title: Global DNA methylation changes in Nile tilapia gonad during high-temperature induced masculinization

status: Public on Aug 27 2015

city: Tai'an

first: Xiangshan

last: Ji

address: 61 Daizong street

department: Collenge of animal science and technology

institute: Shandong Agricultural University

summary: In fish, the sex determining mechanisms can broadly be classified as genotypic (GSD), temperature-dependent (TSD), or genotypic plus temperature effects (GSD+TE). For the fish species with TSD or GSD+TE, extremely high or low temperature can affect its sex determination and differentiation. For long time, the underlying changes in DNA methylation that occur during high or low temperature induced sex reversal have not been fully clarified. In this study, we used Nile tilapia as a model to perform a genome-wide survey of differences in DNA methylation in female and male gonads between control and high temperature induced groups using methylated DNA immunoprecipitation (MeDIP). We identified the high temperature induction-related differentially methylated regions (DMRs), and performed functional enrichment analysis for genes exhibiting DMR. These identified differentially methylated genes were potentially involved in the connection between environmental temperature and sex reversal in Nile tilapia.

overall_design: In this study, four samples (control females, CF; control males, CM; induced females, IF; induced males, IM) were analyzed.

first: Xiang

middle: S

first: Li

middle: X

last: Sun

first: Yi

middle: Y

last: Wang

first: Yan

last: Zhao

first: Ning

last: Li

first: Hui


title: Differential expression of microRNA and snoRNA of normal mucosa in patients with solitary and synchronous primary colorectal cancer

status: Public on Aug 01 2015

city: Chengdu

first: Wen-Jian

last: Meng

state: Sichuan Province

address: No. 37, Guoxue Street

department: Department of Gastrointestinal Surgery

country: China

institute: West China Hospital, Sichuan University

summary: We evaluated the expression profile of miRNA and snoRNA of normal mucosa in five patients with synchronous CRCs and seven patients with solitary CRCs using the Affymetrix GeneChip miRNA 1.0 array. We found that global dysregulated miRNAs and snoRNAs in normal mucosa between solitary and synchronous CRC. Our findings represent the first comprehensive miRNA and snoRNA expression signatures in normal mucosa between solitary and synchronous CRC, which increases the understanding of the molecular basis of synchronous CRC, and firstly implicates the difference of genetic background in patients with solitary and synchronous CRC.

overall_design: Examination of microRNA and snoRNA expression of normal mucosa in patients with solitary and synchronous CRC.

first: W

middle: J

first: L

last: Yang

first: Q

last: Ma

first: Z

middle: Q

first: C

first: Y

last: Yu

middle: G

last: Zhou

first: X

middle: F


title: A microRNA and snoRNA expression profile in the synchronous colorectal cancer

summary: We evaluated the profile of miRNA and snoRNA expression in 5 synchronous CRC and matched normal colorectal tissues using the Affymetrix GeneChip miRNA 1.0 array. A total of 24 miRNA differential expressed transcripts which represent 27 mature miRNAs, including an oncogenic miR-17-92a and oncosuppressive miR-143-145 cluster, and a global up-regulation of snoRNAs were revealed in cancer tissues compared with matched normal tissues. Global miRNA expression could distinguish synchronous cancer from normal mucosa. Our findings represent the first comprehensive miRNA and snoRNA expression signatures for synchronous CRC, which increase the understanding of the molecular basis of synchronous CRC, and firstly implicate that dysregulation of snoRNAs and miRNA clusters may present therapeutic targets for synchronous CRC.

overall_design: Examination of microRNA and snoRNA expression in synchronous CRC and matched normal colorectal tissues

first: H

last: Zhang

first: G

last: Adell

last: Arbman


title: Expression data of Actinobacillus pleuropneumoniae 4074 in response to serum, epinephrine, norepinephrine and dopamine

status: Public on Sep 30 2015

city: Wuhan

first: Lu

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

summary: Bacteria can actively respond to host stress hormones (catecholamines), thereby regulate their growth, metabolism, virulence and other behaviors. This phenomenon provides new explanations of the fact that stress can influence the occurrence and development of infectious disease. Actinobacillus pleuropneumoniae is an important swine respiratory pathogen which has caused great economic losses worldwide. In our previous study, it has been discovered that catecholamines can regulate the expression of a great number of genes of A. pleuropneumoniae. In this study, the effect of catecholamines on A. pleuropneumoniae growth was detected using chemically defined medium (CDM). The results showed that in CDM, serum inhibited A. pleuropneumoniae growth, while epinephrine (Epi), norepinephrine (NE) and dopamine (DA) promoted A. pleuropneumoniae growth in the CDM containing serum. The known bacterial adrenergic receptor QseC didn’t play role in this process. According to growth features after supplementation of ions and genes expression changes caused by serum, Epi, NE and DA, it was discovered that serum established iron-restricted conditions for A. pleuropneumoniae and catecholamines removed the restrictions of iron. Apo-transferrin but not holo-transferrin also inhibited the growth of A. pleuropneumoniae in CDM. Catecholamines induced growth of A. pleuropneumoniae in the CDM containing apo-transferrin. Hence transferrin was one of the components in the serum that caused growth inhibition and was used by catecholamines to facilitate growth. In addition, TonB2 of A. pleuropneumoniae played essential roles in this process. The investigations in this study indicated that catecholamines promoted A. pleuropneumoniae growth by regulating iron acquisition and metabolism, which could be important during pathogenic processes.

sample_organism: Actinobacillus pleuropneumoniae serovar 1 str. 4074

overall_design: Five condition experiment, 4074 cultured in chemically defined medium (CDM) as control, in CDM+serum, in CDM+serum+epinephrine, in CDM+serum+norepinephrine, in CDM+serum+dopamine, respectively. Each condition has three biological replicates. Bacteria were harvested at mid-log phase and total RNA were extracted.

first: Zhaohui

last: Chen

first: Zhuofei

last: Xu

first: Rui


title: Select correlative genes involved in pathogenesis of idiopathic interstitial pneumonia by high-throughput sequencing analysis

status: Public on Sep 19 2015

city: Shanghai

first: Xianghua

last: Yi

address: NO.389, Xincun Rd, Putuo distrct

department: pathology

institute: Tongji hospital

type: Expression profiling by high throughput sequencing

summary: We report abonormally expressed genes of idiopathic interstitial pneumonia by RNA-seq analysis. BMP3 was found down-regulated in idiopathic intestital pneumonia patients, and it closely correlated with pathogenesis of disease. The role of BMP3 in advancement of idiopathic interstitial pneumonia was verified by a series of experiments.

overall_design: Examination of differentially expressed genes in idiopathic interstitial pneumonia. Verification the function of selected gene in pathogenesis of idiopathic interstitial pneumonia in vivo and invitro.

first: Xinghua

first: Aibin

last: Liang

first: Yi


title: Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas)

city: Cincinnati

first: Rong-Lin

address: 26 W MLK Dr

country: USA

institute: US EPA

summary: Fathead minnow and zebrafish are among the most intensively studied fish species in environmental toxicogenomics.  To aid the assessment and interpretation of subtle transcriptomic effects from treatment conditions of interest, there needs to be a better characterization and understanding of the natural variation in gene expression among fish individuals within populations.  Little effort, however, has been made in this area.  Leveraging the transcriptomics data from a number of our toxicogenomics studies conducted over the years, we conducted a meta-analysis of nearly 600 microarrays generated from the ovary tissue of untreated, reproductively mature fathead minnow and zebrafish samples.  As expected, there was considerable batch-to-batch transcriptomic variation; this “batch-effect” appeared to impact the fish transcriptomes randomly.  The overall level of variation within-batch was quite low in fish ovary tissue, making it a suitable system for studying chemical stressors with subtle biological effects.  The within-batch variation, however, differed considerably among individual genes and molecular pathways.  This difference in variability is probably both technical and biological, thus suggesting a need to take into account both the expression levels and variance in evaluating and interpreting the transcriptional impact on genes and pathways by experimental conditions.  There was significant conservation of both the genomes and transcriptomes between fathead minnow and zebrafish.  The conservation to such a degree would enable not only a comparative biology approach in studying the mechanisms of action underlying environmental stressors, but also effective sharing of a large amount of existing public transcriptomics data for future development of toxicogenomics applications.

overall_design: total RNA from the ovary tissue of treated or control fish labeled in single color was hybridized to Agilent fathead minnow microarray (design 019597)

first: David

middle: C

last: Bencic

first: Natàlia

last: Garcia-Reyero

first: Edward

last: Perkins

first: Daniel

middle: L

last: Villeneuve

first: Gerald

middle: T

last: Ankley

first: Adam

middle: D

last: Biales


title: Transcriptome comparison between Bacillus cereus ATCC 14579 wildtype (WT), RpoN (Sigma 54) deletion mutant and the complemented strain.

status: Public on Jul 28 2015

city: Ede

first: Jos

last: Boekhorst

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

summary:
RpoN was shown to have a pleiotropic role in different microorganisms. This study was performed to elucidate role in B. cereus.
In this study we compared the transcriptomic profiles of the WT, rpoN mutant and the complemented strain in aerated and static growth conditions.

overall_design: Matrix is compatible with the Agilent-017343 array design. Aerated cultures were sampled at two time points, upon reaching OD (600 nm) values of 0.2 (t1) and 1.0 (t2), which corresponded to mid-exponential and transition growth phases, respectively. Statically grown cultures were sampled at OD=0.2 (600 nm) corresponding to exponential growth (exp/static). Two independent biological replicates were hybridized on the arrays with either 2 (WT) or 3 (Δrpon and ΔrpoN-comp) technical replicates for each biological replicate.

first: Hasmik

last: Hayrapetyan

first: Marcel

last: Tempelaars

first: Masja

last: Nierop Groot

first: Tjakko

last: Abee


title: Thrombospondin 1 in a model of colorectal carcinogenesis

status: Public on Aug 26 2015

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
By using a model of inflammation-induced carcinogenesis the effects of TSP-1 in induced tumors were analyzed. Mice received a single injection of azoxymethane (AOM) and multiple cycles of dextran sodium sulfate (DSS) for inducing chronic inflammation-related cancers. Proliferation and angiogenesis status were analyzed as well as their transcript profile by using a gene microarray approach.
We used Affymetrix GeneChips to determine the changes in the genetic profile between WT and TSP-1 deficient tumors in a model of colorectal carcinogenesis. We identified differentially expressed genes between WT and TSP-1 deficient tumors.

overall_design: WT and TSP-1 deficient mice were with a single injection of AOM and were drinking 1.5%DSS (dextran sulfate sodium) to induce colitis in four cycles. Wt mice drinking water only was used as reference. Mice were sacrificed and tumors excised for these studies and morphological analyses

first: Linda

last: Gutierrez

first: Zenaida

last: Lopez-Dee


title: Inhibition of ZEB1 expression induces redifferentiation of adult human β cells expanded in vitro

status: Public on Jul 27 2015

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: In-vitro expansion of functional adult human β-cells is an attractive approach for generating insulin-producing cells for transplantation. However, human islet cell expansion in culture results in loss of β-cell phenotype and epithelial-mesenchymal transition (EMT). This process activates expression of ZEB1 and ZEB2, two members of the zinc-finger homeobox family of E-cadherin repressors, which play key roles in EMT. Downregulation of ZEB1 using shRNA in expanded β-cell-derived (BCD) cells induced mesenchymal-epithelial transition (MET), β-cell gene expression, and proliferation attenuation. In addition, inhibition of ZEB1 expression potentiated redifferentiation induced by a combination of soluble factors, as judged by an improved response to glucose stimulation and a 3-fold increase in the fraction of C-peptide-positive cells to 60% of BCD cells. Furthermore, ZEB1 shRNA led to increased insulin secretion in cells transplanted in vivo. Our findings suggest that the effects of ZEB1 inhibition are mediated by attenuation of the miR-200c target genes SOX6 and SOX2. These findings, which were reproducible in cells derived from multiple human donors, emphasize the key role of ZEB1 in EMT in cultured BCD cells and support the value of ZEB1 inhibition for BCD cell redifferentiation and generation of functional human β-like cells for cell therapy of diabetes.

overall_design: Effect of inhibition of ZEB1 on individual's islet cells gene expression.

first: Elad

last: Sintov

first: Gili

last: Nathan

first: Sarah

last: Knoller

first: Holger

middle: A

last: Russ

first: Shimon

last: Efrat


title: Intragraft transcriptional profiling of renal transplant patients with tubular dysfunction reveals biological mechanisms underlying graft fibrosis and outcome after distinct immunosuppressive regimens

status: Public on Jul 31 2015

city: São Paulo

first: Hatylas

last: Azevedo

state: Sao Paulo

address: Doutor Arnaldo Avenue, 455

department: Pediatrics

country: Brazil

institute: University of São Paulo

summary: Intragraft transcriptional profiles were investigated in patients with tubular dysfunction to disclose subclinical mechanisms underlying graft deterioration. Moreover, we analyzed whether individualization of immunosuppression could modify this profile while improving renal function after 12 months of regimen modification.

overall_design: 33 renal transplant patients were enrolled in the study considering their high urinary levels of retinol binding protein, a biomarker of proximal tubular dysfunction (PTD). They were divided in two groups regarding immunosuppressive therapy. At time zero (t0), 33 patients were biopsied and 18 patients had their immunosuppression regimen modified, namely, reduction of cyclosporine dosage and introduction of mycophenolate mofetil (MYF), while 15 patients remained under azathioprine (AZA) schema. All patients were followed-up for 12 months (t12) and then re-biopsied. Microarray experiments were performed using biopsies from 17 patients. Molecular changes due to elevated uRBP levels and immunosuppressive therapies were interpreted via transcriptional network analysis.

first: Hátylas

first: Paulo

last: Renesto

first: Rogerio

last: Chinen

first: Erika

last: Naka

first: Ana Cristina

last: Matos

first: Marcos

last: Cenedeze

first: Carlos

last: Moreira-Filho

first: Niels

middle: O

last: Câmara

first: Alvaro

middle: P

last: Filho


title: Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio)

first: Rong-Lin

last: Wang

type:
Expression profiling by array
Third-party reanalysis

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

overall_design: Refer to individual Series


title: Genome-wide identification of E2f3 and Myc DNA binding sites in normal and Rb-deficient intestines

status: Public on Jul 20 2015

city: Columbus

first: Gustavo

middle: W.

last: Leone

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To explore how Myc and E2f3 might coordinate gene expression programs that drive  normal cell cycles in wild type intestines and ectopic cell cycles in Rb-deficient small intestines, we compared Myc and E2f3 chromatin occupancy in these tissues.

overall_design: Examination of DNA binding of 2 transcription factors (E2f3 and Myc) in normal and Rb-deficient villus cells.

first: Huayang

last: Liu

first: Xing

last: Tang


title: Promoter methylomes of monochorionic twin placentas reveal intrauterine growth restriction specific methylation profiles

status: Public on Aug 31 2015

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

type: Methylation profiling by high throughput sequencing

summary: Intrauterine growth restriction (IUGR) is one of the most common adverse pregnancy outcomes with high risk of perinatal morbidity and mortality, and affects up to 7% of pregnancies. Here, seven pairs of placentas were employed for whole genomic promoter DNA methylation profiling and some of the candidate differentially methylated promoters were further validated in additional twelve pairs of samples. Consistent with previous report, our results further indicated that IUGR associated placentas harbored a distinct promoter DNA hypomethylation pattern and the result was further confirmed byultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS)

overall_design: In this study, seven pairs of MC twins that were diagnosed as severely growth-discordant (one twin with IUGR but another one was normal) were enrolled for DNA methylation identification.Promoters are defined as the regions crossing the upstream 2200bp and downstream 500bp of the transcriptional start site. A complete set of 34163 genes located in the 22 autosomes and the XY sex chromosomes were prepared based on the RefSeq gene files (http://genome.ucsc.edu/, hg19). The promoters overlapped with each other were merged to form a large region, resulting in 20882 merged candidate regions ranging from 2700bp to 8864bp. The capture probes were designed and synthesized by Roche Nimblegen Incorporation, consisted of 150,407 oligonucleotides.

first: Hanlin

last: Lu

first: Junwen


title: Expression data from control, Rb KO and Rb/Myc DKO tissues (villi and crypts)

summary:
Loss of Myc corrects abrrant transcription in Rb KO villi, while these genetic manipulation does not lead to major gene expression changes in crypts.
We used Affymetrix microarrays to profile the global gene expression changes caused by loss of Rb and Rb/Myc.

overall_design: Rb and Myc were conditionally ablated in the small intestine of mice and villi or crypts were harvested 5 days after. Total RNA was isolated from control, Rb KO and Rb/Myc DKO groups and profiled.

first: Arunima

last: Srivastava


title: The early effects of rapid androgen deprivation on human prostate cancer

status: Public on Oct 16 2015

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

summary: The androgen receptor (AR) is the dominant growth factor in prostate cancer.  Understanding how it regulates the human transcriptome is of paramount importance.  The early effects of castration on human prostate cancer have not previously been  studied. In this study 27 patients were medically castrated with degarelix seven days  before radical prostatectomy. Resected tumour was compared with matched  controlled untreated prostate cancer tissue by means of mass spectrometry,  immunohistochemistry and gene expression array (validated by RT-PCR). All  patients had castrate levels of serum androgen with reduced levels of intra-prostatic  androgen at prostatectomy. Differential expression of known androgen regulated  genes (TMPRSS2, KLK3, CAMKK2, FKBP5) was observed. We identified 749 genes  downregulated and 908 genes upregulated following castration. AR regulation of  AMACR expression and three other genes (FAM129A, RAB27A and KIAA0101) was  confirmed. Up-regulation of oestrogen receptor alpha (ESR1) expression was  observed in malignant epithelia. This was associated with differential expression of  ESR1 regulated genes and correlated with proliferation (Ki67 expression).

overall_design:
In total, 27 patients with D'Amico high-risk prostate cancer were administered 240mg degarelix S.C. (donated by Ferring) 7 days before radical prostatectomy . These patients were matched for risk factors (age, serum PSA, tumor grade and stage) with 20 patients undergoing radical prostatectomy without neoadjuvant degarelix . Study and control patients underwent surgery contemporaneously using standard operative technique, with similar ischemic time before sampling described. This GEO submission dataset comprises gene expression data of tumor and benign tissues from Study patients with acceptable RNA quality (RIN > 8). Control samples (GSM181*) have been previously submitted as part of GSE70768.
NOTE: The previously deposited Control samples from GSE70768 have not been reprocessed. They are exactly the same values that have already been submitted.
Supplementary file Matrix_normalized_68samples.csv represents the entire dataset.

first: Greg

last: Shaw

first: Mark

last: Dunning


title: Stress response of Cupriavidus metallidurans strains (AE104 delta 7)

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

country: Germany

summary: Response of Cupriavidus metallidurans  AE104(delta zupT) mutant to Zn/EDTA stress

overall_design: In this study 2 different treatments were performed to acquire expression profiles of the total genome of Cupriavidus metallidurans

last: Grosse

first: Dietrich

middle: H

last: Nies


title: E2f and Myc transcriptional programs and chromatin binding landscapes in the small intestines


title: Comparison of gene expression changes in AML cells after SMARCA4, SMARCD2 or DPF2 knock-down

status: Public on Jul 12 2015

city: Copenhagen

first: Kristian

last: Helin

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: Copenhagen University

summary: We explored the role of SMARCA4 and the two Brahma associated factors SMARCD2 and DPF2 in leukaemia. We observed the selective requirement for these factors for leukemic cell expansion, as well as extended survival of mice transplanted with leukaemic cells with reduced expression of these genes. Gene expression profiling revealed largely similar alterations with the down-regulation of each of these three factors, suggesting a concerted function in transformed blood cells. These changes included loss of pluripotency-associated signature but did not correlate with c-MYC down-regulation.

overall_design: Human acute monocytic leukemia cells (THP-1, ACC 16) were lentivirally transduced with pLKO-puro vectors carrying shRNAs against SMARCA4, SMARCD2 or DPF2. As a negative control, THP-1 cells were transduced with pLKO-puro-shScr (Scrambled). All samples were prepared as biological triplicates.

first: V

last: Cruickshank

first: Patrycja

last: Sroczynska


title: Targeting of SMARCA4 bromodomain selectively inhibits leukemic cell proliferation


title: Gene expression changes in MV4-11 cells upon SMARCA4 knock-down and PFI-3 treatment

summary:
Pharmacological inhibition of the SMARCA4 bromodomain inhibited human leukemic cell proliferation, phenocopying SMARCA4 knockdown in these cells.
We performed microarray analysis of global gene expression changes in MV4-11 cells after 6 days of PFI-3 treatment and after SMARCA4 knock-down. With this analysis we identified several genes whose expression was similarly up- or down-regulated upon inhibitor treatment and SMARCA4 depletion.

overall_design: Human acute monocytic leukemia cells (MV4-11, ACC 102) were lentivirally transduced with shRNA taregting SMARCA4 (KD) or with a negative control shRNA (Scr). In a parallel experiment MV4-11 cells were treated for 6 days with 10μM PFI-3, which is SMARCA4, SMARCA2 and PBRM1 bromodomain inhibitor, or DMSO as a negative control. All sample types were prepared in triplicates.


title: Affymetrix 6.0 SNP arrays interrogated to detect allele-specific DNA modification in the brain

status: Public on Jul 29 2015

city: Toronto

first: Arturas

last: Petronis

address: 250 College Street

country: Canada

institute: Centre for Addiction and Mental Health

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

summary:
It has long been hypothesized that knowledge of allele-specific modification (ASM; "modification" is used to denote various types of epigenetic cytosine marks, not only methylation) can supplement and inform GWAS of complex diseases and traits.
To explore the relationship between GWAS subthreshold SNPs and ASM, we identified brain ASM-SNPs from Caucasian control individuals (n=76) and Caucasian patients affected by schizophrenia (n=65) or bipolar (n=67) using the Affymetrix SNP 6.0 microarray, one of the most common GWAS platforms which has also been thoroughlyt validated for ASM mapping.

overall_design: The brain samples (N=230, all ethnicities) were interrogated twice on Affymetrix SNP 6.0 microarrays. First, regular SNP genotyping was performed following the manufacturer's protocol. Second, we investigated allelic differences in DNA methylation by enriching the unmodified DNA fraction using DNA methylation-sensitive restriction enzymes.


title: Expression data from foam cells of apolipoprotein E-deficient mice

status: Public on Jul 09 2015

city: Albany

first: Antonio

last: Paul

address: Center for Cardiovascular Sciences

institute: Albany Medical College

summary:
Hypercholesterolemai is a major contributor to atherosclerosis development. To assess the effects of hypercholesterolemia on the transcriptional profiling in foam cells, mice were fed regular chow, or WD for 2 or 14 weeks prior to sacrifice.
We used microarrays for broad analysis of gene expression in the 3 experimental groups. Each group included 5 mice.

overall_design: ApoE-/- mice were fed regular mouse chow to the age of 22 weeks (CHOW) or a western-type diet for 2 weeks between weeks 22 and 24 (2w-WD) or for 14 weeks between weeks 8 and 22 (14w-WD). Foam cells in cross-sections of the aourtic sinus were isolated by laser-capsure microdissection (n=5 per group). RNA was amplified by in vitro transcription, biotinylated, and hybridized to Affymetrix Mouse Genome 430 2.0 Arrays.


title: Comparative transcriptomics of Central Asian Vitis vinifera accessions reveals distinct defense strategies against powdery mildew

city: Davis

first: Dario

last: Cantu

state: CA

address: One Shields Ave

department: Viticulture & Enology

institute: University of California, Davis

summary: Grape powdery mildew (PM), caused by the biotrophic ascomycete Erysiphe necator, is a devastating fungal disease that affects most Vitis vinifera cultivars. We have previously identified a panel of V. vinifera accessions from Central Asia with partial resistance to PM that possess a Ren1-like local haplotype. In this study we show that in addition to the typical Ren1-associated late post-penetration resistance, these accessions display a range of different levels of disease development suggesting that alternative alleles or additional genes contribute to determining the outcome of the interaction with the pathogen. To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time-points of PM infection. Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype. Responses to E. necator in all resistant accessions were characterized by an early up-regulation of 13 genes, most encoding putative defense functions, and a late down-regulation of 32 genes, enriched in transcriptional regulators and protein kinases. Potential Ren1-dependent responses included a hotspot of co-regulated genes on chromosome 18. We also identified 81 genes whose expression levels and dynamics correlated with the phenotypic differences between the most resistant accessions ?Karadzhandahal?, DVIT3351.27, and O34-16 and the other genotypes. This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs.

sample_organism:
Vitis vinifera
Vitis vinifera subsp. sylvestris

overall_design: Eight varieties (7 resistant to powdery mildew, 2 of which are V. vinifera spp. sylvestris, 5 of which are V. vinifera spp. sativa) are infected with powdery mildew (E. necator) at two timepoints (1 dpi and 5 dpi) with three replicates for each timepoint for each condition (uninfected vs. infected), for a total of 96 samples

first: Katherine

last: Amrine

first: Summaira

last: Riaz

first: Barbara

last: Blanco-Ulate

first: Laura

last: Jones

first: Daniel

last: Pap

first: Abraham

last: Morales-Cruz

first: Rosa

last: Figueroa

first: M

last: Walker


title: 8-Oxoguanine DNA glycosylase-1 DNA repair-signaling induces gene expression associated to airway remodeling

status: Public on Jul 03 2015

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

summary:
Purpose: The aim of this study is to test whether global gene expression induced by multiple challenges with OGG1-BER product 8-oxoG in mouse airways is linked to airway remodeling.
Methods: RNAs extracted from individual mouse lungs (experimental group: n=5) were pooled and a total 1 μg RNA was used for Next-Generation Sequencing (NGS) analyses on an Illumina HiSeq 1000 sequencing system. Sequence analyses were performed in duplicate. First- and second-strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq Sample Preparation Kit as recommended by the manufacturer (Illumina). Library quailty was evaluated by using an Agilent DNA-1000 chip on an Agilent 2100 Bioanalyzer. Library DNA templates were quantitated by qPCR using known reference standards. Cluster formation of the library of DNA templates was performed using the TruSeq PE Cluster Kit v3 (Illumina) and the Illumina cBot workstation. Paired-end, 50-base sequencing was performed with a TruSeq SBS kit v3 (Illumina) on the Illumina HiSeq 1000 by protocols defined by the manufacturer. Base call conversion to sequence reads was performed using CASAVA-1.8.2. Sequence data were analyzed with the Bowtie2, Tophat2 and GFOLD programs. Processed data are presented as reads per kilobase transcript per million (RPKM), normalized to the experimental control (RNA from saline challenged lungs) and reported as fold change (test/control).
Results: We mapped an average of 31.41 million sequence reads per sample and identified 23,337 transcripts in total RNA extracted from lungs of Balb/cJ mice as described in Methods. Approximately 14% of the transcripts showed differential expression between the saline-challenged control and 8-oxoguanine-challeged mouse lungs, with a fold change ≥3.0. We validated the expression changes of 18 selected EMT-related genes of interest for our studies by qRT-PCR. Hierarchical clustering followed by Protein ANalysis THrough Evolutionary Relationships database (PANTHER) analysis of differentially expressed genes was done using GENE-E online software from Broad Institute (http://www.broadinstitute.org/cancer/software/GENE-E/). Results from PANTHER analysis of upregulated transcripts (fold change ≥3.0) showed overrepresentation of various biological functions (GO terms) including developmental process (GO:0032502, P=4.58E-33), system development (GO:0048731, P=9.16E-33), cellular process (GO:0009987, P= 5.52E-31), cell adhesion (GO:0007155, P= 8.63E-28) among others. Pathway analysis (PANTHER) indicated that the most overrepresented pathways were: cadherin signaling (P00012, P=6.62E-07), wnt signaling (P00057, P= 5.81E-06), integrin signaling (P00034, P= 1.09E-05) among others. In addition to gene expression analysis, we confirmed airway remodeling by histological examination (Hematoxylin and Eosin, Masson's trichrome staining)  of lung sections at seven days from the last challenge (day 11).
Conclusions: This is the first study showing a link between gene expression at whole-transcriptome level induced by chronic OGG1-BER (mimicked by multiple challenges with 8-oxoG) and airway remodeling, supported by histological structural changes in lungs.

overall_design: Balb/cJ mice (5 per group) were intranasally challenged with 8-oxoguanine (1 µM, 60 µl) for three times at days 0, 2 and 4. Control group mice were intranasally challenged with saline (60 µl). At 30, 60 and 120 min after the third challenge (day 4), mice were sacrificed and lungs were processed for RNA extraction. RNAs from individual mice within the same group were pooled and subjected to deep-sequencing analysis in duplicate using NSG on an Illumina HiSeq 1000 sequencing system. After alignment and processing, the resulting RPKM from treatment groups (8-oxoG-challenged) were normalized to control group (saline-challenged).

first: Leopoldo

last: Aguilera-Aguirre

first: Thomas

last: Wood

first: Steven

last: Widen


title: Effect of GW4064 on primary cultured mouse kidney proximal tubule cells

status: Public on Jun 26 2015

city: Zurich

first: Zhibo

last: Gai

state: Schweiz

address: Wagistrasse 14

department: Department of Clinical Pharmacology and Toxicology

country: Switzerland

institute: University Hospital Zurich

summary: Global gene expression in primary cultured mouse kidney proximal tubule cells treated with either DMSO or 1uM GW4064 (an FXR agonist) was compared. Results provide insight into mechanisms underlying effects of FXR activation on gene expression in mouse kidney proximal tubule cells.

overall_design:
Male C57/BJ mice aged 6 weeks were sacrificed under anesthesia and kidney proximal tubule cells were cultured until confluent. Cells were treated with either GW4064 (1uM) or equal amount of DMSO and incubated for 24 hours. 4 total RNA samples per group were analyzed and gene expression was compared between the groups.
GW4064 is a compound which activates FXR, a bile acid nuclear receptor. The natural FXR agonists are usually bile acids, such as cholic acid and CDCA. GW4064 is an artificial FXR agonist which is synthesized by Sigma-Aldrich.

first: Ting

last: Gui


title: Assessment of MEK-ERK pathway targeting by BRAF, NRAS and KRAS gene mutations in plasma cell dyscrasias [Patient samples]

status: Public on Jul 01 2015

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary:
Multiple myeloma (MM) is a malignant disorder characterized by the clonal proliferation of plasma cells (PCs) in the bone marrow (BM). The genetic background and clinical course of the disease are largely heterogeneous, and MM pathophysiology ranges from the premalignant condition of monoclonal gammopathy of undetermined significance (MGUS) to smoldering MM, symptomatic MM, and extramedullary MM/plasma cell leukemia (PCL). Recent genome-wide sequencing efforts have provided the rationale for molecularly aimed treatment approaches, identifying mutations that can be specifically targeted, such as those in the mitogen-activated protein kinase (MAPK) pathway, which represent the most prevalent mutations in MM. Among these, mutations affecting BRAF gene, detected in 4-15% of patients, are of potential immediate clinical relevance due to the availability of effective inhibitors of this serine-threonine kinase which are in fact being explored also in myeloma.
In this study, we screened by next generation sequencing (NGS) a large and representative series of intramedullary and extramedullary MM patients, including primary and secondary plasma cell leukemia (pPCL and sPCL, respectively), for mutations in BRAF, NRAS and KRAS genes. We evaluated the relationship of identified variants with other clinical and biological features and determined the transcriptional signature associated with MAPK pathway activation in MM.

overall_design: To identify transcriptomic profiles possibly related to BRAF, NRAS and KRAS mutations found in our study, we investigated by Affymetrix microarray technology a large fraction (n=142) of the samples analyzed by NGS, including wild-type patients for all the three genes and cases carrying mutations in at least one of them. Assuming that alterations present in a very limited number of malignant PCs might not appreciably affect gene expression, we chose to arbitrarily establish 20% as the lower variant allele frequency cut-off to perform supervised analyses.

first: Marta

last: Lionetti

first: Marzia

last: Barbieri

first: Katia

last: Todoerti

first: Simona

last: Marzorati

first: Serena

last: Galletti

first: Giulia

last: Milesi

first: Martina

last: Manzoni

first: Sonia

last: Fabris

first: Mara

last: Mazzoni

first: Maria

last: Greco

first: Giovanni

last: Tonon

first: Agostino

last: Cortelezzi

last: Baldini

last: Palumbo

first: Pellegrino

last: Musto

first: Antonino

last: Neri


title: Assessment of MEK-ERK pathway targeting by BRAF, NRAS and KRAS gene mutations in plasma cell dyscrasias

last: Agnelli


title: Expression data from control, E2f TKO, Myc KO and E2f/Myc QKO crypts

first: Gustavo

last: Leone

summary:
Combined ablation of Myc and E2f1-3 results in disruption of crypt-villus integrity in the small intestine due to a S-G2 cell cycle blockade.
We used Affymetrix microarrays to profile the global gene expression changes caused by loss of Myc and/or E2f1-3.

overall_design: Myc and/or E2f1-3 were conditionally ablated in the small intestine of mice and crypts were harvested 2 days after. Total RNA was isolated from control, E2f TKO, Myc KO and E2f/Myc QKO groups and profiled.

first: Huayang

last: Liu

first: Arunima

last: Srivastava


title: An analysis fo genomic structural alterations in iPS cells derived from xeroderma pigmentosum patients

status: Public on Jun 24 2015

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

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

summary: To elucidate frequencies of genomic structural alterations, we performed an analysis using a SNP genotyping array (Illumina HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit) for iPS cells derived from xeroderma pigmentosum patients (XP3OS, XP40OS, and XPEMB-1). Samples were collected after 10 to 25 passages to detect structural mutations occurred during the cell cultivation processes. Our results suggested a higher mutation rate of the iPS cells compared to those from normal cells.

overall_design: The iPS-cell samples were collected after several passages togerther with their precursor cell samples and subjected to the SNP genotyping array. We searched for structural mutations occurred during the culture of the iPS cells.

first: Kazuhiro

last: Nakabayashi

first: Kohji

last: Okamura

first: Yoriko

last: Takahashi

first: Kenichiro

last: Hata


title: Expression analysis of a full SlrV locus 1 knockout in Haemophilus influenzae strain PittII

status: Public on Jun 23 2015

city: Philadelphia

first: Benjamin

last: Janto

state: PA

institute: Drexel University College of Medicine

summary: Investigation of whole genome gene expression differences between a full (four-gene) SlrV locus 1 deletion compared to the WT PittII strain. Removal of the four SlrV genes (aka macrophage survival factors :  Δmsf) results in a competetive defect with the WT strain in in vitro biofilms and in the otitis media chinchilla model. It also results in an inability to persist within macrophages long-term in vitro and to escape from the middle-ear space and infect other sites in the chinchilla model.

overall_design: WT and Δmsf strains were grown in a chemically defined media (CDM) to early stationary phase (OD ~1.0). RNA was extracted from two separate cultures (biological replicates). 3-13 probes represent each subcluster(gene) and two replicate probe sets are included on each custom NTHi supragenome chip (technical replicates) thus under each sampling condition 4 separate values are obtained per strain and used for WT:Msf-KO comparisons.

first: Jennifer

last: Kress-Bennett

first: Luisa

middle: N

last: Hiller

first: Rory

last: Eutsey

first: Evan

last: Powell

first: Mark

last: Longwell

first: Todd

last: Hillman

first: Tenisha

last: Blackwell

first: Barbara

last: Byers

first: Joshua

last: Mell

first: Christopher

last: Post

first: Fen

middle: Z

last: Hu

first: Garth

last: Ehrlich


title: Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline

status: Public on Jun 18 2015

city: Cincinnati

first: Satoshi

last: Namekawa

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary:
The male germline transcriptome changes dramatically during the mitosis-to-meiosis transition to activate late spermatogenesis genes and to transiently suppress genes commonly expressed in somatic lineages and spermatogenesis progenitor cells, termed somatic/progenitor genes.
These changes reflect epigenetic regulation. Induction of late spermatogenesis genes during spermatogenesis is facilitated by poised chromatin established in the stem cell phases of spermatogonia, whereas silencing of somatic/progenitor genes during meiosis and postmeiosis is associated with formation of bivalent domains which also allows the recovery of the somatic/progenitor program after fertilization. Importantly, during spermatogenesis mechanisms of epigenetic regulation on sex chromosomes are different from autosomes: X-linked somatic/progenitor genes are suppressed by meiotic sex chromosome inactivation without deposition of H3K27me3. Our results suggest that bivalent H3K27me3 and H3K4me2/3 domains are not limited to developmental promoters (which maintain bivalent domains that are silent throughout the reproductive cycle), but also underlie reversible silencing of somatic/progenitor genes during the mitosis-to-meiosis transition in late spermatogenesis.

overall_design: 29 samples analyzed by ChIP-Seq

first: Sin

last: Hosu

first: Andrey

last: Kartashov

first: Kazuteru

last: Hasegawa

first: Artem

last: Barski


title: sRNA sequencing to study assorted processing of synthetic trans-acting siRNAs and its activity in antiviral resistance

status: Public on Jun 17 2015

city: Mutilva Baja

first: Junkal

last: Garmendia

address: Pamplona, 123

country: Spain

institute: Instituto de Agrobiotecnologia, Consejop Superior de Investigaciones Científicas

type: Non-coding RNA profiling by high throughput sequencing

summary: The use of syn-tasiRNAs has been proposed as an RNA interference technique alternative to those previously described: hairpin based, virus induced gene silencing or artificial miRNAs. In this study we engineered the TAS1c locus to impair Plum pox virus (PPV) infection by replacing the five native siRNAs with two 210-bp fragments from the CP and the 3´NCR regions of the PPV genome. Deep sequencing analysis of the small RNA species produced by both constructs in planta has shown that phased processing of the syn-tasiRNAs is construct-specific. While in syn-tasiR-CP construct the processing was as predicted 21-nt phased in register with miR173-guided cleavage, the processing of syn-tasiR-3NCR is far from what was expected. A 22-nt species from the miR173-guided cleavage was a guide of two series of phased small RNAs, one of them in an exact 21-nt register, and the other one in a mixed of 21-/22-nt frame. In addition, both constructs produced abundant PPV-derived small RNAs in the absence of miR173 as a consequence of a strong sense PTGS induction. The antiviral effect of both constructs was also evaluated in the presence or absence of miR173 and showed that the impairment of PPV infection was not significantly higher when miR173 was present. The results show that syn-tasiRNAs processing depends on construct-specific factors that should be further studied before the so-called MIGS (miRNA-induced gene silencing) technology can be used reliably.

overall_design: Two samples were analyzed. The control sample has no presence of miR173.

first: Mingmin

last: Zhao

first: David

last: San León

first: Frida

last: Mesel

first: Juan

last: García

first: Carmen

last: Simón-Mateo


title: Gene expression in Rainbow trout (Oncorhynchus mykiss) fry gonads after a chronic exposure to a range of  17α-ethynylestradiol concentrations

status: Public on Jun 25 2015

city: Namur

first: Sophie

last: Depiereux

state: Namur

address: Rue de Bruxelles, 61

country: Belgium

institute: University of Namur

summary: Sex steroids play a key role in triggering sec differentiation in fish and the use of exogenous hormone treatment leads to partial or complete sex reversal. This phenomenon has attracted attention since the discovery taht even low environmental doses of exogenous steroids can adversely affect gonad morphology (ovotestis development) and induce reproductive failure. Modern genomic-based technologies have enhanced opportunities to find mechanisms of action (MOA) and dentify biomarkers for the toxic action of a compound. The goal of this study are to improve the understanding of feminization in fish by analyzing gene expression patterns in the gonads of rainbow trout fry after a chronic exposure to several doses (0.01, 0.1, 1 and 10 μg/L) of ethynylestradiol (EE2) and to offer target genes as potential biomarkers of ovotestis development.

overall_design: An all-male population of Rainbow trout fry was exposed during 76 days (from 60 to 136 days post-fertilization (dpf)) to five nominal concentrations of 17α-ethynylestradiol (0-solvent control-, 0.01, 0.1, 1 and 10 μg EE2/L of water), using 3 tanks per condition. In total, 30 samples were analyzed independantly: 6 samples per concentration tested (two samples per tank, three tanks per concentration), each sample being a pool of 10 pairs of gonads.

first: Patrick

last: Kestemont

first: Eric


title: Mouse expression data of epididymal white adipose tissue at Zeitgeber time (ZT) 18 comparison control vs. Sleep restriction

status: Public on Jun 15 2015

city: Goettingen

first: Jana

last: Husse

address: Am Fassberg 11

institute: Max Planck Institute for Biophysical Chemistry

summary:
We hybridzed cRNA from epididymal white adipose tissue collected at ZT18 of control animals and TSR animals (TSR: these mice were sleep restricted for 6 hours every day by gentle handling for 5 consecutive days and killed on the last day at ZT18)
mice used in this study were C57BL/6

overall_design: control mice were compared to timed sleep restriction mice (TSR: these mice were sleep restricted for 6 hours every day by gentle handling for 5 consecutive days and killed on the last day at ZT18)

first: Henrik

last: Oster


title: Fluidigm C1 + Illumina HiSeq quantitative whole transcriptome analysis of unsorted population of E16.5 lung cells

status: Public on Jun 11 2015

first: Yan

last: Xu

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cicinnati children's Hospital Medical Center

summary: We used microfluidic single cell RNA-seq on mixed e16.5 mouse lung cells in order to determine the potential cell types present based on differential transcriptional profiles of the entire population using minimal cell selection bias.

overall_design: whole lung mouse e16.5 cells were pooled and loaded onto the Fluidigm C1 device.  microwells that contained intact single cells were recorded, the labchip was processed for the generation of cDNA from each cell, and cDNA generated from each accepted well was used to generate amplified and barcoded DNA library that was loaded into an Iluumina HiSeq machine for HTS analysis.

first: P

last: Dexheimer

first: B

last: Aronow

first: J

last: Whitsett

first: S

last: Potter

first: E

last: Brunskill

last: Shannon

first: Y

first: M

last: Guo

last: Du


title: Assessment of MEK-ERK pathway targeting by BRAF, NRAS and KRAS gene mutations in plasma cell dyscrasias [U266 human myeloma cell line]

first: Luca

last: Agnelli

overall_design: To further elucidate the transcriptional programs modulated by BRAF activation in MM, we used the PLX4032 drug to inhibit BRAF activity in U266 human myeloma cell line (HMCL), carrying K601N mutation and showing constitutive activation of MEK/ERK signaling. After confirming its ability to suppress MAPK pathway and myeloma cell proliferation in culture in the U266 cell line, we investigated the specific modulation of gene expression induced by the drug. U266 cells were treated with PLX4032 (30 µM) or DMSO for 12 hours and subjected to gene expression profiling (GEP) analysis by using Affymetrix GeneChip Human Gene 1.0ST arrays.

first: Marta

last: Lionetti

first: Marzia

last: Barbieri

first: Katia

last: Todoerti

first: Simona

last: Marzorati

first: Serena

last: Galletti

first: Giulia

last: Milesi

first: Martina

last: Manzoni

first: Sonia

last: Fabris

first: Mara

last: Mazzoni

first: Maria

last: Greco

first: Giovanni

last: Tonon

first: Agostino

last: Cortelezzi

last: Baldini

first: Antonio

last: Palumbo

first: Pellegrino

last: Musto

first: Antonino

last: Neri


title: Expression data of sleeping, waking, and sleep deprived adult heterozygous aldh1l1 – eGFP-L10a mice

status: Public on Jul 08 2015

city: Madison

first: Michele

last: Bellesi

state: WI

address: 6001 Research Park Blvd

institute: University Wisconsin-Madison

summary:
Transcriptomic studies revealed that hundreds of mRNAs show differential expression in the brains of sleeping versus awake rats, mice, flies, and sparrows. Although these results have offered clues regarding the molecular consequences of sleep and sleep loss, their functional significance thus far has been limited. This is because  the previous studies pooled transcripts from all brain cells, including neurons and glia.
In the following experiment, we studied the specific effects of sleep and wake conditions on glia cells of mouse cerebral cortex using the genetically targeted translating ribosome affinity purification (TRAP) methodology. We used bacterial artificial chromosome (BAC) transgenic mice expressing EGFP tagged ribosomal protein L10a in astrocytes which constitute a defined cellular population of the mouse brain. Using this approach, we could extract only the astrocytic mRNAs, and only those already committed to be translated into proteins (L10a is part of the translational machinery).

overall_design: Six mice for each vigilant state group (sleep (S), waking (W), and sleep deprivation (SD)) were considered. For each animal, cerebral cortex was dissected and immediately processed. Samples were immunoprecipitated to isolate astrocytes. The precipitated portion formed the bound sample (IP) containing astrocytes and the remaining part formed the unbound sample (UB) containing all the remaining cell types (neurons and other glia cells). Then, both IP and UB samples were processed and RNA was extracted. All the IP samples (n=18) were then hybridized to  Affymetrix GeneChip Mouse Genome 430 2.0 arrays, while UB samples were pooled together in two biological replicates (UB1+UB2+UB3 and UB4+UB5+UB6) for each group (n=6 in total) and then hybridized to  Affymetrix GeneChip Mouse Genome 430 2.0 arrays.

first: Luisa

last: de Vivo

first: Giulio

last: Tononi

first: Chiara

last: Cirelli


title: Transcriptome analysis upon TFIIS4 silencing during autogamy time course

status: Public on Jun 12 2015

city: Gif-sur-Yvette

first: Olivier

last: ARNAIZ

address: avenue de la terrasse

country: France

institute: CNRS

summary: At each sexual cycle, during development of the somatic macronucleus (MAC) from the germline micronucleus (MIC), the genome of the ciliate Paramecium tetraurelia is massively rearranged through the reproducible elimination of germline-specific sequences. It has been reported previously that targeting of these sequences is mediated by non-protein-coding RNAs including different classes of small RNAs and longer non-coding transcripts. Using RNA interference, we showed that TFIIS4 gene encoding development-specific TFIIS elongation factor is essential for the formation of a functional somatic genome. We demonstrated that genome rearrangements taking place during MAC development were inhibited in TFIIS4-depleted cells, which led to high lethality in the sexual progeny. The role of TFIIS4 elongation factor in coding transcription at the genome-wide level was studied by performing a microarray hybridization experiment using RNA samples extracted during vegetative growth and at five time points during the progression of the sexual cycle (autogamy).

overall_design: Total RNA samples were extracted during vegetative growth and at five different time points of autogamy from mass cultures fed with bacteria producing dsRNA to induce TFIIS4 or ICL7a silencing. TFIIS4 gene encodes TFIIS elongation factor and is strongly induced during autogamy, a self-fertilization process. RNAi against TFIIS4 leads to strong lethality in post-autogamous progeny. ICL7a is a non-essential gene; the loss of function of this gene by with dsRNA feeding results in mutant phenotypes: absence of intraciliary lattice and defect in calcium-induced cell contractility.

first: Kamila

last: Maliszewska-Olejniczak

first: Jacek

middle: K

last: Nowak


title: Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer

status: Public on Jun 08 2015

city: University of Helsinki

first: Henna

last: Heinonen

address: PO Box 63

country: Finland

institute: University of Helsinki

summary: We report the chromatin binding sites of HOXB7 transcription factor in BT-474 breast cancer cell line using ChIP-sequencing. We validated the chromatin binding sites in BT-474, MDA-MB-361, MCF7 and T-47D breast cancer cell lines using ChIP-qPCR. The ChIP experiments have been performed using HOXB7 antibody and IgG non-specific antibody as a negative control. The direct downstream target genes of HOXB7 were identified by analyzing the expression of genes located nearby HOXB7 binding sites in HOXB7 knockdown versus control cells using qRT-PCR.

overall_design: Examination of chromatin binding sites of HOXB7 in BT-474 breast cancer cell line using ChIP-seq. Four parallel IgG samples were sequenced, merged together and used as a control data set. Two parallel HOXB7 ChIP samples were sequenced and merged for each replicate, AF1 and AF2. Both HOXB7 ChIP replicates (AF1 and AF2) contained approximately the same amount of reads as the merged IgG control data set.

first: Tatiana

last: Lepikhova

first: Biswajyoti

last: Sahu

last: Pehkonen

first: Päivi

last: Pihlajamaa

first: Riku

last: Louhimo

first: Ping

last: Gao

first: Gong-Hong

last: Wei

first: Sampsa

last: Hautaniemi

first: Olli

last: Jänne

first: Outi

last: Monni


title: Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with Pseudomonas syringae pv. tomato DC3000.

status: Public on Jun 02 2015

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

institute: The Genome Analysis Centre

summary: High-resolution temporal transcriptomic analysis of Arabidopsis thaliana leaves during infection by Pseudomonas syringae DC3000 and DC3000hrpA-thaliana

overall_design: RNA was extracted from Arabidopsis leaves after mock-inoculation, infection with P. syringae DC3000 and infection with P. syringae DC3000hrpA-. 13 time points (0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 14, 16, 17.5 hours post inoculation) were sampled from each treatment and four biological replicates (a single leaf) were harvested at each time point for each treatment. This led to 156 biological samples (13 time points x 3 treatments x 4 biological replicates). Four technical replicates of each biological sample were generated (624). The microarrays were two-channel CATMA arrays and hence two samples are hybridized to each array resulting in 312 arrays used in the experiment. A “loop design” was developed to enable efficient extraction of information about sample comparisons. Half the arrays were used to directly compare samples at different time points within the same treatment, and half directly compared the same time point and adjacent time points between treatments. This design maximizes the power of data comparisons over time and between treatments.

first: Laura

last: Lewis

first: Krzysztof

last: Polanski

first: Marta

last: de Torres-Zabala

first: Siddarth

last: Jayaraman

last: Bowden

first: Christopher

last: Penfold

first: Dafyd

middle: J

last: Jenkins

first: Claire

last: Hill

last: Baxter

first: Satish

last: Kulasekaran

first: William

last: Truman

first: George

last: Littlejohn

first: Justyna

last: Pruskinska

first: Andrew

last: Mead

first: Jens

last: Steinbrenner

first: Richard

last: Hickman

first: David

last: Rand

last: Wild

first: Sascha

last: Ott

first: Vicky

last: Buchanan-Wollaston

first: Nick

last: Smirnoff

first: Jim

last: Beynon

first: Katherine

last: Denby

first: Murray

last: Grant


title: SAHA Rat Dental Pulp

status: Public on Jun 16 2015

city: Dublin

first: Hnery

middle: Fergus

last: Duncan

address: Lincol Place

department: Restorative Dentistry

country: Ireland

institute: Dublin Dental University Hospital, Trinity College Dublin

summary:
Transcriptional response of rat dental pulp cells (DPCs) cultured with SAHA at early and late mineralisation time points
Transcript profiling of DPC identified several novel genes expression induced and supressed by HDACi at 24 hrs and 14 days under mineralising conditions. SAHA induces several members of the MMP family of endopepsidases (TIMP-1, MMP-9, MMP-13) and other members of the endochondral ossification pathway at 24 h.

overall_design: 8 experiemental parameters were analysed, each carried out in quadruplicate

first: Henry


title: Identifying Non-Invasive Molecular Correlates relevant to Irradiation-Skin Burn Combined Injuries

status: Public on May 15 2015

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

summary:
Currently there is growing concern with respect to scenarios where people are likely to be presented with radiation exposure along with many kinds of other injuries such as trauma and infection. The potential for such scenarios was brought to reality with the events and aftermath of the Fukushima nuclear disaster in Japan. As such medical complications arising from such exposures would be poorly dealt with as no evidence-based guidelines exist for their rehabilitation or recovery.
Our research intends to differentially characterize combined radiation and burn injuries and identify novel pathways and biomarkers. Such findings will lead to better medical practices in the diagnosis, care and rehabilitation of affected individuals. The study includes four groups of mice: 1) Control sham mice group (n=4), 2) Skin burn injury mice group (n=6), 3) Radiation injury mice group (n=6), 4) Combined radiation and burn injury mice group (n=6).

overall_design: We propose to characterize the effects of combined radiation and burn injuries using microRNA microarray analysis. Our primary aim is to identify novel molecular pathways and biomarkers specific to whole blood samples (serum) from mice exposed to combined radiation and burn injuries. B6D2F1/J female mice will be used. 30 days following combined radiation and burn injuries arterial blood will be harvested from euthanized mice. 200ul of serum from whole blood samples will be used for microRNA microarray experiments (Affymetrix).

first: Aminul

last: Islam


title: Genome wide DNA methylation profiling of normal breast, normal adjacent and breast cancer tissue

city: London

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

institute: University College London

type: Methylation profiling by genome tiling array

summary:
The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in a total of 407 samples, including  50 normal samples from healthy women, 42 matched normal-adjacent breast cancer pairs (84 samples), 263 unmatched breast cancers, 7 normal samples from BRCA1 carriers and 4 BRCA1 breast cancers.

***WARNING: incomplete metadata supplied for this study***

overall_design: Bisulphite converted DNA from the 407 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Martin

last: Widschwendter


title: Expression data from prostate tumor of TRAMPxNOD/ShiLtJ F2 cross

city: Bethesda

first: Kendra

last: Williams

state: MD

address: 50 South Dr, Bldg 50

department: NHGRI

institute: NIH

summary:
We hypothesize that germline variation influences susceptibility to aggressive prostate tumor
We examined the changes in gene expression in tumors obtain from TRAMPxNOD/ShiLtJ F2 mice in groups exhibiting metastasis versus no metastasis

overall_design: Transgene-positive (Tg+) F2 males were bred by crossing Tg- sires to Tg+ dames. 126 tumor samples were analyzed, which were obtained from the Tg+ F2 male

first: Minnkyong

last: Lee

first: Ying

last: Hu

first: Jonathan

last: Andreas

first: Shashank

last: Patel

first: Suiyuan

last: Zhang

first: Abdel

last: Elkahloun

first: Settara

last: Chandrasekharppa

first: Silvio

last: Gutkind

first: Alfredo

last: Molinolo

first: Nigel

last: Crawford


title: MiRNA profiling in aortas of Apoe-/- mice with an specific knock-out of Dicer in endothelial cells compared to control mice after 12 weeks of a high-fat diet

status: Public on May 31 2015

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

institute: Ludwig-Maximilians-University

summary: Increased monocyte adhesion to dysfunctional endothelial cells (ECs) orchestrated by chemokines plays an important role in arterial inflammation during atherosclerosis. Endothelial microRNAs (miRNAs) processed by the RNase Dicer1 determine the phenotype of ECs by posttranscriptional regulation of gene expression. However, the impact of endothelial miRNAs on endothelial inflammation and atherosclerosis is currently unclear. To study the effect of Dicer-dependent miRNAs in ECs on atherosclerosis, Apoe-/- mice with an inducible, EC-specific knock-out of Dicer (EC-Dicerflox) and control mice (EC-DicerWT) mice were treated with tamoxifen to induce Cre-recombinase activity and fed with a high fat-diet (HFD) for 12 weeks. The comparison of the miRNA expression profile in the aortas of EC-Dicerflox and EC-DicerWT mice after 12 weeks of a HFD was performed to identify EC-specific miRNAs that may play a role in the EC function during atherogenesis.

overall_design: VE-Cadherin-CreERT2 mice were crossed with Dicer1flox/flox/Apoe-/- to obtain VE-Cadherin-CreERT2Dicer1WT/flox/Apoe-/-. VE-Cadherin-CreERT2Dicer1flox/flox/Apoe-/- (EC-Dicerflox) mice and VE-Cadherin-CreERT2Dicer1WT/WT/Apoe-/- (EC-DicerWT) littermates were used for experiments. Cre-recombinase activity was induced by Tamoxifen (TMX) treatment (2 mg/20 g body weight, dissolved in neutral oil) for 5 consecutive days (i.p. injection). One week after the last TMX injection, 6-8 week old females were fed a high-fat diet (HFD) comprising 21% crude fat, 0.15% cholesterol and 19.5% casein for 12 weeks. The aortas were harvested after in situ perfusion with RNAlater and total RNA was isolated using mirVana microRNA Isolation Kit. The Dicer knockout in EC-Dicerflox mice was confirmed by quantification of Dicer1 mRNA expression in the aortas of EC-DicerWT and EC-Dicerflox by qRT-PCR.

first: Petra

last: Hartmann

first: Zhou

last: Zhe


title: Transcriptome Profiling of patients with 16p11.2 rearrangements

status: Public on May 10 2015

city: Lausanne

first: Alexandre

last: Reymond

address: Dorigny

department: CIG

institute: UNIL

summary:
The 600kb BP4-BP5 16p11.2 CNV (copy number variant) is associated with neuroanatomical, neurocognitive and metabolic disorders.  These recurrent rearrangements are associated with reciprocal phenotypes such as obesity and underweight, macro- and microcephaly, as well as autism spectrum disorder (ASD) and schizophrenia. Here we interrogated the transcriptome of individuals carrying reciprocal CNVs in 16p11.2.
The genome-wide transcript perturbations correlated with clinical endophenotypes of the CNV and were enriched for genes associated with ASD. We uncovered a significant correlation between copy number changes and expression levels of genes mutated in ciliopathies.

overall_design: Transcriptome profiles of lymphoblastoid cell lines of 50 16p11.2 deletion carriers, 31 16p11.2 duplication carriers and 17 controls.

first: Eugenia

last: Migliavacca

first: Katrin

last: Mannik


title: Single-cell chromatin accessibility data using scATAC-seq

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Cell-to-cell variation is a universal feature of life that impacts a wide range of biological phenomena, from developmental plasticity to tumor heterogeneity. While recent advances have improved our ability to document cellular phenotypic variation the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of cellular DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells via assay of transposase accessible chromatin sequencing (ATAC-seq). Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single-cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provides insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type specific accessibility variance across 6 cell types. Targeted perturbations of cell cycle or transcription factor signaling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome topological domains de novo, linking single-cell accessibility variation to three-dimensional genome organization. All together, single-cell analysis of DNA accessibility provides new insight into cellular variation of the “regulome.”

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Profiles of single cell epigenomes, assayed using scATAC-seq, across 8 cell types and 4 targeted cell manipulations. The complete data set contains a total of 1,632 assayed wells.


title: Expression data from  wildtype and Tfr1 skeletal muscle KO mice

status: Public on May 08 2015

city: Durham,

first: Tomasa

last: Barrientos

state: NC

address: 308 Research Drive, LSRC C127

department: Pharmacology and Cancer Biology

institute: Duke University Medical Center

summary:
Tfr1 is important for iron uptake in red blood cells. We deleted Tfr1 in skeletal muscle to determine the role of Tfr1 in iron uptake in skeletal muscle.
We used microarrays to identify global gene changes associated with deletion of Tfr1 in skeletal muscle

overall_design: We used skeletal muscle and liver from wild type and Tfr1 skeletal muscle KO mice at postnatal day 5 and postnatal day 9. mRNA was extracted from the tissues, labaled and hibridized to Affymetrics microarrays.

first: Nancy

middle: C

last: Andrews


title: MiRNA expression profile in the aortas of  Apoe-/- mice with an specific knock-out of Dicer in endothelial cells compared to control mice after 4 weeks of a high-fat diet

summary: Increased monocyte adhesion to dysfunctional endothelial cells (ECs) orchestrated by chemokines plays an important role in arterial inflammation during atherosclerosis. Endothelial microRNAs (miRNAs) processed by the RNase Dicer1 determine the phenotype of ECs by posttranscriptional regulation of gene expression. However, the impact of endothelial miRNAs on endothelial inflammation and atherosclerosis is currently unclear. To study the effect of Dicer-dependent miRNAs in ECs during the development of atherosclerosis, Apoe-/- mice with an inducible, EC-specific knock-out of Dicer (EC-Dicerflox) and control mice (EC-DicerWT) mice were treated with tamoxifen to induce Cre-recombinase activity and fed with a high fat-diet (HFD) for 4 weeks. The comparison of the miRNA expression profile in the aortas of EC-Dicerflox and EC-DicerWT mice after 4 weeks of a HFD was performed to identify EC-specific miRNAs that may play a role in the EC function during atherogenesis.

overall_design: VE-Cadherin-CreERT2 mice were crossed with Dicer1flox/flox/Apoe-/- to obtain VE-Cadherin-CreERT2Dicer1WT/flox/Apoe-/-. VE-Cadherin-CreERT2Dicer1flox/flox/Apoe-/- (EC-Dicerflox) mice and VE-Cadherin-CreERT2Dicer1WT/WT/Apoe-/- (EC-DicerWT) littermates were used for experiments. Cre-recombinase activity was induced by Tamoxifen (TMX) treatment (2 mg/20 g body weight, dissolved in neutral oil) for 5 consecutive days (i.p. injection). One week after the last TMX injection, 6-8 week old males were fed a high-fat diet (HFD) comprising 21% crude fat, 0.15% cholesterol and 19.5% casein for 4 weeks. The aortas were harvested after in situ perfusion with RNAlater and total RNA was isolated using mirVana microRNA Isolation Kit. The Dicer knockout in EC-Dicerflox mice was confirmed by quantification of Dicer1 mRNA expression in the aortas of EC-DicerWT and EC-Dicerflox by qRT-PCR.


title: Expression data from mutant p53 breast cancer cell line SK-BR-3

status: Public on Jun 01 2015

city: New Brunswick

first: Emmanuel

middle: S.

last: Zachariah

state: New Jersey

address: 125 Paterson Street

department: CINJ Functional Genomics Facility

institute: Rutgers

summary:
Tumor associated mutant p53 proteins often gain new functions for tumorigenesis and tumor progression.  It has been shown that mutant p53 can transcriptionally regulate a group of genes, which in turn contributes to mutant p53 gain of function.  A mutant p53 interacting protein Pontin binds to mutant p53 and promotes its gain of function.  This experiment tests whether the interaction of Pontin with mutant p53 regulates the transcriptional activity of mutant p53.
We used a breast cancer cell line containing endogenous mutant p53 (SK-BR-3) with or without knockdown of mutant p53 by shRNA to identify genes regulated by mutant p53.  We then knocked down endogenous Pontin in SK-BR-3 cells, and compared the transcriptional levels of these genes in cells with and without mutant p53 knockdown to investigate the effect of Pontin on mutant p53-dependent transcriptional regulation.

overall_design: Four types of cells were used in this experiments: SK-BR-3 breast cancer cells transfected with control shRNA, SK-BR-3 cells transfected with p53 shRNA, SK-BR-3 cells with transfection of siRNA against Pontin, SK-BR-3 cells transfected with p53 shRNA and siRNA against Pontin.  Cells were collected to extract total RNA for Affymetrix microarray analysis.

first: Wenwei

last: Hu

first: Yuhan

last: Zhao

first: Cen


title: Functional Networks Of Praziquantel-Induced Differentially Expressed Genes In Schistosoma mansoni And Synergy Of Omeprazole And Praziquantel In Vitro Against Adult Worms

status: Public on May 01 2015

city: São Paulo

first: Giulliana

middle: Tessarin

last: Almeida

state: SP

address: Av Prof Lineu Prestes, 748

department: Departamento de Bioquímica

institute: University of São Paulo - Instituto de Química

summary: Background: Treatment and morbidity control of schistosomiasis relies on a single drug, praziquantel. Therefore, there is a pressing need to explore the effects of PZQ on the parasites at the molecular level and to pursue alternative and/or or synergistic drugs against schistosomiasis.   Methodology: We used a custom-designed Schistosoma mansoni oligo-microarray to explore the effects of a sublethal dose of praziquantel on S. mansoni adult worms’ gene expression. We used functional analysis of gene interaction networks to identify differentially expressed genes that are known targets of other drugs already tested in humans for diverse disease conditions. Omeprazole, a proton pump inhibitor drug that is widely prescribed, was tested in combination with praziquantel. We comparatively assessed the efficacy of praziquantel or omeprazole alone and in combination against S. mansoni adult worms in vitro over a period of 120 hours.   Principal Findings: We identified sets of genes that were affected by praziquantel on both paired and unpaired females, however with opposite gene expression patterns (up-regulated in paired and down-regulated in unpaired females), indicating that the transcriptomics changes induced by praziquantel are heavily influenced by the mating status. We also identified genes that were similarly affected by praziquantel in males and females. The use of sublethal doses of praziquantel together with omeprazole showed a significantly enhanced worm mortality in vitro compared to praziquantel alone, thus evidencing a synergic effect.   Conclusions: Functional analysis of gene interaction networks is an important approach to identify genes whose expression is affected by one drug and that are at the same time known targets of other drugs already tested in humans for diverse disease conditions, thus pointing the latter as possible synergic drugs. Combined treatment with omeprazol increases the efficacy of praziquantel against S. mansoni adult worms in vitro, and additional in vivo studies are warranted.

overall_design: Two-condition experiment, PZQ-treated vs. untreated . Biological replicates: 2 with dye-swap

last: Tessarin-Almeida

first: Regina

last: Lage

first: Thiago

middle: M

last: Venancio

first: Helder

middle: I

last: Nakaya

first: Leticia

last: Anderson

first: Patrícia

last: Miyasato

first: Henrique

last: Rofatto

first: Adhemar

last: Zerlotini

first: Eliana

last: Nakano

first: Guilherme

last: Oliveira

first: Sergio

last: Verjovski-Almeida


title: Regulation of gene expression by JMJD5 in LNCaP prostate cancer cells

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: The goal of this study was to define the cohort of genes whose expression is regulated by JMJD5 function in prostate cancer.  Towards this goal, LNCaP sublines stably expressing wld-type JMJD5 (LNCaP-JMJD5) were established.  In addition, a control subline(LNCaP-Vector) was generated by transfection with empty vector.  Both sublines were cultured in either androgen-deprived medium or in the presence of dihydrotestosterone (DHT).  Subsequently, total RNA was isolated and then subjected to microarray gene expression profiling with Affymetrix GeneChip HG-U133 Plus 2.0 Arrays.

overall_design: A total of 4 samples were analyzed in this study.  The study included two cell lines, LNCaP-Vector and LNCaP-JMJD5, that were cultured under conditions of androgen depivation (-DHT) or supplementation with dihydrotestosterone (+DHT).  The LNCaP-Vector cell line served as the control for the study.

first: Hsing-Jien

last: Kung

middle: G


title: Microarray Profiling of Long Non-coding RNA (lncRNA) Associated with Hypertrophic Cardiomyopathy

city: Chengdu

first: Haixiang

last: Wu

address: No. 55, People’s South Road

department: Department of Ultrasonics

country: China

institute: the Second Hospital of Sichuan

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

summary: Approximately 1426 lncRNAs (965 up-regulated and 461 down-regulated) and 1715 mRNAs (896 up-regulated and 819 down-regulated) were aberrantly expressed in HCM patients with fold change > 2.0

overall_design: Myocardial tissues were obtained from 7 HCM patients and 5 disease-free individuals, and lncRNA and mRNA expression profiles were analyzed using the CapitalBio Human LncRNA Microarray v2.0.


title: Neural Stem/Progenitor Cell Properties of Glial Cells in the Adult Auditory Nerve [ouabain]

status: Public on Apr 30 2015

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

country: USA

institute: MUSC

summary: Spiral ganglion neurons (SGNs) and the associated components of the auditory nerve are primary carriers of auditory information from hair cells to the brain.  Loss of SGNs occurs with many pathological conditions, resulting in permanent sensorineural hearing loss.  Neural stem/progenitors (NSPs) have been well-characterized in several locations of adult brain and retina.  However, it is unclear whether NSPs are present in the adult auditory nerve.  Here we examined the self-renewal potential of the adult auditory nerve using ouabain application as a well-established mouse model of acute SGN injury.  The observed increase in cell proliferation, alteration in enchromatin/heterochromatin ratio and down-regulation of histone deacetylase expression in glial cells suggest that the quiescent glial cells convert to an activated state after SGN degeneration.  This was further confirmed by global gene expression analysis of injured auditory nerves, which showed up-regulation of numerous neurogenesis- and/or development-associated genes shortly after ouabain exposure.  These genes include molecular markers commonly used for the identification of NSPs.  Under a strict culture regimen, auditory nerve-derived cells of adult mouse ears gave rise to neurospheres, suggesting that multipotent NSPs are present in adult cochlear nerve.  Neurosphere assays on Sox2 transgenic mice revealed that Sox2+ glial cells are the source for NSPs.  Our data also showed that acute injury or hypoxia enhances neurosphere formation.  Taken together, our study revealed that glial cells of adult cochlea exhibit several NSP characteristics, and hence these mature non-neuronal cells may be important targets for promoting self-repair of degenerative auditory nerves.

overall_design: Adult Mice (CBA/CaJ, aged 8 to 12 weeks) were anesthetized and subjected to survival surgery to expose the bulla of the right ear. A ouabain solution (3 mM, approximately 10 ul) was administered in the round window niche. This solution was wicked away and replaced with fresh ouabain approximately every 10 min during a cummulative exposure period of 60 min. The left ears (i.e., contralateral) were not surgically manipulated and were used as controls. Mice were maintained for 3 days or 7 days following treatments, then euthanized, and the oubain-treated and contralateral cochleas were removed. Cochleas underwent microdissection to remove the outer bony cochlear shell and cochlear lateral wall, thus preserving the modiolus portion of cochlea which contains mainly the auditory nerve. All sample types were prepared in experimental triplicate (n=3).

first: Hainan

last: Lang

middle: L


title: Neural Stem/Progenitor Cell Properties of Glial Cells in the Adult Auditory Nerve [development]

overall_design: Analysis was conducted on auditory nerve samples from stages encompassing maturation and onset of hearing. Cochleas were collected from euthanized mice (CBA/CaJ) at perinatal (P) stages P0, P3, P7, P10, P14 and P21. Cochleas underwent microdissection to remove the outer bony cochlear shell and cochlear lateral wall, thus preserving the modiolus portion of cochlea which contains mainly the auditory nerve. Paired cochleas (i.e., from left and right ears) from each mouse were pooled to make individual samples. All sample types were done in experimental duplicate (n=2).


title: Comparison of the expression profiles of wild-type (WT), Tyk2-deficient (Tyk2-/-) and kinase-inactive Tyk2 mutant (Tyk2K923E) NK cells

status: Public on Apr 28 2015

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary:
Define the impact of Tyk2 and Tyk2K923E on the transcriptome of NK cells
Tyrosine kinase 2 (TYK2) is a Janus kinase (JAK) that is crucially involved in inflammation, carcinogenesis and defense against infection. The cytotoxic activity of natural killer (NK) cells in TYK2-deficient (Tyk2-/- ) mice is severely reduced, although the underlying mechanisms are largely unknown. Using Tyk2-/- mice and mice expressing a kinase-inactive version of TYK2 (Tyk2K923E), we show that NK cell function is partly independent of the enzymatic activity of TYK2. Tyk2-/- and Tyk2K923E NK cells develop normally in the bone marrow, but the maturation of splenic Tyk2-/- NK cells (and to a lesser extent of Tyk2K923E NK cells) is impaired. In contrast, the production of interferon γ (IFNγ) in response to interleukin 12 (IL-12) or to stimulation through NK cell-activating receptors strictly depends on the presence of enzymatically active TYK2. The cytotoxic activity of Tyk2K923E NK cells against a range of target cells in vitro is higher than that of Tyk2-/-  NK cells. Consistently, Tyk2K923E mice control the growth of NK cell-targeted tumors significantly better than TYK2-deficient mice, showing the physiological relevance of the finding. Inhibitors of TYK2’s kinase activity are being developed for the treatment of inflammatory diseases and cancers, but their effects on tumor immune surveillance have not been investigated. Our finding that TYK2 has kinase-independent functions in vivo suggests that such inhibitors will leave NK cell mediated tumor surveillance largely intact and that they will be suitable for use in cancer therapy.

overall_design: Splenic NK cells derived from WT, Tyk2-/- and Tyk2K923E mice (DX5-MACS enriched from 3-4 mice per genotype) were grown in the presence rhIL-2 (5000 U/ml) for 7 days. Three independent expreiments (= biological replicates)

first: Michaela

last: Prchal-Murphy

first: Agnieszka

last: Witalisz-Siepracka

first: Karoline

middle: T

last: Bednarik

first: Eva

last: Putz

first: Dagmar

last: Gotthardt

first: Katrin

last: Meissl

first: Veronika

last: Sexl

first: Mathias

last: Müller

first: Birgit

last: Strobl


title: Neural Stem/Progenitor Cell Properties of Glial Cells in the Adult Auditory Nerve [cultured auditory nerve cells]

status: Public on Apr 29 2015

overall_design: Auditory nerves were removed from the temporal bones of adult CBA/CaJ mice, aged 8 to 12 weeks. Tissues were either collected and used directly as the tissue samples or dissociated and used for the cell culture samples. Dissociated auditory nerve cells were propagated and grown to full confluency (5-7 days), constituting the cultured cell samples. For neurosphere samples, growth medium was changed to neurosphere formation medium and the cells were cultured for an additional 12 days. All samples were prepared in triplicate (n=3).


title: Neural Stem/Progenitor Cell Properties of Glial Cells in the Adult Auditory Nerve

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

overall_design: Refer to individual Series


title: MicroRNA expression profiles associated with anti-schistosome features in Microtus fortis

status: Public on Jun 10 2015

city: Shanghai

first: hongxiao

last: han

address: No. 518, Ziyue Road,

department: Shanghai Veterinary Research Institute

institute: Chinese Academy of Agricultural Sciences

summary: Microtus fortis (M. fortis) is the only mammal in which the growth, development and maturation of schistosomes (Schistosoma japonicum) is prevented, resulting in the failure of the parasite to mature and complete its life cycle. MicroRNAs (miRNAs) are a class of endogenous, non-coding small RNAs, has been found to introduce a whole new layer of gene regulation in eukaryotes. The anti-schistosomiasis mechanosm of M. fortis may require the participation of miRNA-mediated gene expression. In the present study, the difference pathological change of different tissue such as liver, spleen and lung of M. fortis were observed by using haematoxylin-eosin staining. Also, the miRNA expression in different tissue of M. fortis and mice before challenge and 10 days post-infection with schistosomes were first compared using microRNA microarray analysis. Histological analyses showed that S. japonicum infection in M. fortis resulted in more intensive inflammatory response and pathologic change than mice. The microarray investigations showed that 388 miRNAs detected common expressed in the two species, and 11 miRNAs in liver, 25 miRNAs in spleen and 28 miRNAs in lung differentially expressed in non-permissive M. fortis while increased, decreased or nearly fixed in mice. Further studies of the differentially expressed miRNAs demonstrated that many important signal pathway were triggered after the S. japonicum infection in M. fortis rather than the mouse, such as the metabolism of some nutrient material such as fatty-acid, cholesterol, lipid, insulin, and carbohydrate; immune response such as B and T cell differentiation, monocyte differentiation, the inflammation, NF-kappaB binding, even the in innate immune system; Cell differentiation and apoptosis such as erythrocytic differentiation and targeting proapoptotic and antiapoptotic proteins. These results may provide new insights into general mechanisms of regulation in non-permissive M. fortis, exploit the potential miRNA regulatory networks and the interaction between parasites and different hosts, which provide valuable new information on schistosome biology and valuable information for the better understanding of schistosome development and host-parasite interactions.

sample_organism:
Mus musculus
Rattus norvegicus
Alexandromys fortis

platform_organism:
Cricetulus griseus
Mus musculus
Rattus norvegicus

overall_design: We collected liver, spleen and lung from control and 10 days post-infection with schistosomes of M. fortis, mice and rat, respectively.

first: Hongxiao

last: Han

first: Jinbiao

last: Peng

first: Yang

last: Hong

first: Min

last: Zhang

first: Yanhui

first: Zhiqiang

last: Fu

first: Jinjun

last: Xu

first: Jianping

last: Tao

first: Jiaojiao

last: Lin


title: Transcriptomics Analyses of soybean leaves and roots sample during water-deficit

status: Public on Apr 26 2015

city: Dallas

first: Paul

last: Rushton

address: 17360 Coit Road

institute: Texas A&M AgriLife Research & Extension Center

summary: Microarray experiments were performed on the roots and leaves samples seperately using custom based Nimblgen platform (12plex). This is a time-course study. The plants were grown in controlled growth chamber condiditons ambiient to soybean growth and development using a hydrophonics system. The tissues were harvested after 30days of growth in six time points- 0min, 30mins, 1hour, 2hours, 3hours and 5hours of dehydration.

overall_design: We used a hydrophonics system for the trancriptomics analysis of the soybean(William -82) root and leaves samples to study the reponse during water- deficit or drought. Plants were grown in controlled growth chamber conditions and harvested after 30days in six time-points. The plants were transferred to empty pots without touching to nullify any possibility of wounding and harvested subsequently. For 0mins, plants were taken out of the well-watered conditions and transfered to empty boxes and immediately harvested for both tisses and hence called 0-min dehydrated tissue. Similarly other time-points were processed (for instance, 2hrs of dehydration, plants were dehydrated for 2hours after being taken out from well-waterted pots and then harvested). Tissues for three biological replicates and three plants per biological replicates were collected for each time-point (n=9). RNA was islolated from both tissues using RNeasy Kit from Qiagen and quality was accessed with Nano-drop as well as with Agilent-Bioanalyzer using RNA-600 kit. 20ug of sample was processed at Micro Array Facility.

first: Prateek

last: Tripathi

first: Roel

last: Rabara


title: A comprehensive genomic, transcriptomic and proteomic analysis of a hyperosmotic stress sensitive α-proteobacterium.

status: Public on Apr 21 2015

city: Greifswald

first: Christian

last: Kohler

address: Martin Luther Strasse 6

department: Medical Microbiology University Medicine

institute: Friedrich Loeffler Institute for Medical Microbiology

summary:
BACKGROUND: With the aim of remaining viable, bacteria must deal with changes in environmental conditions, including increases in external osmolarity. While studies concerning bacterial response to this stress condition have focused on soil, marine and enteric species, this report is about Caulobacter crescentus, a species inhabiting freshwater oligotrophic habitats.
RESULTS:
A genomic analysis reported in this study shows that most of the classical genes known to be involved in intracellular solute accumulation under osmotic adaptation are missing in C. crescentus. Consistent with this observation, growth assays revealed a restricted capability of the bacterium to propagate under hyperosmotic stress, and addition of the compatible solute glycine betaine did not improve bacterial resistance. A combination of transcriptomic and proteomic analyses indicated quite similar changes triggered by the presence of either salt or sucrose, including down-regulation of many housekeeping processes and up-regulation of functions related to environmental adaptation. Furthermore, a GC-MS analysis revealed some metabolites at slightly increased levels in stressed cells, but none of them corresponding to well-established compatible solutes.
CONCLUSION:
Despite a clear response to hyperosmotic stress, it seems that the restricted capability of C. crescentus to tolerate this unfavorable condition is probably a consequence of the inability to accumulate intracellular solutes. This finding is consistent with the ecology of the bacterium, which inhabits aquatic environments with low nutrient concentration.

overall_design: Three experimental procedures, each of them performed in three replicates. A total of nine independent biological samples were used

first: Rogério

middle: F

last: Lourenço

first: Jörg

last: Bernhardt

first: Dirk

last: Albrecht

first: Julia

last: Schüler

first: Michael

last: Hecker

first: Suely

last: Gomes


title: Expression data from rat lung-resident mesenchymal stem cells and bone marrow-derived mesenchymal stem cells

status: Public on Apr 25 2015

first: Lin

last: Tong

address: 180 Fenglin Road

department: Department of Pulmonary Medicine

institute: Zhongshan Hospital, Fudan University

summary:
Rat lung-resident mesenchymal stem cells (LR-MSCs) were isolated via bronchoalveolar lavage from fibroblast growth factor-10 (FGF-10) pretreated lungs. We characterized the similarity and diversity between LR-MSCs and bone marrow-derived mesenchymal stem cells (BM-MSCs) by transcriptional profiling of these two types of cells.
In this dataset, we include the expression data obtained from LR-MSCs and BM-MSCs cultured under similar conditions at passage 5. These data are used to obtain genes that are differentially expressed by these two types of cells.

overall_design: 6 Total samples were analyzed. Both LR-MSCs and BM-MSCs are in three replicates.

first: Yuanlin

last: Song


title: Gene microarray data for HT-29 monolayer and spheroids

status: Public on Apr 01 2015

city: Richmond

first: Bhaumik

middle: B

last: Patel

state: VA

address: 1201 Broad Rock Blvd

institute: Hunter Holmes McGuire VA Medical Center

summary:
Colorectal cancers have a rare population of cells that express specific cell surface markers, and are referred to as cancer stem cells (CSC). Targeting CSCs, implicated in tumor relapse, is a paradigm shifting approach for colorectal cancer.
We used gene microarray to analyze gene expression in HT-29, a colon cancer cell line, grown as monolayer and spheroid and identify metabolic pathways that are upregulated.

overall_design: HT-29 monolayer cells were grown in DMEM/F12 media supplemented with 10% FBS, and 1X Antibiotic-Antimycotic liquid (AA); and spheroids were grown in stem cell media [DMEM:F12, 1X AA, 1X B27, epidermal growth factors, and fibroblast growth factor for five days. Total RNA was isolated using the mirVana™ miRNA Isolation Kit according to the manufacturer's protocol. RNA intergrity was confirmed on the Nanodrop ND-1000 and analyzed with Agilent 2100 bioanalyzer. The arrays were scanned with the Affymetrix 3000 7G plus scanner.

first: Chetna

last: Sharon

first: Somesh

last: Baranwal

first: Nirmita

first: Daniel

last: Rodriguez-Agudo

first: William

last: Pandak

first: Adhip

middle: P

last: Majumdar

first: Geoffrey

last: Krystal


title: Dynamic mRNA gene expression during a nutritional upshift from proline to glutamine

status: Public on Apr 07 2015

city: Zurich

first: Uwe

last: Sauer

address: Auguste-Piccard-Hof 1

department: Institute of Molecular Systems Biology

institute: ETH Zurich

summary: Dynamic mRNA gene expression from the wildtype YSBN6 during a nutritional upshift from proline to glutamine. Glutamine was added to yeast cells growing exponentially on proline as the sole nitrogen source.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design:
A sample was taken at steady-state 10 minutes before the shift, and then 3, 7, 10, 14, 24, 56 and 120 minutes after the glutamine addition. Biological triplicate gene expression was measured for samples -10, 7 and 24 minutes after shift, for a total of 14 chips. Changes were generally evaluated relative to the steady-state point (-10 minutes). Biological variability can be assessed from the replicates time points.
Other dynamic omics data are associated with this dataset. Consult the publication for more details.

first: Ana

last: Oliveira


title: Gene Expression by Mouse Inner Ear Hair Cells During Development

status: Public on Mar 24 2015

city: Boston

first: David

middle: P.

last: Corey

address: 220 longwood avenue

department: Neurobiology Department

institute: Harvard Medical School

summary: Hair cells of the inner ear are essential for hearing and balance. As a consequence, pathogenic variants in genes specifically expressed in hair cells often cause hereditary deafness.  Hair cells are few in number and not easily isolated from the adjacent supporting cells, so the biochemistry and molecular biology of hair cells can be difficult to study. To study gene expression in hair cells, we developed a protocol for hair cell isolation by FACS sorting.  With nearly pure hair cells and surrounding cells, from cochlea and utricle and from embryonic day 16 to postnatal day 7, we performed a comprehensive cell-type-specific RNA-Seq study of gene expression during mouse inner ear development. Expression profiling revealed new hair-cell genes with distinct expression patterns:  some are specific for vestibular hair cells, others for cochlear hair cells, and some are expressed just before or after maturation of mechanosensitivity. We found that many of the known hereditary deafness genes are much more highly expressed in hair cells than surrounding cells, suggesting that genes preferentially expressed in hair cells are good candidates for unknown deafness genes.

overall_design: 3' tags of mRNA profiles of hair cells and surrounding cells from  E16, P0, P4, and P7 cochlear and utricular sensory epithelia were generated by deep sequencing, using Illumina GAIIx

first: Deborah

last: Scheffer

first: Jun

last: Shen

first: Zheng-Yi

last: Chen


title: Rlf, a widely-spaced zinc finger protein, is involved in maintaining epigenetic marks at CpG island shores and enhancer elements across the genome

city: Bundoora

first: Harald

last: Oey

state: Vic

address: Kingsbury Drive

department: Genetics

country: Australia

institute: La Trobe University

summary: We recently identified a novel protein, Rearranged L-myc fusion (Rlf), that is required for DNA hypomethylation (and transcriptional activity) at certain regions of the mouse genome known to be sensitive to epigenetic gene silencing. Here we report the analysis of 12 whole genome bisulphite sequencing datasets across three different embryonic tissues/stages from mice with and without Rlf. We find that its absence has effects at thousands of differentially methylated regions.

overall_design: Whole genome bilsulphite sequencing, RNAseq and H3K4me1 ChIP-seq for wild type and mice homozygous null for Rlf (MommeD28/MommeD28)

first: E

last: Whitelaw

first: H

first: S

last: Harten