sleeping Beauty-mediated somatic mutagenesis screens provided supportive evidence for 184 of these as candidate driver mutations. Pathway based analysis recapitulated clustering of mutations in core signalling pathways in PC, and identified multiple new components in each, particularly in DNA damage repair mechanisms (ATM, TOP2A, TLM, RPA1). We also identified frequent somatic aberrations in genes involved in novel mechanisms including chromatin modification (SWI/SNF complex members, SETD2, EPC1), and axon guidance (Semaphorin, Slit, Netrin and Ephrin signalling), extending the number of core perturbed pathways in PC. Aberrant expression of axon guidance genes co- segregated with poor patient survival, and in animal models was associated with disease development and progression, further implicating perturbation of the axon guidance pathway as a novel mechanism important in PC.
This dataset includes gene expression data from 90 primary tumour samples, 88 of which were used in this manuscript for survival analysis. Much of this data is also available through the International Cancer Genome Consortium (ICGC) Data Portal (http://dcc/icgc.org), under the project code: "Pancreatic Cancer (QCMG, AU)". Access to the strictly restricted clinical data must be made through the ICGC Data Access Compliance Office (http://www.icgc.org/daco).

overall_design: This dataset contains expression array data from 90 primary pancreatic ductal adenocarcinoma samples. One sample is present with two biological replicates, all others have 1 biological replicate.

first: Andrew

last: Biankin

first: Nicola

last: Waddell

first: Karin

last: Kassahn

first: Marie-Claude

last: Gingras

first: Amber

last: Johns

first: David

last: Miller

first: Peter

last: Wilson

first: Ann-Marie

last: Patch

last: Chang

first: Mark

middle: J

last: Cowley

first: Brooke

last: Gardiner

first: Sarah

last: Song

first: Ivon

last: Harliwong

first: Senel

last: Idrisoglu

first: Craig

last: Nourse

first: Ehsan

last: Nourbakhsh

first: Suzanne

last: Manning

first: Shivangi

last: Wani

first: Milena

last: Gongora

first: Marina

last: Pajic

first: Christopher

last: Scarlett

first: Anthony

last: Gill

first: Elizabeth

middle: A

last: Musgrove

first: Robert

last: Sutherland

first: Andreia

last: Pinho

first: Ilse

last: Rooman

first: Matthew

last: Anderson

first: Oliver

last: Holmes

first: Conrad

last: Leonard

first: Darrin

last: Taylor

first: Scott

last: Wood

first: Christina

last: Xu

first: Katia

last: Nones

first: Lynn

last: Fink

first: Angelika

last: Christ

last: Bruxner

first: Nicole

last: Cloonan

first: Gabriel

last: Kolle

first: Felicity

last: Newell

last: Pinese


title: Comparison of Atlantic salmon individuals with different outcomes of cardiomyopathy syndrome (CMS)

status: Public on Mar 30 2012

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Experimentally infected Atlantic salmon post-smolts exhibited different outcomes of disease (CMS). High responder (HR) fish were characterized with sustained and increased viral load and pathology in heart tissue. Low responder (LR) fish showed declining viral load from 6-10 weeks post infection (wpi) and absence of pathology. Global gene expression analyses were performed to compare these groups. Virus-responsive genes involved in early antiviral and innate immune responses were upregulated equally in LR and HR at the first stage (2-4 wpi), reflecting the initial increase in virus replication. Repression of heart muscle development indicated the early onset of pathology. By six weeks both responder groups had comparable viral loads, while increased pathology was observed in HR fish. This was reflected by induced expression of genes implicated in apoptosis and cell death, presumably related to lymphocyte regulation and survival. In contrast, LR fish showed earlier activation of NK cell-mediated cytotoxicity and NOD-like receptor signaling pathways. At the late stage of infection, increased pathology and viral load in HR was accompanied by a broad activation of genes involved in adaptive immunity and particularly T cell responses, probably reflecting the increased infiltration and homing of virus-specific T cells to the infected heart. This was in sharp contrast to LR fish, where recovery and reduced viral load was associated with a significantly reduced transcription of adaptive immunity genes and activation of genes involved in energy metabolism.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Atlantic salmon post smolts (average weight 50g) were challenged with the putative CMS causing pathogen (PMCV). Heart was sampled from challenged and control fish at 2, 4, 6, 8 and 10 wpi. Heart pathology was detectable earliest at 6 wpi and from this time-point, individuals were assigned to HR and LR.

first: Gerrit

last: Timmerhaus

first: Sven

middle: M

last: Jørgensen

first: Sergey

last: Afanasyev

first: Harald

last: Takle


title: Transcript level responses of Plasmodium falciparum to antimycin A

status: Public on Apr 20 2012

city: London

first: Sarah

last: Tarr

address: Gower Street

department: ISMB

institute: UCL

summary: Abstract: The mitochondrial electron transport chain is essential to Plasmodium and is the target of the antimalarial drug atovaquone.  The mitochondrial genomes of Plasmodium sp. are the most reduced known, and the majority of mitochondrial proteins are encoded in the nucleus and imported into the mitochondrion post-translationally.  Many organisms have signalling pathways between the mitochondria and the nucleus to regulate the expression of nuclear-encoded mitochondrially-targeted proteins, for example in response to mitochondrial dysfunction.  We have studied the gene expression profiles of synchronous Plasmodium falciparum treated with an LD50 concentration of the complex III inhibitor antimycin A, to investigate whether such pathways exist in the parasite.  There was a broad perturbation of gene expression.  Some effects were attributable to a delay in the gene expression phase of drug-treated parasites.  However, our data also indicated regulation of mitochondrial stress response genes and genes involved in pyrimidine biosynthesis.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: 3 biological replicates each for treated and untreated: control (1/2000 DMSO) and LD50 antimycin A, respectively.  Normalised microarray data for antimycin A-treated parasites were contrasted against untreated (DMSO) controls.

first: R

middle: E

last: Nisbet

first: Christopher

last: Howe


title: Immunodominant myelin basic protein fragments induce mechanical hypersensitivity.

status: Public on Mar 03 2012

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: An insulating myelin sheath ensures saltatory conduction of mechanosensory A  afferents. Myelin damage results in the electrical instability of A  fibers and the ability to generate pain in response to light touch/pressure (mechanical allodynia). We have hypothesized and then established that the release of T cell epitopes of myelin basic protein (MBP) enables nociceptive circuitry in myelinated fibers. Thus, mass spectrometry analysis of the rat sciatic nerve proteome followed by bioinformatics examination of the datasets revealed a loss of MBP and activation of T-helper cell signaling in the nerves undergoing chronic constriction injury (CCI). Matrix metalloproteinase-9 (MMP-9) proteolysis resulted in the MBP digest peptides, including the MBP84-104 and MBP68-86 regions, which exhibit prominent immunogenic epitopes. Myelin-forming Schwann cells and paranodal areas accumulated MHCII, MMP-9 and the degraded MBP at the sciatic nerve injury site. Administration of the immunodominant MBP84-104 and MBP68-86 peptides but not of the control peptides in a naïve rat sciatic nerve produced robust mechanical allodynia. Allodynia was accompanied by the T cell infiltration and an increase in MHCII, IL-17A and TNF-  levels at the nerve injection site and the segmental ganglia. The pro-nociceptive activity of the synthetic MBP84-104 diminished in athymic nude rats lacking T cells. SB-3CT, an antagonist of MMP-9, inhibited mechanical allodynia, neuroinflammation and spinal sensitization after CCI. Collectively, our novel data implicate, for the first time, MMP-mediated cleavage of MBP and the resulting MBP digest fragments as a major cause of neuropathic pain.

overall_design: Gene extression profiling of total RNAs extracted from rat sciatic nerves, dorsal root ganglion and spinal cords after MBP84-104 peptide injection

first: Veronica

last: Shubayev

first: Alex

middle: Y

last: Strongin


title: Differential lipid partitioning between adipocytes and tissue macrophages modulates macrophage lipotoxicity and M2/M1 polarization in obese mice.

status: Public on Mar 22 2012

city: Valencia

first: David

last: Montaner

address: C/ Eduardo Primo Yufera, 3

department: Bioinformatics

institute: CIPF

summary: Obesity-associated insulin resistance is characterized by a state of chronic, low-grade inflammation that is associated with the accumulation of M1 proinflammatory macrophages in adipose tissue. Although different evidence explains the mechanisms linking the expansion of adipose tissue and adipose tissue macrophage (ATM) polarization, in the current study we investigated the concept of lipid-induced toxicity as the pathogenic link that could explain the trigger of this response. We addressed this question using isolated ATMs and adipocytes from genetic and diet-induced murine models of obesity. Through transcriptomic and lipidomic analysis, we created a model integrating transcript and lipid species networks simultaneously occurring in adipocytes and ATMs and their reversibility by thiazolidinedione treatment. We show that polarization of ATMs is associated with lipid accumulation and the consequent formation of foam cell–like cells in adipose tissue. Our study reveals that early stages of adipose tissue expansion are characterized by M2-polarized ATMs and that progressive lipid accumulation within ATMs heralds the M1 polarization, a macrophage phenotype associated with severe obesity and insulin resistance. Furthermore, rosiglitazone treatment, which promotes redistribution of lipids toward adipocytes and extends the M2 ATM polarization state, prevents the lipid alterations associated with M1 ATM polarization. Our data indicate that the M1 ATM polarization in obesity might be a macrophage-specific manifestation of a more general lipotoxic pathogenic mechanism. This indicates that strategies to optimize fat deposition and repartitioning toward adipocytes might improve insulin sensitivity by preventing ATM lipotoxicity and M1 polarization.

overall_design: 15 samples; 2 genotypes and 2 time points

first: Antonio

last: Vidal-Puig

first: Xavier

last: Prieur

first: Joaquin

last: Dopazo