title: Repertoire of BALB/c mice natural anti-carbohydrate antibodies

status: Public on Mar 29 2017

city: Hospitalet de Llobregat

first: Rafael

last: Manez

state: Barcelona

address: Feixa Llarga s/n

institute: HUB

summary: One of the most common genetic backgrounds for mice used as model to investigate human diseases is the BALB/c strain. This work is aimed to characterize the pattern of natural anti-carbohydrate antibodies present in serum of BALB/c mice by printed glycan array technology. Natural antibodies from serum of BALB/c mice interacted with at least 70 glycans from a library of 419 different carbohydrate structures. However, only a restricted number of these (12, ~17%) were highly recognized by natural antibodies, and shared by more than 80% of mice under examination. This conserved pattern differed dramatically from that of humans. This finding together with not identical repertoires of antibodies between individual mice should be specially considered when mouse models are intended to be used for investigation of human natural antibodies in different biomedical research and diagnostic contexts.

overall_design: To study the repertoire of natural circulating anti-carbohydrate antibodies, serum from 20 BALB/c mice was evaluated by printed glycan-array technology (PGA). Microarrays were prepared by Semiotik LLC (Moscow, Russia) from 419 different amine-functionalized glycans, using N-hydroxysuccinimide-derivatized glass slides H Schott-Nexterion (Germany). All glycans were printed in 6 replicates. The glycan library included blood group antigens and other most frequent terminal oligosaccharides and their cores of mammalian N- and O-linked glycoproteins and glycolipids, tumour-associated carbohydrate antigens.

first: Daniel

last: Bello-Gil

last: Mañez


title: LPS response during systemic Chlamydia infection

status: Public on Mar 07 2017

city: Davis

first: Stephen

middle: J.

last: McSorley

state: CA

address: Center for Comparative Medicine, County Rd 98 & Hutchison Dr.

country: USA

institute: UC Davis

summary:
The overall study examines the mechanism and role of innate re-stimulation of T cells after activation and differentiation during infection.
This particular study is focused on the restimulation of Th1 cells activated during Chlamydia infection, using in vivo LPS stimulation to increase the response. The study was conducted to compare the expression profile after LPS stimulation during Chlamydia infection to that seen after LPS stimulation during Salmonella infection (submitted as a separate dataset).

overall_design:
Six female C57BL/6 mice were infected iv with Chlamydia muridarum, then 7 days post-infection (at the peak of T cell activation) 3 of the 6 mice were injected iv with LPS. All of the mice were cervically dislocated 4 hours later, and the spleens were removed and flash frozen for mRNA extraction. The Affymetrix GeneChip 'Mouse Gene 1.0 ST Array' was used to compare mRNA expression in total splenocytes for all murine genes that were well-annotated at the time of GeneChip purchase (2012). Biological replicates were averaged within each group and the fold-change difference between the averages was assessed for statistical significance by dChip software to determine which genes were up- or down-regulated in the spleen after LPS stimulation during Chlamydia infection.
Total RNA was DNase treated, quantified, and assessed for quality, then submitted to the UC Davis Microarray Core Facility for RNA processing, hybridization, chip scanning, and initial data processing

first: Hope

last: O'Donnell


title: Genomic and epigenomic architecture of hepatocellular carcinoma

status: Public on Mar 03 2017

city: Los Angeles

first: Huy

middle: Q

last: Dinh

state: California

address: 8700 Beverly Blvd

department: Center for Bioinformatics and Functional Genomics

institute: Cedars Sinai Medical Center

type: Methylation profiling by genome tiling array

summary: Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. Understanding of the intratumoral heterogeneity of HCC is instructive for developing personalized therapy and molecular biomarkers. We applied whole exome sequencing to a total of 63 samples from 11 patients to resolve the genetic architecture and subclonal diversification. Notably, spatial genomic diversity was found in all 11 HCC cases, with 33% of the driver mutations being heterogeneous. Temporal dissection of mutational signatures suggested that exogenous and endogenous factors have different contributions in shaping the mutational spectrum during the development of HCC. Moreover, we observed extensive intratumoral epigenetic heterogeneity in HCC, and showed that integrative analysis of both genetic and epigenetic phylogenies could generate more robust resolution of clonal architecture than single profiling approach. Our results also demonstrated prominent epigenetic subclonal diversification even in a stable HCC genome. Together, these findings highlight the widespread intratumoral heterogeneity at both genomic and epigenomic levels in HCC, and provide important molecular foundation for better understanding of the biology and pathogenesis of this malignancy.

overall_design: We examined a total of 22 tumor tissues and 4 morphologically-normal liver tissues (3 out of 4 were matched normal livers) from 5 HCC patients  using Illumina Infinium HumanMethylation450K platform (Illumina, San Diego, CA).

first: De-Chen

last: Lin

first: Benjamin

middle: P

last: Berman

first: H

last: Koeffler


title: LPS response in Salmonella infected mice

summary:
The overall study examines the mechanism and role of innate re-stimulation of T cells after activation and differentiation during infection.
This particular study is focused on the restimulation of Th1 cells activated during Salmonella infection, using in vivo LPS stimulation to increase the response.

overall_design:
Six female C57BL/6 mice were infected iv with attenuated Salmonella Typhimurium (BRD509), then 14 days post-infection (at the peak of T cell activation) 3 of the 6 mice were injected iv with LPS. All of the mice were cervically dislocated 4 hours later, and the spleens were removed and flash frozen for mRNA extraction. The Affymetrix GeneChip 'Mouse Gene 1.0 ST Array' was used to compare mRNA expression in total splenocytes for all murine genes that were well-annotated at the time of GeneChip purchase (2012). Biological replicates were averaged within each group and the fold-change difference between the averages was assessed for statistical significance by dChip software to determine which genes were up- or down-regulated in the spleen after LPS stimulation during Salmonella infection.
Total RNA was DNase treated, quantified, and assessed for quality, then submitted to the UC Davis Microarray Core Facility for RNA processing, hybridization, chip scanning, and initial data processing

middle: J


title: The eutherian-specific miR-290/miR-371 cluster modulates placental growth and maternal-fetal transport

status: Public on Mar 04 2017

city: Wuerzburg

first: Alireza

last: Paikari

address: Biocenter

country: Germany

institute: Wuerzburg University

type: Expression profiling by high throughput sequencing

summary: A family of vertebrate-specific microRNAs called the ESCC microRNAs regulates proliferation and differentiation of embryonic stem cells. The ESCC microRNAs arise from two genetic loci in mammals, the miR-290/miR-371 and miR-302 loci. While the miR-302 locus is found broadly among vertebrates, the miR-290/miR-371 locus is unique to eutherian species, suggesting a role in placental development. Here, we evaluate that role. A knockin reporter for the mouse miR-290 gene is expressed throughout the embryo until gastrulation, at which time it becomes specifically expressed in extraembryonic tissues and the germline. In the placenta, expression is limited to the trophoblast lineage, where it remains highly expressed until birth. Deletion of the miR-290 gene results in reduced trophoblast progenitor cell proliferation and a reduced DNA content in endoreduplicating trophoblast giant cells. A reduction in placental size precedes a reduction in fetal size and prenatal death of most knockout embryos. The vascular labyrinth shows disorganization with thickening of the barrier between maternal and fetal blood associated with reduced diffusion of a radioactive tracer. Multiple mRNA targets of the cluster miRNAs are upregulated. Together, these data uncover a critical function for the miR-290 in the regulation of a network of genes required for normal placental development, suggesting a central role for this microRNA cluster in the evolution of eutherian species.

overall_design: mRNA expression in miR-290 knockout and wild-type placenta.

first: Robert

last: Blelloch


title: LPS response during systemic infection

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

overall_design: Refer to individual Series


title: Transcriptional and accessible chromatin profiles during conversion process of alternatively activated macrophages (ATAC-Seq)

status: Public on Apr 24 2017

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Whether inflammatory macrophages can adopt features of the tissue resident niche and what mechanisms mediate phenotypic conversion remain unclear. In this study, we show by cell surface phenotyping, as well as by RNA-Seq transcriptional profiling and ATAC-Seq open chromatin regions profiling, that inflammatory monocyte can adopt a tissue resident phenotype, which is also accompanied by re-programming of the transcriptional profiles and remodeling of the open chromatin landscape. The conversion process is dependent on Vitamin A, suggesting that Vitamin A deficiency may lead to the failure to resolve inflammation, as inflammatory macrophages accumulate without adopting a tissue residency phenotype.

overall_design: Monocyte-derived (N=3), tissue converted (N=3) and tissue resident (N=3) mouse peritoneal macrophages were FACS-sorted for RNASeq and ATACSeq.

first: Uma

last: Mahesh Gundra

first: Natasha

middle: M

last: Girgis

first: Michael

last: Gonzalez

first: Mei

last: San Tang

first: P'ng

last: Loke


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT MRSA USA300 Infected HEKn and HaCaT Transcriptomes

status: Public on Feb 21 2017

city: New York

first: Alice

last: Prince

state: New York

institute: Columbia University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Method: HaCaTs and primary keratinocytes were infected with WT USA300 S. aureus (MOI 100:1) for 1 hour before cell lysates were prepared. Poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and to proceed to library preparation by using Illumina TruSeq RNA prep kit. Libraries were then sequenced using Illumina HiSeq2500 at Columbia Genome Center. The samples were multiplexed in each lane, which yields targeted number of singleend/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane. The raw read files were not available for submission because they have been deleted by the core facility.
Results: Using an optimized data analysis workflow, we identified 15,780 transcripts in the skin of both HEKn and HaCaT cells.  Expression values were analyzed using Ingenuity Pathway Analysis (IPA).
Conclusions: Our study represents the first detailed analysis of HEKn and HaCaT transcriptomes, with biologic replicates, generated by RNA-seq technology after WT MRSA USA300 infection. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Skin mRNA profiles of HEKn and HaCaT cells were generated by deep sequencing, in triplicate, using Illumina HiSeq2500


title: Analyses of Long Non-coding RNA and mRNA Profiles using Microarray Platform in Mice Brain during Japanese Encephalitis Virus Infection

status: Public on Feb 11 2017

city: wuhan

first: li

middle: yun

last: chuan

state: hubei

address: No.1,Shizishan Street,Hongshan District

country: China

institute: Huazhong Agricultural University

summary:
Japanese encephalitis virus (JEV) is the leading cause of epidemic encephalitis worldwide. JEV-induced neuroinflammation is characterized by profound neuronal cells damage accompanied by activation of glial cells.
Albeit long non-coding RNAs (lncRNAs) have been emerged as important regulatory RNAs with profound effects on various biological processes, it is unknown how lncRNAs regulate JEV-induced inflammation. Here, using microarray approach, we identified 618 lncRNAs and 1007 mRNAs differentially expressed in JEV-infected mice brain.

overall_design: Six adult BALB/C mice (six weeks old) were randomly assigned to two groups: the JEV-infected group and the control group, each group have three mice for the following experiments. For the infection group, mice were inoculated intracranially with 200 PFU JEV (P3 strain) in 20μl DMEM, whereas mice belonging to the control group were injected intracranially with equal volume of DMEM. On day 6 post-infection, mice infected with JEV showed signs of acute encephalitis. Mice from both groups were euthanized, and brain samples were collected for further RNA extraction and hybridization on Affymetrix microarrays.

first: Yunchuan

last: Li

first: Hao

last: Zhang


title: ATAC-seq and RNA-seq of adult mouse rods and cones

status: Public on Feb 09 2017

city: St. Louis

first: Joseph

last: Corbo

address: 660 S. Euclid

institute: Washington University School of Medicine

summary: Rod photoreceptors are specialized neurons that mediate vision in dim light and are the predominant photoreceptor type in nocturnal mammals. The rods of nocturnal mammals are unique among vertebrate cell types in having an 'inverted' nuclear architecture, with a single dense mass of heterochromatin in the center of the nucleus rather than dispersed clumps at the nuclear periphery. We hypothesized that this unique chromatin organization would correlate with a unique epigenomic landscape as defined by chromatin accessibility. To test this idea, we performed open chromatin profiling (ATAC-seq) on purified mouse rods and their most closely related cell type, cone photoreceptors, which revealed that thousands of loci are selectively closed in rods. Comparison with open-chromatin maps from >60 additional cell types and tissues demonstrated that rods have by far the most closed chromatin architecture. To explore how the unique epigenomic landscape of rods is controlled, we profiled photoreceptors purified from mice lacking the rod master regulator Nrl. We find that the open-chromatin profile of Nrl-/- photoreceptors is nearly indistinguishable from that of native cones, indicating that Nrl is necessary to achieve selective chromatin closure in rods. Finally, we identified distinct enrichments of transcription factor binding sites in rods and cones, suggesting specific mechanisms by which rods and cones encode cell type-specific information in regulatory DNA. Taken together, these data provide new insight into the development and maintenance of photoreceptor identity, and highlight rods as an attractive system for studying the relationship between nuclear organization and local changes in chromatin accessibility.

overall_design: ATAC-seq of adult (eight-week-old) mouse rods, green cones, and Nrl-/- photoreceptors (two biological replicates each) purified from transgenic reporter lines via fluorescence-activated cell sorting (FACS). RNA-seq of adult (eight-week-old) mouse rods and Nrl-/- photoreceptors (three biological replicates each) purified from transgenic reporter lines via FACS.

first: Andrew

middle: E

last: Hughes

first: Jennifer

last: Enright

first: Connie

middle: A

last: Myers

first: Susan

last: Shen

middle: C


title: Analysis of differentially expressed genes in HepG2 after transfection with miR-192,miR-204 and siHOTTIP

city: Beijing

first: Yunxia

last: Ge

address: NO.15 Of North Three-ring East Road,Chao Yang District  BEIJING,CHINA

institute: Beijing Universicty of Chemicl Technology

summary: This study aimed to identify differential expressed genes before and after transfection with miR-192,miR-204 and siHOTTIP, using the HepG2 liver cancer cell line as a model.

overall_design: There were a total of 4 samples examined.

first: Ming

last: Yang


title: Gene expression-signatures for non-small cell lung cancer patients with different ALK mutational status.

status: Public on Feb 07 2017

first: Xiao-Qing

last: Liu

address: 8 Dongda Road

department: Department of Lung Cancer

institute: Affiliated Hospital of Academy of Military Medical Sciences

summary: To identify a plasma microRNA panel that could help to distinguish ALK positive with  ALK negative NSCLC patients, plasma samples of 3 ALK-positive, 3 ALK-negative NSCLC, and 3 Healthy Subjects were selected for Agilent miRNA microarray analysis to detect differences in the expression levels of circulating miRNAs (n = 2568) between the above cohorts.

overall_design: In the study presented here, plasma samples of 3 ALK-pos, 3 ALK-neg, and 3 Healthy subjects were selected for the Agilent microRNA array expression profiles with a total of 2568 unique miRNAs. The significantly dysregulated miRNAs between the above cohorts were then validated by qRT-PCR.

first: Liang-Liang


title: The effects of Lactobacillus plantarum on small intestinal barrier function and mucosal gene transcription; a randomized double-blind placebo controlled trial

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: The aim of this study was to investigate the effects of three Lactobacillus plantarum strains on in-vivo small intestinal barrier function and gene transcription in human subjects. The strains were selected for their differential effects on TLR signalling and tight junction protein rearrangement, which may lead to beneficial effects in a stressed human gut mucosa. Ten healthy volunteers participated in four different intervention periods: 7-day oral intake of either L. plantarum WCFS1, CIP48 (CIP104448), TIFN101 (CIP104450) or placebo, proceeded by a 4 weeks wash-out period. Lactulose-rhamnose ratio (an indicator of small intestinal permeability) increased after intake of indomethacin, which was given as an artificial stressor of the gut mucosal barrier (mean ratio 0.06±0.04 to 0.10±0.06, p=0.001), but was not significantly affected by the bacterial interventions. However, gene transcription pathway analysis in small intestinal biopsies, obtained by gastroduodenoscopy, demonstrated that particularly L. plantarum TIFN101 modulated cell-cell adhesion with high turnover of genes involved in tight- and adhesion junction protein synthesis and degradation (e.g. actinin alpha-4, metalloproteinase-2). These effects were less pronounced for L. plantarum WCFS1 and CIP104448. In conclusion, L. plantarum TIFN101 induced the most pronounced probiotic properties with specific effects on repair processes in the compromised intestine of healthy subjects.

overall_design: Ten healthy volunteers participated in a randomized double-blind placebo-controlled cross-over trial in which four different interventions were evaluated: 7-day oral intake of either L. plantarum WCFS1, CIP48 (CIP104448), TIFN101 (CIP104450), or placebo; after which mucosal biopsies from the duodenum were obtained for gene expression profiling.

first: Z

last: Mujagic

first: P

last: de Vos

first: M

middle: V

last: Boekschoten

first: C

last: Govers

first: H

middle: H

last: Pieters

first: N

last: de Wit

last: Bron

first: A

last: Masclee

first: F

last: Troost


title: Deciphering transcriptome profiles of porcine PBMCs in response to porcine reproductive and respiratory syndrome virus vaccine

status: Public on Feb 14 2017

city: Bonn

first: Chritiane

last: Neuhoff

state: NRW

address: Endenicher Allee 15

department: Institute of Animal Science

institute: University of Bonn

summary: In vivo microarray study of global gene expression changes in peripheral blood mononuclear cells (PBMCs) of German Landrace pigs during the innate immune response to porcine reproductive and respiratory syndrome virus vaccination.

overall_design: PBMCs samples collected at four time points (0, 6, 24 and 72 hpv) from PRRSV vaccinated and three time points (6, 24 and 72 hpv) from unvaccinated pigs were subjected hybridization of 21 arrays. Samples from each  time points were hybridized with three biological replications. To characterize the gene expression changes, we compared the PBMCs transcriptome profiles in two phenotypic dimensions. I. Between vaccinated and unvaccinated pigs (6 hpv_vaccinated vs. 6 hpv_unvaccinated and 24 hpv_vaccinated vs. 24 hpv_unvaccinated). II. Within the vaccinated group between before (0h- control) and the three post vaccination time points (6, 24 and 72 hpv).

first: Aminul

last: Islam

first: Karl

last: Schellander

first: Christiane


title: Global transcriptional analysis reveals unique and shared responses in Arabidopsis thaliana exposed to combined drought and pathogen stress

city: Delhi

first: Muthappa

last: Senthil-Kumar

state: New Delhi

address: Aruna Asaf Ali Road

department: Plant-microbe interaction

country: India

institute: National institute of plant genome research

summary:
With frequent fluctuations in global climate, plants often experience co-occurring dry-wet cycles and pathogen infection and this combination adversely affects plant survival. In the past, some studies indicated that morpho-physiological responses of plants to the combined stress are different from the individual stressed plants. However, interaction of drought stressed or drought recovered plants with pathogen has not been widely studied at molecular level. Such studies are important to understand the defense pathways that operate as part of combined stress tolerance mechanism. In this study, Arabidopsis plants were exposed to individual drought stress (soil drying at 40% FC, D), Pseudomonas syringae pv tomato DC3000 (PStDC3000), infection and their combination. Plants recovered from drought stress were also exposed to PStDC3000. Beside we have also infiltrated P. syringae pv tabaci (PSta, non-host pathogen) individually or in combination with drought stress. Using Affymetrix WT gene 1.0 ST array, global transcriptome profiling of plants leaves under individual drought stress and pathogen infection was compared with their combination. Results implicate that plants exposed to combined drought and pathogen stress experience a new state of stress where each combination of stressor and their timing defines the plant responses and thus should be studied explicitly.
Global transcriptional analysis in Arabidopsis leaves exposed to individual and combined drought and pathogen stress.

overall_design: Microarray based global gene expression analysis was carried out in Arabidopsis leaves after exposure to individual and combined stress treatments. Arabidopsis plants were exposed to drought stress (D), PStDC3000 infection (P, 1d and 6d), PSta infection (NH, 1d). For treatments involving combined stress, PStDC3000 was infiltrated on drought stressed plants (DP, 1d), plants were exposed to drought stress upon PStDC3000 infiltration (PD, 1d), PSta was infiltrated on drought stressed plants (DNH, 1d), and PStDC3000 was infiltrated on drought recovered plants (DRP). Six plants per treatment were used such that leaf tissue from three plants made one biological replicate. Two biological replicates were hybridized for each treatment.

first: Aarti

last: Gupta


title: Dysregulation of long non-coding RNAs in mouse testis and sperm after exposure to cadmium

status: Public on Feb 08 2017

city: Nanchang

first: Xiaoning

last: Zhang

address: 999 Xuefu R.D., Nanchang

institute: Nanchang University

type: Non-coding RNA profiling by high throughput sequencing


title: Total RNA sequencing in multiple Sus Scrofa tissues reveals novel long non-coding RNAs functioning in skeletal muscle development

first: Zhonglin

last: Tang

address: No. 2 Yuanmingyuan West Road, Beijing, 100193, P.R.China,

institute: Chinese Academy of Agricultural Sciences

summary: Long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. However, the landscape of lncRNAs is largely unclear in Sus scrofa. Here we performed stranded RNA-seq on total RNA libraries from over 100 samples of Sus scrofa tissues. We identified 10,813 lncRNAs in Sus scrofa, of which 9,075 are novel. 57% of these lncRNAs were conserved in both human and mouse. These conserved lncRNAs tend to be more tissue-specific than pig-specific lncRNAs, and enriched in reproducible organs (i.e. testis and ovary). We characterized a group of lncRNAs potentially involved in the skeletal muscle development. One such lncRNA, a homolog of maternally expressed gene 3 (MEG3), was specifically expressed in the skeletal muscle at early developmental stage. And its expression pattern is conserved in pig and mouse. By over-expressing and knocking down MEG3 in mouse myoblast cell lines, we demonstrated its novel function as a myoblast proliferation suppressor.

overall_design:
A comprehensive lncRNA profile in pig by total RNA sequencing

Please note that 'TCONS_000nnnn' identifiers in the *RPKM.txt processed data files are the new lncRNAs we identified in our study and that the 'sus_lncRNA.fa' contains the sequence information for each feature.

first: Kui

last: Li


title: Hypertonic saline attenuates the cytokine-induced pro-inflammatory signature in primary human lung epithelia

status: Public on Feb 06 2017

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: HTS inhibits inflammation of lung epithelium

overall_design: This study was designed to interrogate the global transcriptional responses induced by HTS and provides insight into the underlying molecular mechanisms and pathways affected by HTS. In this study, RNA sequencing was employed to explore early changes in transcriptional response, identify key mediators, signaling pathways, and transcriptional modules that are affected by HTS in the presence of a strong inflammatory stimulus.

first: Sanchayita

last: Mitra

first: Anirban

last: Banerjee


title: Transcriptome-wide analysis of roles for tRNA modifications in translational regulation

status: Public on Jun 29 2017

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation Street

department: Biochemistry & Molecular Pharm

institute: UMass Medical School

summary: Covalent nucleotide modifications in noncoding RNAs such as tRNAs affect a plethora of biological processes, with new functions continuing to be discovered for even well-known tRNA modifications. To systematically compare the functions of a large set of ncRNA modifications in gene regulation, we carried out ribosome profiling and RNA-Seq in budding yeast for 57 nonessential genes involved in tRNA modification.

overall_design: Yeast strains were treated with cycloheximide and proceeded to ribosome profiling. For ribosome-protected footprints (RPF), 80S monosome fractions were isolated after RNase I treatment, and 27-34 nt RPF were isolated by denaturing PAGE. For RNA-Seq, total RNA was depleted of rRNA using Ribo-Zero, followed by zinc-based fragmentation. RNA fragments and RPF are constructed into Illumina deep-sequencing libraries by RNA 3’ adaptor ligation and cDNA circularization. Barcoded libraries were sequenced on an Illumina NextSeq 500. Raw fastq reads were de-multiplexed and removed of adaptor sequence. RPF reads were mapped to S. cerevisiae rDNA and the mapping reads were discarded. The remaining RPF reads and RNA-seq reads were mapped to sacCer3 genome. Uniquely mapping reads in length of 27-34 nt (RPF) or 27 nt (RNA-seq) were quantified as RPKM.

first: Hsin-Jung

last: Chou


title: Impact of plfB delation on the transcriptome of Streptococcus pneumoniae D39

status: Public on Jan 26 2017

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Galactose is an important sugar for in vivo survival and virulence of important human pathogen Streptococcus pneumoniae, and pyruvate formate lyase (PFL) activity is crucial for galactose metabolism. Thus, the regulation of genes important for active PFL synthesis, pflA and pflB, was investigated. We identified six transcriptional regulators differentially expressed in ΔpflB and hypothesised that they are important for pflA or pflB regulation. Among these, CcpA, MerR2 and GntR family transcriptional regulators were directly involved in the regulation of pflA, pflB or both. It was found that CcpA is the transcriptional activator of pflB, and is the repressor of pflA on galactose. CcpA’s interaction with pflB did not require HPr-[Ser-P] but is enhanced by sodium formate, produced by the activity of PFL. The MerR2 is a repressor of both pflA and pflB, and sodium formate decreases MerR2 affinity for pflB promoter. In addition, MerR2 mediates ccpA expression mainly on glucose and to lesser degree on galactose, and MerR2 and CcpA interact for regulation of pflB. It was shown that both CcpA and MerR2 are required for pneumococcal colonisation and virulence. We also found that GntR represses pflB expression but its expression is not induced by any of the tested sugars, suggesting sugar independent regulation of pflB.

overall_design:
Transcriptome comparison of the Streptococcus pneumoniae D39 ΔplfB  to D39 wild type grown in CDM with 55mM Galactose
One condition design comparision of two strains including a dye swap

first: Hasan

last: Yesilkaya

first: Oscar

last: Kuipers


title: Transcriptomic Profiling of Early Drosophila Embryogenesis Reveals Similarities in Replication Checkpoint and Histone mRNA Processing Mutants

status: Public on Jan 20 2017

city: Montreal

first: Fabio

middle: Alexis

last: Lefebvre

state: Quebec

address: 110 Ave des Pins

department: RNA biolog

country: Canada

institute: IRCM

summary: In higher eukaryotes, maternally provided gene products drive the initial stages of embryogenesis until the zygotic transcriptional program takes over, a developmental process called the midblastula transition (MBT). In addition to zygotic genome activation, the MBT involves alterations in cell-cycle length and the implementation DNA damage/replication checkpoints that serve to monitor genome integrity. Previous work has shown that mutations affecting histone mRNA metabolism or DNA replication checkpoint factors severely impact developmental progression through the MBT, prompting us to characterize and contrast the transcriptomic impact of these genetic perturbations. In this study, we define gene expression profiles that mark early embryogenesis in Drosophila through transcriptomic analyses of developmentally staged (early syncytial vs late blastoderm) and biochemically fractionated (nuclear vs cytoplasmic) wild-type embryo. We then compare the transcriptomic profiles of loss-of-function mutants of the dChk1/Grapes replication checkpoint kinase and the Stem Loop Binding Protein (SLBP), a key regulator of replication-dependent histone mRNAs. Our analysis of RNA spatial and temporal distribution during embryogenesis offers new insights into the dynamics of early embryogenesis. Moreover, we find that grp and slbp mutant embryos display profound and highly similar defects in gene expression, most strikingly in zygotic genome activation, compromising the transition from a maternal to a zygotic regulation of development.

overall_design: We performed RNA-seq (Ribodepletion, Illumina) on collections of staged (0-45 min AEL and 90-180 min AEL) and biochemically fractionnated (cytoplasmic and nuclear extracts) wt (ORER) Drosophila embryos to derive a global spatiotemporal index of RNA distributions. In addition, we generated RNA-seq data of total embryo extracts (0-180 min AEL) derived from transheterozygous mothers bearing the grpfs1, Slbp10/12 and Slbp10/15 mutations.

first: Louis

last: Bouvrette

first: Julie

last: Bergalet

first: Éric

last: Lécuyer


title: Whole translatome profiling of Human Hepatoma culture Huh7.5 and Huh7.5M

status: Public on Feb 01 2017

city: HYDERABAD

first: KRISHNAN

middle: HARINIVAS

last: HARSHAN

address: HABSIGUDA

institute: CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY

summary: Huh7.5 cells, when grown in presence of 1-2mg/ml of Geneticin, generarated colonies with cells that were morphologically distinct from the parental cells. These cells were substantially smaller in size, had spindle like features and grew faster. They expressed mesenchymal markers and were named as Huh7.5M cells.

overall_design: Agilent-027114 Genotypic Technology designed Custom Human Whole Genome 8x60k Microarray


title: Mitochondrial and oxidative stress genes are differentially expressed in neutrophils of sJIA patients treated with tocilizumab: a pilot microarray study

status: Public on Jan 25 2017

city: London

first: Ebun

last: Omoyinmi

address: 30 Guilford Street

department: Infection, Inflammation and Rheumatology

country: United Kingdom

institute: UCL, Institute of Child Health

summary:
We hypothesised that neutrophil pathways could be also be important in the pathogenesis of sJIA. We therefore studied the gene profile in both PBMC and neutrophils of sJIA patients treated with tocilizumab.
We demonstrate that neutrophils from sJIA patients showed significantly different changes in gene expression in response to tocilizumab.

overall_design: We studied the transcriptomes of peripheral blood mononuclear cells (PBMC) and neutrophils from eight paired samples obtained from 4 sJIA patients taken before and after tocilizumab treatment.


title: Transcriptome assembly and candidate genes involved in nutritional programming in Xiphophorus multilineatus

status: Public on Jan 15 2017

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

summary:
Nutritional programming takes place in early development. Variation in the quality and/or quantity of nutrients in early development can influence long-term health and viability. However, little is known about the mechanism of nutritional programming. The live-bearing fish Xiphophorus multilineatus, has the potential to be a new model for understanding these mechanisms, given evidence of both genetic and nutritional programming influences on juvenile growth rate.
To study the molecular signatures of nutritional programming, we assembled a de novo transcriptome for X. multilineatus, and used RNA-Seq to profile gene expression in the brains of males reared in low and high quality juvenile environments.
We found131 genes were differentially expressed, including metabolism and appetite master regulator agrp gene.

overall_design: Xiphophorus multilineatus were read in High Quality Juvenile Environment (HQJE:fish were housed individually after 14 days of age, and were fed Tetramin and brine shrimp, ad libitum) or Low Quality Juvenile Enviroment (LQJE; densities > 6 fish per liter, N = 23. Fish in this group were fed Tetramin once a day) . 2 biological replicates for each treatment were performed.

first: Charlotte

last: Klimovich

first: Kalen

last: Robeson

first: William

last: Boswell

last: Rios-Cardenas

first: Ronald

middle: B

last: Walter

first: Molly

middle: R

last: Morris


title: Patient-Specific and Genome-Edited Induced Pluripotent Stem Cell-Derived Cardiomyocytes Elucidate Single-Cell Phenotype of Brugada Syndrome

status: Public on Jan 12 2017

city: Stanford

first: Jared

last: Churko

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

summary: This study recruited 2 patients with type 1 BrS carrying 2 different sodium voltage-gated channel alpha subunit 5 variants as well as 2 healthy control subjects. We generated iPSCs from their skin fibroblasts by using integration-free Sendai virus. We used directed differentiation to create purified populations of iPSC-CMs. BrS iPSC-CMs showed reductions in inward sodium current density and reduced maximal upstroke velocity of action potential compared with healthy control iPSC-CMs. Furthermore, BrS iPSC-CMs demonstrated increased burden of triggered activity, abnormal calcium (Ca2+) transients, and beating interval variation. Correction of the causative variant by genome editing was performed, and resultant iPSC-CMs showed resolution of triggered activity and abnormal Ca2+ transients. Gene expression profiling of iPSC-CMs showed clustering of BrS compared with control subjects. Furthermore, BrS iPSC-CM gene expression correlated with gene expression from BrS human cardiac tissue gene expression.

overall_design: RNA-seq of  hiPSC-CMs from control and Brugada patient lines

first: Karim

last: Sallam

first: Ping

last: Liang


title: Study on the effects of cytoskeletal modifying compounds on stem cell differentiation

status: Public on Dec 30 2016

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: We report genome-wide expression changes that occur in mouse bone marrow-derived mesenchymal stem cells treated in triplicate for 24 hours with or without Cytochalasin D and/or CK666. mRNA-Seq analysis shows that both cell surface and the nucleus undergo phenotypic changes. Cytochalasin D enhanced expression of genes involved in pathways known to regulate osteoblast differentiation, including genes involved in development and cell signaling, including calcium ion binding, WNT and PI3K/AKT pathway. In summary, RNA-seq data reveal that the CytoD activates genes linked to osteogenesis, while CK666stimulates adipogenic genes.

overall_design: Bone marrow-derived MSCs were maintained in MEM containing 10% fetal bovine serum, 100 μg/ml penicillin/streptomycin. For experiments, the cells were plated at a density of 10,000 cells/cm2 in 6-well culture plates and cultured for 1 day prior to application of treatments. Cells were treated with CytochalasinD and/or CK666 for 24h followed by preparation for RNA isolation. Purified RNA was then submitted for RNA-sequencing.

first: Andre

last: van Wijnen

first: Amel

last: Dudakovic


title: Epigenetic effects of RRx-001: a possible unifying mechanism of anticancer activity

status: Public on Dec 31 2016

first: Hongjuan

last: Zhao

address: 300 Pasteur Dr

department: Urology

summary: RRx-001 (also known as ABDNAZ, 1-bromoacetyl-3,3-dinitroazetidine) is a novel aerospace-derived compound currently under investigation in several ongoing Phase II studies.  In a Phase I trial, it demonstrated anti-cancer activity and evidence of resensitization to formerly effective therapies in heavily pre-treated patients with relapsed/refractory solid tumors.  With a pharmacologically unprecedented dinitroazetidine scaffold, RRx-001 generates reactive oxygen and nitrogen species (ROS and RNS) and nitric oxide (NO), elicits changes in intracellular redox status, modulates tumor blood flow, hypoxia and vascular function and triggers apoptosis in cancer cells.  Here, the effect of RRx-001 on the epigenome of SCC VII cancer cells was investigated. RRx-001 at 0.5 and 2 μM significantly decreased global DNA methylation, i.e., 5-methylcytosine levels, in SCC VII cells determined by analysis with an enzyme-linked immunosorbent assay (ELISA).  Consistently, 0.5-5 μM RRx-001 significantly decreased Dnmt1 and Dnmt3a protein expression determined using Western blot in a dose- and time-dependent manner.  In addition, global methylation profiling identified differentially methylated genes in SCC VII cells treated with 0.5, 2, and 5 μM RRx-001 compared to control cells.  Twenty-three target sites were hypomethylated and 22 hypermethylated by >10% in the presence of at least two different concentrations of RRx-001.  Moreover, RRx-001 at 2 μM significantly increased global acetylated histone H3 and H4 levels in SCC VII cells after 24 hour treatment determined by a fluorometric assay, suggesting that RRx-001 regulates global acetylation in cancer cells.  These results demonstrate that, in contrast to the traditional “one drug one target” paradigm, RRx-001 has multi(epi)target features, which contribute to its anti-cancer activity and may rationalize the resensitization to previously effective therapies observed in clinical trials and serve as a unifying mechanism for its anticancer activity.

overall_design: Exponentially growing cells were plated in 100-mm dishes with 5-10 x 105 cells per dish in DMEM culture media and grown overnight.  Cells were treated with RRx-001, 5-azacytidine or 0.025% DMSO as a vehicle control for one to three days.  Media containing RRx-001, 5-azacytidine, or DMSO were replaced daily over the 3-day period.

first: Shoucheng

last: Ning

first: Jan

last: Scicinski

first: Bryan

last: Oronsky

first: Susan

last: Knox

first: Donna

last: Peehl


title: Murine NIH3T3 Cells: Wild vs. BRAFV600E Transfected

status: Public on Jan 01 2017

city: Xi’an

first: Yiping

last: Qu

address: The First Affiliated Hospital of Xi’an Jiaotong University

department: Department of Endocrinology

summary: Transcriptional profiling of mouse NIH3T3 cells comparing control NIH3T3 cells transfected with a pEFm6-BRAF with cells transfected with pEFm6-BRAFV600E. Goal was to determine the effects of BRAFV600E gene transfection on global mouse NIH3T3 cells gene expression.

overall_design: Two-condition experiment, Wild vs. BRAFV600E TransfectedNIH3T3 cells.

first: Peng

last: Hou


title: Pre- and Post-hatch transcriptomic response of chicken Musculus gastrocnemius to transient variation of incubation temperature

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

summary: After elevated and reduced incubation temperature during embryonic days (ED) 7-10 and 10-13 changes of gene expression were determined  at ED 10, ED 13, and post-hatch at day (D) 35

overall_design: Broiler eggs were incubated at a lower or higher temperature (36.8°C, 38.8°C) relative to control (37.8°C) over two developmental intervals, embryonic days (ED) 7-10 and 10-13. Global gene expression of Musculus gastrocnemius was assayed at ED 10, ED 13, and slaughter age [post-hatch day (D) 35] (6 groups; 3 time points; 8 animals each) by microarray analysis and treated samples were compared to controls within each time point

first: Watcharapong

last: Naraballobh

first: Nares

last: Trakooljul

first: Eduard

last: Muráni

first: Siriluck

last: Ponsuksili


title: Improved post thaw function and genetic changes for mesenchymal stromal cells cryopreserved using multicomponent osmolyte solutions

summary: We report genome-wide expression changes that occur in H9-iMSCs frozen with different freezing methods that include DMSO and non-DMSO experimental solutions such as SGC (sucrose-glycerol-creatinine, SMC (sucrose-mannitol-creatinine), and SGI (sucrose-mannitol-isoleucine). mRNA-Seq analysis shows that DMSO samples cluster with fresh samples in the same clade, while all samples using the experimental solutions cluster together. In addition, we also see that cells frozen using experimental solutions have upregulation of a number of key molecular function pathways including extracellular matrix structural genes, receptor binding, and growth factor expression.

overall_design: H9 MSCs were cultured in alpha-MEM base (Life Technologies), 10% FBS (qualified), and 1% non-essential amino acids (Life Technologies). Culture flasks were coated with 0.01% porcine gelatin (Fisher) for a minimum of 2 hours before H9 MSC seeding.  H9 MSCs were seeded in gelatin-coated flasks at a density of approximately 2500 cells/cm2.  Cells were split when they reached 70% confluence and were used for experiments only from passages 8 to 12.  Control cells in media were similarly combined stepwise with DMSO at a 1:1 final volume ratio.  Each of these vials was incubated at room temperature for 0, 1, or 2 hours.  Experimental solutions were frozen using a 3°C/min cooling rate while DMSO solutions were frozen using a 1°C/min cooling rate. Samples were submerged in a 37ºC bath to just under cap level, and agitated until only a small ice crystal was present. The cells were combined with acridine orange/propidium iodide (AO/PI) and enumerated using a hemocytometer. Samples were diluted, centrifuged and supernatant was aspirated, followed by preparation for RNA isolation. Purified RNA was then submitted for RNA-sequencing.

first: Rebekah

last: Samsonraj


title: Genome-wide maps of H3K27 state in transfected NIH3T3 cells.

institute: The First Affiliated Hospital of Xi’an Jiaotong University

summary: Epigenetic H3k27me3 changes of mouse NIH3T3 cells comparing control NIH3T3 cells transfected with a pEFm6-BRAF with cells transfected with pEFm6-BRAFV600E. By obtaining over 30 Million bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of BRAF transfected. We find that global lysine 3 and lysine 27 trimethylation levels changed under the condition of activated ERK by BRAFV600E, and specific genes might be downregulated for the hight level of H3K27me3 induced by BRAFV600E

overall_design: Examination global levels of H3K27me3 in the 2 transfected cells.


title: Expression data from HCT 116 colorectal cancer cells treated with oncolytic virus M1

status: Public on Dec 27 2016

city: Guang Zhou

first: Jing

last: Cai

address: Zhongshan School of Medicine, Sun Yat-sen University   74 Zhongshan 2nd Road

institute: Sun yat-sen university

summary:
Virus infection is a kind of immune stimulation, except anti-viral factors, virus also induce tumor cells to secret cytokines which act on neighboring cells. Figuring out the exact cytokines upregulated by M1 virus is of great significance.
We used microarry data to detail the expression of cytokines, chemokines and Inflammasomes regulated by oncolytic virus M1.

overall_design: HCT116 tumor cells were treated with oncolytic virus M1 for 0h or 24h, and we used microarray data to detail the expression of cytokines, chemokines and Inflammasomes regulated by oncolytic virus M1.

first: Xiao

last: Xiao


title: Transcriptomic landscape of S. cerevisiae x S. kudriavzevii hybrids in low temperature winemaking.

status: Public on Dec 03 2016

city: Paterna

first: Jordi

last: Tronchoni

address: Avda. Agustín Escardino, 7

country: Spain

institute: CSIC

summary: Comparative genome-wide gene expression analysis between two industrial wine yeast hybrid strains belonging to the species S. cerevisiae x S. Kudriavzevii, in natural must fermentations.

sample_organism: Saccharomyces cerevisiae x Saccharomyces kudriavzevii

overall_design: RNA samples taken from wine fermentations at 12ºC and 28ºC at the beginning of exponential phase. Three biological replicates.

first: Jose-Manuel

last: Guillamón

first: Amparo

last: Querol

first: Roberto

last: Pérez-Torrado


title: CGH analysis of mouse mammary gland tumors from eight genetically-engineered mouse models

status: Public on Nov 18 2016

city: Bethesda

first: Jeffrey

last: Green

state: MD

address: Rm 4054, 37 Convent Drive

institute: NCI

summary:
Background. Oncogene overexpression in primary cells often triggers the induction of a cellular safeguard response promoting senescence or apoptosis. Secondary cooperating genetic events are generally required for oncogene induced tumorigenesis to overcome these biologic obstacles.  We employed array CGH for 8 genetically-engineered mouse models of mammary cancer to identify loci that might harbor genes that enhance oncogene-induced tumorigenesis.
Results. Unlike many other mammary tumor models, the MMTV-Myc tumors displayed few CNVs except for amplification of distal mouse chromosome 11 in 80% of the tumors (syntenic to human 17q23-qter often amplified in human breast cancer). Analyses of candidate genes located in this region identified JMJD6 as an epigenetic regulatory gene that cooperates with Myc to enhance tumorigenesis.  It suppresses Myc-induced apoptosis under varying stress conditions through inhibition of p19ARF mRNA and protein, leading to reduced levels of p53.  JMJD6 binds to the p19ARF promoter and exerts its inhibitory function through demethylation of H4R3me2a.  JMJD6 overexpression in MMTV-Myc cell lines increases tumor burden, induces EMT and greatly enhances tumor metastasis.  Importantly, we demonstrate that co-expression of high levels of JMJD6 and MYC is associated with poor prognosis for human ER+ breast cancer patients.
Conclusions.  A novel epigenetic mechanism has been identified for how JMJD6 cooperates with Myc during oncogenic transformation. Combined high expression of Myc and JMJD6 confers a more aggressive phenotype in mouse and human tumors. Given the pleotropic pro-tumorigenic activities of JMJD6, it may be useful as a prognostic factor and a therapeutic target for Myc-driven mammary tumorigenesis.

overall_design: 5-6 mammary gland tumors for each model were subjected to CGH analysis.  The same mouse mammary gland tumor models were used as described in Zhu M, Yi M, Kim CH, Deng C, Li Y, Medina D, Stephens RM, Green JE: Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage. Genome Biol 2011, 12:R77.

first: Jeff

first: Olga

last: Aprelikova

first: Min

last: Zhu


title: Macrophage Colony Stimulating Factor derived from CD4+ T cells aids in control of an intracellular infection [RNA-seq]

status: Public on Nov 12 2016

city: San Francisco

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary:
Background: In malaria, parasites of the genus Plasmodium elicit robust host expansion of macrophages and monocytes, but the underlying mechanisms remain unclear. In a microarray analysis of pooled, activated CD4+ T cells from mice infected with P. chabaudi, we detected inducible expression of Csf1, which promotes macrophage proliferation. To better characterize Csf1-producing T cells, single-cell RNA-Seq was performed.
Results: Robust Csf1 expression was detected in a subset of sampled CD4+ T cells (n = 14/35), whereas the remainder of cells had no detectable Csf1. Further, we identified ~ 400 genes that were differentially expressed between Csf1+ and Csf1- T cells.
Conclusions: This work defines the transcriptional landscape of a subset of activated CD4+ T cells that produce the cytokine Csf1. These cells are expected to be important in infections with intracellular pathogens such as Plasmodium.

overall_design: Antigen-experienced (CD11a+ CD49d+) CD4+ T cells were isolated by double-sorting from the blood of C57BL/6 adult female mice 6 days post-infection with Plasmodium chabaudi.   Single cells were isolated and processed for RNA sequencing using a Fluidigm C1 integrated fluidic circuit chip.  35 biological replicates were analyzed.

first: Charles

first: Mary

middle: F

last: Fontana


title: Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

status: Public on Dec 06 2016

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

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

overall_design: Refer to individual Series


title: Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [Capture-C]

overall_design: Capture-C protocol on embryonic limb bud.

first: Robert

last: Schöpflin


title: Transcriptional profiling of CD4+ T cells activated in murine malaria.

summary:
CD4+ T cells are critical for defense against the Plasmodium parasites that cause malaria. To better understand CD4+ T cell effector mechanisms during malaria, we performed microarray analysis of CD4+ T cells from naïve and infected mice.
Comparison of activated (CD44 hi CD62L lo) CD4+ T cells from infected mice to bulk CD4+ T cells from naïve mice revealed a subset of genes that were upregulated by infection with Plasmodium chabaudi. These results help generate a more complete picture of CD4+ T cell function in malaria.

overall_design: Total CD4+ T cells were double-sorted from the blood of adult naïve female mice; activated (CD44 hi CD62L lo) CD4+ T cells were double-sorted from the blood of adult female mice 6 d post-infection with P. chabaudi. Four independent biological replicates were performed per condition.


title: Expression data of colon cancer COLO320DM cells and tankyrase inhibitor-resistant variant 320-IWR cells

status: Public on Nov 01 2016

city: Tokyo

first: Tetsuo

last: Mashima

address: 3-8-31, Ariake,Koto-ku

country: Japan

institute: JFCR

summary: Wnt/β-catenin signaling is activated in colorectal cancer (CRC) and is involved in CRC growth. Tankyrase, a poly(ADP-ribose) polymerase family member, destabilizes Axin and positively regulates the Wnt/β-catenin signaling. Tankyrase inhibitors efficiently suppress CRC cell proliferation. We established 320-IWR cells, which showed resistance to tankyrase inhibitor IWR-1, from human CRC COLO-320DM cells. We analyzed gene expression profile of 320-IWR cells (320IWR_1,_2) and parental COLO-320DM cells (COLO320_1,_2).

overall_design: We continuously treated COLO-320DM cells with a tankyrase inhibitor IWR-1 and established a tankyrase inhibitor-resistant cell line, 320-IWR. We compared gene expression between COLO-320DM (COLO320_1,_2) and 320-IWR (320IWR_1,_2) cells.

first: Yoko

last: Taneda

first: Hiroyuki

last: Seimiya


title: Luminal B breast cancer subtype displays a dichotomic epigenetic pattern

status: Public on Dec 18 2016

city: Adelaide

first: Naiara

middle: G

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

country: Australia

institute: The University of Adelaide

summary: Purpose In breast cancer, specific aberrant methylation patterns have been associated with different BC histologic and molecular subtypes and data suggest that DNA methylation profiles may play an important role in the development and progression of distinct breast subtypes. However, the epigenome of the newly defined luminal B and luminal B-HER2 positive breast cancers has not yet been characterized. Therefore the main goal of the current study is to deciphered the aberrant DNA methylation profiles associated with these breast cancer subtypes.  Experimental Design 29 luminal subtype breast cancer samples along with 8 control tissue were epigenetically interrogated using the HumanMethylation27 DNA Analysis BeadChip. Results Luminal B-HER2 + subtype displays the most aggressive phenotype and shows the highest number of aberrantly methylated CpG markers. On the other hand, the luminal B subtype harbours an heterogeneous DNA methylation profile that seems to be half way between the luminal A and luminalB-HER2+ subtypes. Conclusions The heterogeneous epigenetic and genetic profile of the luminal B subtype, might indicate that a further stratification has to be done for this specific breast cancer subtype.

overall_design:
Bisulphite converted DNA from the 29 breast cancer samples and 8 control samples were hybridised to the Illumina Infinium 27
k Human Methylation Beadchip v1.217

first: Elena

last: Beristain

first: Borja

last: Calvo


title: Exercise-induced transcriptome changes in skeletal muscle adapted to aerobic training

status: Public on Oct 27 2016

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

summary: We sequenced mRNA in vastus lateralis muscle samples from two amateur endurance-trained males (V’O2max 57 ml/min/kg) before and after acute endurance exercise

overall_design: Examination of mRNA prior to, 4 h, and 8 h after acute intensive cycling session (70 min, 70% V’O2max )

first: P

last: Makhnovskii

first: D

last: Popov


title: LncRNA/mRNA expression profiling for 10 human samples

city: Shanghai

first: Zhang

last: Zi-Zhen

address: Department of General Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, 1630 Dongfang Road, Shanghai 200127, China

institute: Department of General Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, P.R. China

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

summary: By using the method of “small samples for high throughput screening + large samples for validation”, to find the risk-related long non-coding RNAs and encoding-genes in gastric cancer. To improve the level of clinical diagnosis and treatment of gastric cancer by studying the biological function and its molecular mechanism of these molecules

overall_design: Identification of risk-related coding RNAs and lncRNAs that are diffrentially expressed in gastric cancer by comparing 5 gastric cancer tissues and 5 adjancent normal tissues.

first: Zi-Zhen

last: Zhang


title: Progressive retinal atrophy in the Hungarian Puli

status: Public on Oct 31 2016

city: Darlington

first: Tracy

last: Chew

state: NSW

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

institute: University of Sydney

summary: Progressive retinal atrophy (PRA) is a common cause of blindness in many pure and mixed breed dogs (Canis lupus familiaris). The typical onset of PRA begins with gradual night vision loss followed by day vision loss due to the death of rod and cone receptors, respectively. There are currently no mutations or genes reported to be causative or associated with PRA in the Hungarian Puli. In this study, we use an extensive list of 53 known PRA genes to screen for putative causal variants in this breed of dog.

overall_design: 2 cases, 12 controls

first: Bianca

last: Haase

first: Rosyln

last: Bathgate

first: Cali

last: Willet

first: Maria

middle: K

last: Kaukonen

first: Lisa

last: Mascord

first: Hannes

middle: T

last: Lohi

first: Claire

last: Wade


title: DNA methylation variation of human-specific Alu repeats

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences Bldg

department: Biological Sciences

institute: Louisiana State University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is the major repression mechanism for human retrotransposons, such as the Alu family. Here, we have derived methylation levels regarding 5238 loci belonging to two Alu subfamilies, AluYa5 and AluYb8, using High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS). The results indicate that ~90% of loci are repressed by high methylation levels. Of the remaining loci, many of these hypomethylated elements are found near gene promoters and show high levels of DNA methylation variation. We have characterized this variation in the context of tumorigenesis and inter-individual differences. Comparison of a primary breast tumor and its matched normal tissue revealed early DNA methylation changes in ~1% of AluYb8 elements in response to tumorigenesis. At the same time, AluYa5/Yb8 elements proximal to promoters also showed differences in methylation of up to one order of magnitude even between normal individuals. Overall, the current study demonstrates that early loss of methylation occurs during tumorigenesis in a subset of young Alu elements, suggesting their potential clinical relevance. However, techniques such as deep-bisulfite-sequencing of individual loci using HT-TREBS are required to distinguish clinically relevant loci from the background observed for AluYa5/Yb8 elements in general with regard to high levels of inter-individual variation in DNA methylation.

overall_design: HT-TREBS has been used with the Ion Torrent PGM platform to analyze the DNA methylation of 5238 AluYa5/Yb8 elements in a locus-specific manner in human skin-derived fibroblast cells, and a matched normal breast and primary tumor

first: Arundhati

last: Bakshi

first: Scott

last: Herke

first: Mark

last: Batzer


title: Intracoronary imaging, cholesterol efflux and transcriptomes after intensive statin treatment

status: Public on Oct 29 2016

city: New York City

first: Joel

last: Dudley

state: NY

address: 770, Lexington Ave, 15th Floor

department: Genetics and Genomics Sciences

institute: Mount Sinai Health System

summary:
The relation of serial changes in plaque morphology of obstructive nonculprit lesions to HDL efflux, inflammation and transcriptome perturbations in response to high-dose statin therapy (YELLOW II study). YELLOW II is a prospective single center study. Stable patients who were scheduled for elective coronary angiography and/or coronary artery stenting were screened for this study. The final target population were patients with multivessel disease requiring staged intervention, culprit vessel initially and non-culprit vessel later, with maxLCBI4mm greater than 150 by NIRS. Patients underwent PCI for a culprit lesion followed by OCT and NIRS/IVUS of an obstructive non-culprit lesion (NCL). All subjects received rosuvastatin, 40 mg every day for 8-12 weeks. The NCL was reimaged and underwent intervention as a part of staged intervention. Blood samples were obtained for cholesterol efflux capacity (CEC) quantification and peripheral PBMC isolation.
Despite the extensive evidence for the beneficial effects of statins on clinical outcomes, the mechanisms underlying these effects in remain elusive. In a prospective study, 85 patients with stable multivessel coronary artery disease underwent percutaneous coronary intervention for a culprit lesion followed by intracoronary multi-modality imaging including optical coherence tomography (OCT) of an obstructive NCL. All subjects received 40 mg of rosuvastatin every day for 8-12 weeks, when the NCL was reimaged and intervention was performed. Blood samples were drawn at both times to assess cholesterol efflux capacity (CEC) and transcriptomic profile in peripheral blood mononuclear cells (PBMC).

overall_design: Paired, sibship enabled study with baseline and followup expression data analyses.

first: Annapoorna

middle: S

last: Kini

first: Yuliya

last: Vengrenyuk

first: Khader

last: Shameer

first: Akiko

last: Maehara

first: Meerarani

last: Purushothaman

first: Takahiro

last: Yoshimura

first: Mitsuaki

last: Matsumura

first: Melissa

last: Aquino

first: Nezam

last: Haider

first: Kipp

middle: W

last: Johnson

first: Ben

last: Readhead

first: Brian

last: Kidd

first: Jonathan

last: Feig

first: Prakash

last: Krishnan

first: Joseph

last: Sweeny

first: Mahajan

last: Milind

first: Pedro

last: Moreno

first: Roxana

last: Mehran

first: Jason

last: Kovacic

first: Usman

last: Baber

first: Jagat

last: Narula

first: Samin

last: Sharma


title: Gene expression in the tail tissue of tadpoles [Rana pirica] by larvae salamander or dragon fly

status: Public on Oct 24 2016

city: Fujisawa

first: Tsukasa

last: Mori

state: Kanagawa

address: Kameino 1866

department: Bioresource Sciences

institute: Nihon University

summary:
Tadpoles of the anuran species Rana pirica can undergo predator-specific morphological responses. Exposure to a predation threat by larvae of the salamander Hynobius retardatus results in formation of a bulgy body (bulgy morph) with a higher tail.  Whereas, dragon fly also induced higher tail tadpole.  The tadpoles revert to a normal phenotype upon removal of the larval salamander or dragon fly threat.
The objective of the present study was to use Affymetrix Xenopus Genechip to profile gene expression in the tail tissue by different predation threat.

overall_design: Tadpoles of Rana pirica treated with larvae salamander for 8days (S1, S2, S3) or dragon fly for 8days (Y1,Y2, Y3) were analyzed with triplicate. Removal experiments were also treated with predators for 4days and then removed predators from tadpoles (-S1,-S2, -S3) or (-Y1,-Y2,-Y3).  Controls were cultured for 8days without predators (C2, C3).  Tails from tadpoles after 8days of each treatment were dissected for RNA extraction and gene expression analysis using Affymetrix Xenopus Genechip arrays.


title: Fish Connectivity Mapping: Linking Chemical Stressors by Their MOA-Driven Transcriptomic Profiles

status: Public on Jan 08 2017

city: Cincinnati

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

institute: US EPA

summary: Modeled on human connectivity mapping (Cmap), this study was undertaken to investigate the potential applications of Cmap approach in ecotoxicology.  Over 3500 zebrafish (Danio rerio) and fathead minnow (Pimephales promelas) transcriptomic profiles, each associated with one of several dozen chemical treatment conditions, were compiled into three distinct collections of rank-ordered gene lists (ROGLs) by species and microarray platforms.  Individual query signatures, each consisting of multiple gene probes differentially expressed in a chemical condition, were used to interrogate the reference ROGLs.  Informative connections were established at high success rates within species when, as defined by their mechanisms of action (MOAs), both query signatures and ROGLs were associated with the same or similar chemicals.  In other words, a simple query signature functioned effectively as an exposure biomarker, without going through a typical time-consuming process of development and validation.  More importantly, a large reference database of ROGLs also enabled a query signature to cross- interrogate other chemical conditions with overlapping MOAs, leading to novel groupings and subgroupings of seemingly unrelated chemicals at a finer resolution.  This approach confirmed the identities of several estrogenic chemicals, as well as a polycyclic aromatic hydrocarbon and a neuro-toxin, in the largely uncharacterized water samples near several waste water treatment plants, and thus demonstrates its future potential in real world applications.  The power of Cmap should grow along with the chemical coverage of its ROGLs, making it a framework easily scalable in the future.  For toxicity extrapolation across fish species, however, a sufficient number of GEPs linked to chemical conditions common to multiple fish species are needed next in order to conduct a more thorough feasibility study of interspecific Cmap.

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, 036574)

first: Adam

last: Biales

first: Natalia

last: Garcia-Reyero

first: Edward

last: Perkins

first: Dan

last: Villeneuve

first: Gerald

last: Ankley

first: David

last: Bencic


title: Microarray data vitiligo patients lesional and non-lesional skin

city: Delhi

first: Vivek

last: Natarajan

state: Delhi

address: Mathura Road

institute: CSIR-IGIB

summary: lesional and non-lesional skin from vitiligo patients

overall_design: there are 30 samples from 15 individuals' lesional and non-lesional skin

first: Rajesh

last: Gokhale

first: Chetan

last: Gadgil

first: Riitta

last: Lahesmaa

first: Rajni

last: Rani

first: Päivi

last: Junni


title: Individuals with excess numbers of germline de novo CNVs [Affymetrix]

status: Public on Oct 14 2016

city: Houston

first: Pengfei

last: Liu

address: 2450 Holcombe Blvd, O270F

institute: Baylor College of Medicine

type: Genome variation profiling by genome tiling array

summary: We describe a multiple de novo CNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional de novo CNVs. Five such families are studied, which consists of four trios and one singleton. Various array platforms are used to interogate these families to identify de novo CNVs.

overall_design: DNAs were isolated from blood samples or cultured lymphoblastoid cell lines. DNAs from each subject and their parents were initially analyzed on both the Agilent SurePrint G3 Unrestricted CGH 1x1M (G4824A) array or an Agilent customized array and the Roche NimbleGen Human CGH 4.2M Whole Genome Tiling Array following the manufacturer’s protocols. The same DNA samples were subsequently analyzed on SNP genotyping arrays including the Illumina HumanOmni2.5-8 Array, the Illumina HumanOmni1-Quad Array, the Affymetrix Genome-Wide Human SNP Array 6.0, and the Affymetrix CytoScan HD Array.

first: James

last: Lupski


title: Individuals with excess numbers of germline de novo CNVs [NimbleGen]

overall_design: DNAs were isolated from blood samples or cultured lymphoblastoid cell lines. DNAs from each subject and their parents were initially analyzed on both the Agilent SurePrint G3 Unrestricted CGH 1x1M (G4824A) array or an Agilent customized array and the Roche NimbleGen Human CGH 4.2M Whole Genome Tiling Array following the manufacturer’s protocols. The same DNA samples were subsequently analyzed on SNP genotyping arrays including the Illumina HumanOmni2.5-8 Array, the Illumina HumanOmni1-Quad Array, or the Affymetrix CytoScan HD Array.


title: Individuals with excess numbers of germline de novo CNVs [Illumina]

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


title: Individuals with excess numbers of germline de novo CNVs


title: Individuals with excess numbers of germline de novo CNVs [Agilent]


title: Hyaluronan and TLR4 Regulate Alveolar Stem Cell Renewal and Prevent Severe Pulmonary Fibrosis

status: Public on Oct 03 2016

city: Los Angeles

first: ting

last: Xie

state: CA

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

summary:
The successful repair of alveolar epithelial injury is required to restore the integrity of gas exchanging regions of the lung and preserve organ function. Severe pulmonary fibrosis is the result of repeated episodes of epithelial injury, activation of fibroblasts, and matrix accumulation. Thus, impaired alveolar epithelial progenitor cell renewal could contribute to the progression of fibrosis. We provide evidence that expression of TLR4 and hyaluronan (HA) on Type 2 alveolar epithelial cells (AEC2s) is necessary for self-renewal. Either deletion of TLR4 or HA synthase 2 leads to impaired regeneration of AEC2s, severe fibrosis and mortality, in part due to blunted production of IL-6. AEC2s from patients with pulmonary fibrosis have reduced cell surface HA, and impaired renewal capacity, suggesting that interactions between HA and TLR4 are key regulators of lung stem cell renewal, repair of lung injury and that severe pulmonary fibrosis is the result of epithelial stem cell failure.
We used microarrays to detail the gene expression of AEC2 cells from WT  and TLR4-/- mice.

overall_design: AEC2 cells were flow sorted from either untreated lungs or the lungs 4 days after bleomycin from WT or TLR4-/- mice. RNA were extracted and hybridized on Affymetrix microarrays.

first: Jiurong

last: Liang

first: Yanli

last: Zhang

first: Ting

first: Huaiyong

last: Chen

first: Christina

last: Barkauskas

first: Barry

last: Stripp

first: Brigid

last: LHogan

first: Dianhua

last: Jiang

first: Paul

last: Noble


title: Microarray data of two ros1 background hda6 alleles of Arabidopsis

status: Public on Oct 01 2016

city: KONGLOON TOON

first: SHOUDONG

last: ZHANG

address: WATERLOO ROAD

department: BIOLOGY

country: Hong Kong

institute: HONG KONG BAPTIST UNIVERSITY

summary: HDA6 is a RPD3-like histone deacetylase.  In Arabidopsis, it mediates transgene and some endogenous target transcriptional gene silencing (TGS) via histone deacetylation and DNA methylation.  Here, we characterized two hda6 mutant alleles that were recovered as second-site suppressors of the DNA demethylation mutant ros1-1.  Although both alleles derepressed 35S::NPTII and RD29A::LUC in the ros1-1 background, they had distinct effects on the expression of these two transgenes.  In accordance to expression profiles of two transgenes, the alleles have distinct opposite methylation profiles on two reporter gene promoters.  Furthermore, both alleles could interact in vitro and in vivo with the DNA methyltransferase1 with differential interactive strength and patterns. Although these alleles accumulated different levels of repressive/active histone marks, DNA methylation but not histone modifications in the two transgene promoters was found to correlate with the level of derepression of the reporter genes between the two had6 alleles.  Our study reveals that mutations in different domains of HDA6 convey different epigenetic status that in turn controls the expression of the transgenes as well as some endogenous loci.

overall_design: In this array, four samples including wild type (C24-Luc), ros1-1 mutant, ros1hda6-9, and ros1hda6-10 were analyzed, and each sample is with two biological replicates. Here ros1-1 single mutant as a reference sample.

first: Shoudong


title: Genetic correction of a LRRK2 mutation in human iPSCs links parkinsonian neurodegeneration to ERK-dependent changes in gene expression.

status: Public on Sep 30 2016

city: Tuebingen

first: Sven

last: Poths

address: Calwerstr. 7

department: Medical Genetics

institute: University hospital Tuebingen

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

summary: Induced pluripotent stem cells generated from Parkinson's disease patients with LRRK2 G2019S

overall_design: retroviral delivery of OCT4, SOX2, KLF4, and C-MYC into primary fibroblasts

first: Jared

last: Sterneckert

first: Peter

last: Reinhardt

first: Thomas

last: Gasser

first: Benjamin

last: Schmid


title: INTRAGRAFT ANTI-VIRAL-SPECIFIC GENE EXPRESSION AS A DISTINCTIVE TRANSCRIPTIONAL SIGNATURE FOR POLYOMAVIRUS-ASSOCIATED NEPHROPATHY

first: Tara

last: Sigdel

address: 513 parnassus

department: Surgery

institute: University of California San Francisco

summary: Polyoma virus nephropathy (PVAN) is a common cause of kidney allograft dysfunction and loss. Microscopic descriptions of PVAN are very similar to T-cell mediated rejection (TCMR) and have unclear underlying molecular mechanisms. To identify PVAN-specific gene expression, we analyzed 162 kidney biopsies with and without PVAN for global gene expression. Unsupervised hierarchical clustering analysis of all 162 biopsies revealed high similarity between PVAN and TCMR gene expression. Increasing the stringency for the specificity (p <0.001 and >2-fold expression) between PVAN and TCMR, 158 and 252 unique PVAN and TCMR injury-specific probesets were observed, respectively. While TCMR-specific probeset were overwhelmingly involved in immune response costimulation (CTLA4, CD28, CD86) and TCR (NFATC2, LCP2) signaling, PVAN-specific probesets were mainly related to viral replication process (IFITM1, LTF, NOSIP, RARRES3), RNA polymerase assembly (POLR2l, TAF10, RPS15) and pathogen recognition receptors (C1QA, C3, CFD). A principal component analysis using these genes further confirmed the most optimal separation between the 3 different clinical phenotypes. Validation of 4 PVAN-specific probesets (RPS15, CFD, LTF, and NOSIP) by QPCR and further confirmation by IHC of 2 PVAN-specific proteins with anti-viral function (LTF and IFITM1) was done, showing significantly higher expression within interstitial cellular infiltrates and in tubuli in PVAN specimens as compared to TCMR and NL kidney biopsies. In conclusion, even though PVAN and TCMR kidney allografts share great similarities on gene perturbation, particular PVAN-specific transcripts were identified with well-known anti-viral properties that provide tools for discerning PVAN and AR as well as attractive targets for rational drug design.

overall_design: A total of 168 kidney biopsies from kidney transplant patients were used. The kidney biopsies included renal biopsies from PVAN (n=10), T cell mediated cellular rejection (n=26), patients with IFTA (n=59), patients with stable grafts (STA) (n=73).

first: Oriol

last: Bestard

first: Nathan

last: Salomonis

first: Szu-Chuan

last: Hsieh

first: Joan

last: Torras

first: Maarten

last: Naesens

first: Tim

middle: Q

last: Tran

first: Silke

last: Roedder

first: Minnie

last: Sarwal


title: Shewanella piezotolerans WP3 wild-type strain at 4°C vs 25°C

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: The WP3 strains were cultured at 4°C and 25°C, respectively. The transcriptional profiles at these two different temperatures were compared.

overall_design: Three biological replicates sample and 6 technical replicates for each experiment

first: Shengkang

last: Li

first: Fengping

last: Wang


title: Whole blood gene expression profiles from a lupus nephritis mouse model: SNF1 (SWR X NZB F1) mice treated with pristane

status: Public on Sep 06 2016

city: Cambridge

first: Agnes

last: Gardet

address: 115 broadway

department: Immunology

institute: Biogen

summary: We characterized the longitudinal gene expression profiles of whole blood from a novel lupus model nephritis: SNF1 (SWR X NZB F1) mice treated with pristane. Genes from interferon, plasma cell, neutrophil, T-cell and protein synthesis signatures were differentially expressed in the pristane-SNF1 model compared to the untreated matched control animals.

overall_design: Whole blood was collected from mice SNF1 (SWR X NZB F1) after pristane treatment at different time points (week 0, week 2, week 4, week 8, week 12, week 14) as well as from matched untreated SNF1 mice and from untreated 36-week old SNF1 mice that show spontaneous disease. The study includes blood samples from at least 8 animal for each condition.


title: Comparative analysis of single-cell RNA sequencing methods

status: Public on Sep 09 2016

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

summary: Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data from 583 mouse embryonic stem cells to evaluate six prominent scRNA-seq methods: CEL-seq2, Drop-seq, MARS-seq, SCRB-seq, Smart-seq and Smart-seq2. While Smart-seq2 detected the most genes per cell and across cells, CEL-seq2, Drop-seq, MARS-seq and SCRB-seq quantified mRNA levels with less amplification noise due to the use of unique molecular identifiers (UMIs). Power simulations at different sequencing depths showed that Drop-seq is more cost-efficient for transcriptome quantification of large numbers of cells, while MARS-seq, SCRB-seq and Smart-seq2 are more efficient when analyzing fewer cells. Our quantitative comparison offers the basis for an informed choice among six prominent scRNA-seq methods and provides a framework for benchmarking further improvements of scRNA-seq protocols.

overall_design: J1 mESC in two replicates per library preparation method.

first: Wolfgang

last: Enard


title: Kidney gene expression profiles from a lupus nephritis mouse model: SNF1 (SWR X NZB F1) mice treated with pristane

summary: We characterized the longitudinal gene expression profiles of kidneys from a novel lupus model nephritis: SNF1 (SWR X NZB F1) mice treated with pristane. Genes from biological processes such as IFN response, complement, Fc gamma receptors, immune recruitment, innate immune pattern recognition, antibody response and fibrosis,were upregulated in diseased kidneys.

overall_design: Kidney tissues were collected from mice SNF1 (SWR X NZB F1) after pristane treatment at different time points (week 0, week 2, week 4, week 8, week 12, week 14) as well as from untreated control mice SNF1 mice. The study includes tissues from at least 8 animal for each condition.


title: Kidney gene expression profiles from a lupus nephritis mouse model: NZB X NZW F1 (BWF1) mice treated with IFN-alpha with adenovirus delivery.

summary: We characterized the longitudinal gene expression profiles of kidneys from a lupus model nephtiris: NZB X NZW F1 (BWF1) mice treated with IFN-alpha using adenovirus delivery. Genes from biological processes such as IFN response, complement, Fc gamma receptors, immune recruitment, innate immune pattern recognition, antibody response and fibrosis,were upregulated in diseased kidneys.

overall_design: Kidneys were collected from NZB X NZW F1 (BWF1) mice after IFNalpha treatment using an adenovirus delivery at different time points (week 1, week 2, week 3, week 5, week 7, week 9 after treatment). The study includes control kidneys from 3 untreated mice and kidneys from 5 treated mice for each time points.


title: Characterization of mouse models of lupus nephritis

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

overall_design: Refer to individual Series


title: Differential gene expression analysis of follistain treated skeletal muscle

status: Public on Sep 03 2016

city: MELBOURNE

first: Jonathan

middle: Robert

last: Davey

state: VIC

address: 75 Commercial Rd

institute: Baker IDI Heart and Diabetes Institute

summary: RNA-Seq analysis was performed to define the associated changes in gene expression of skeletal muscle treated with follistatin

overall_design: Skeletal muscle mRNA profiles from follistatin and control treated tibialis anterior muscles. Acute  (3 day treatment, 3 control  and 4 follistatin replicates) and chronic (7or 14 day treatment, 3 control and 4 follistatin replicates) timepoints were analysed.

first: Paul

last: Gregorevic


title: Expression data of thermally eluted RNA from human primary fibroblasts with non-targeting or GLD4 siRNA treatment

status: Public on Sep 01 2016

city: Philadelphia

first: Bin

last: Tian

state: PA

address: 3601 Spruce Street

institute: the wistar institute

summary: In a screen for downregulated genes in poly(U) chromatography upon GLD4 knockdown, we identified carbohydrate metabolism genes were affected including a glucose transporter, GLUT1

overall_design: human primary fibroblasts are treated with non-targeting siRNA or siGLD4. RNAs were subjected to poly(U) chromatography and eluted at 65C. Differentially expressed genes were identified using illumina microarray.

first: Joel

middle: D

last: Richter


title: Changes in RNA expression in human oral cavity carcinoma cells as a result of LDB1 reduction

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

summary: The study was designed to identify differential expressed genes between human oral cavity carcinoma cell lines with and without LDBI knockout

overall_design: Three parental human oral cavity carcinoma cell lines were used as control, LDB1 was knocked out in the three parent cell lines to create KO cell lines.

first: Elizabeth

middle: A

last: Simonik

first: Stephen

last: Brandt


title: Prospective identification and lineage tracing of top-level hematopoietic stem cells that sustain adult hematopoiesis

status: Public on Aug 30 2016

city: New York

first: Catherine

last: Sawai

state: New York

address: 701 W. 168th Street - HHSC 9-906

institute: Columbia University Medical Center

summary: Hematopoietic stem cells (HSC) sustain long-term reconstitution of hematopoiesis in primary transplantation recipients. Few HSC can serially reconstitute secondary recipients, and their identity and contribution to normal hematopoiesis remain moot. We directed transgene expression to a distinct fraction of HSC in the adult bone marrow. Epxression of the reporter transgene segregated with reconstituting activity during secondary transplantations. The labeled cells had an undifferentiated phenotype and expression profile, were slow-cycling and localized to the vascular niche. Inducible genetic labeling showed the transgene-expressing HSC gave rise to other cells within the HSC populations, confirming their top position in the differentiation hierarchy. Importantly, labeled HSC gave rise to more than two-thirds of all myeloid cells and platelets in adult mice, and this contribution could be further accelerated by interferon response. Thus, the rare "top-level" HSC with serial reconstitution capacity also serve as the major source of endogenous hematopoiesis in adult animals.

overall_design: Sorted LSK CD48- CD150+ Map17-GFP+ and Map17-GFP- HSCs and LSK CD48+ CD150- Map17-GFP-MPPs were sequenced for mRNA profiling.

middle: M

first: Boris

last: Reizis


title: Mitochondrial supplementation at fertilization enhances early developmental outcome

city: Clayton

first: Justin

middle: C

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

institute: Hudson Institute of Medical Research

summary: Competent oocytes can be discriminated by BCB staining. Positive stained oocytes are considered more competent than BCB negative oocyte, and injection of BCB+ oocyte extracted mitochondria into BCB negative oocytse can increase fertilisation and blastocyst rate. Here we have analysed the impact of mitochondrial supplementation on subsequent blastocyst transcriptome using agilent one color microarray that is specificly design to study the porcine embryo preimplantation period. Blastocysts were produced by intra cytoplasmic sperm injection (ICSI) from BCB positive and BCB negative oocytes as well as BCB negative oocytes supplemented with mitochondrial extract during ICSI (mICSI), and 3-4 single blatocyst transcriptomes were analysed for each group.

overall_design: 3-4 single blastocysts were analysed at the RNA level after whole transcriptome amplification, and level of gene expression was compared between groups, i.e ICSI BCB+ blastocysts (4), ICSI BCB- blastocysts (3) and mICSI BCB- blastocysts (4).

first: Gael

last: Cagnone

first: Pamela

last: Matthews

first: Tesha

last: Tsai

first: Matthew

last: McKenzie


title: Genomic analyses of breast cancer cells: 17β-hydroxysteroid dehydrogenase type 1 induces transcriptional changes in estradiol-dependent and independent manners

city: Quebec

first: Ezequiel

middle: L

last: Calvo

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

summary: 17β-HSD1 expression modulates T47D transcript profile in in steroid-deprived medium. The enzyme specifically regulates apoptosis and cancer-related genes  in T47D cells cultured in steroid-deprived medium. Genes that primarily involved in Cell cycle progression, such as the Cyclin A2 gene, CCNA2, are generally down-regulated whereas most genes involved in apoptosis and cell death, such as the proapoptotic gene XAF1 and FGF12, are on the contrary up-regulated by 17β-HSD1 knockdown, and 21% of the modulated genes belong to this latter functional category.  This correborates with its role previously shown in increasing breast cancer cell proliferation (Aka et al, 2010) and indicates that in addition to its direct role as cell proliferation via incresing E2 and decreasing DHT, 17β-HSD1 may also be involved in oncogenesis by favoring its anti-apoptosis pathway in breast cancer cells  17β-HSD1 may also be involved in oncogenesis by favoring anti-apoptosis pathway and/or inhibiting cell survival pathway.  We tested the ability of estrogen to induce or repress endogenous genes of T47D by microarray analysis. A total of 131 genes were found to increase or decrease 1.5-fold or higher in response to 17 beta-estradiol (1 nM for 48 h).  Besides, the gene regulation occuring in steroid-deprived conditions showed that 17β-HSD1 modulates gene expression in steroid-independent manners. Our study thus demonstrates that 17β-HSD1 modulates the E2-independent transcription of endogenous genes in T47D cells. The E2-dependent transcription as well as the E2-independent transcription are significantly modulated by 17β-HSD1 in breast cancer cells  We first report here that breast cancer cell transcript profile is independtly modulated by both 17β-HSD1 and its principale product estradiol.

overall_design: Microarrays was used to study the effect of 17β-HSD1 gene knockdown on gene expression and on endogenous ERG in T47D cells. The sense and antisense sequences of three 17β-HSD1 siRNAs were selected and synthesized. Scramble siRNA was used as control siRNA. Two days before transfection, T47D cells in T75 were cultured in steroid deprived medium. On the transfection day, cells in T75 flasks were trypsined and ressuspended in a fresh charcoal-treated medium. Cells were then reverse-transfected with 17β-HSD1 specific siRNAs or with negative control siRNA.Two days (48 hours) after transfection, cell culture media were replaced by fresh charcoal-treated medium containing either the steroid E2 (1 nM) or ethanol as a vehicle control, and cells were incubated for two more days before RNA extraction.

first: Julliete

last: Aak

first: Sheng-Xiang

last: Lin


title: Molecular Mechanisms Contributing to the Growth and Physiology of an Extremophile Cultured with Dielectric Heating

status: Public on Aug 29 2016

city: Washington

first: Baochuan

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

summary: This study utilized the thermophile Thermus scotoductus SA-01 to determine changes in gene expression based on growth with convective or dielectric microwave heating (2.45 GHz) at 65°C.  A total of 344 genes were identified as significantly differentially regulated across the three time points.  Our results reveal that a large number of genes involved in cell wall recycling and biogenesis were induced, corroborating the elongated cell morphology observed in cells grown with dielectric heating. Genes associated with sugar metabolism were induced across multiple time points, while genes involved in denitrification were repressed, suggesting the different modes of heating influence metabolism. Additionally, an unexpected link was observed with regards to enzymes in which molybdenum serves as a co-factor.

overall_design: T. scotoductus were cultured  at 65°C in a nutrient rich medium under either microwave radiation exposure or convective heating at three different points (8, 14 and 24 hours) of the growth cycle.  Global transcriptional profiling was performed to to determine which genes were differentially expressed at each time point.

first: Kathleen

last: Cusick

first: Anthony

middle: P

last: Malanoski

first: Sarah

last: Strycharz-Glaven

first: Allison

last: Cockrell

first: Lisa

last: Fitzgerald

first: Daniel

last: Barlow

first: Jeffrey

last: Cramer

last: Biffinger


title: Expression profiling and H3K4me3 occupancy in WT and jhd2Δ Saccharomyces cerevisiae cells

status: Public on Aug 09 2016

city: Toronto

first: Maria

last: Soloveychik

state: Ontario

address: 1 king's college circle

department: Molecular Genetics

institute: University of Toronto


title: ChIP seq of H3K4me3 and pan-H3  in WT and jhd2Δ Saccharomyces cerevisiae cells

summary: We describe the landscape of H3K4me3 in WT and jhd2Δ cells in YAR media by ChIP seq

overall_design: To determine the contribution of Jhd2 to the H3K4me3 landscape in respiring yeast cells, we performed H3K4me3 ChIP and normalized to pan-H3 ChIP signal.

first: Kwan-Yin

last: Lee

first: Mengshu

last: Xu

first: Marc

last: Meneghini


title: Whole-Genome Transcriptome Profiling of Microvascular Free Flaps

status: Public on Jul 24 2016

city: Honolulu

first: Yiqiang

last: Zhang

state: HI

address: 651 Ilalo St BSB-311D

department: Anatomy, Biochemistry and Physiology

institute: University of Hawaii Manoa

summary:
Vascular compromise in microsurgical free flap transfers continues to present devastating outcomes in terms of flap failure and increased operating room costs. Current devices to detect early venous congestion have not become widely accepted because of insufficient sensitivity, incisiveness, or practicality.
In our study, we developed a venous obstruction rat model in which the superficial inferior epigastric (SIE) vessels to the lower abdominal flaps was separated and artery or vein was ligated, and the flap reattached. Flaps were harvested 4 hours post-op. Total RNA was isolated and gene expression profiles were compared  by Affymetrix Whole Genome 230 2.0.

overall_design: Flaps from groups of Venous or artery congestion (VC or AC, resp.) and sham operation group, were harvested and RNA extraction and hybridization on Affymetrix microarrays. Other controls including histology assays to assure comparable phenotype within groups.

first: Gerard

last: Nguyen

first: Brian

last: Hwang


title: Transcriptome signature in early biopsies of stably functioning kidney allografts identify patients at risk for chronic injury

status: Public on Jul 20 2016

first: Weijia

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

summary:
Chronic injury in kidney transplants remains a major cause of graft loss. The aim of this study was to identify a predictive gene set capable of classifying renal grafts at risk for progressive injury due to fibrosis.The Genomics of Chronic Allograft Rejection (GoCAR) study is a prospective, multicenter study. Biopsies obtained prospectively 3 months after transplantation from renal allograft recipients (n=159) with stable renal function were analyzed for gene expression by microarray. Genes were sought which correlated with subsequent 12-month Chronic Allograft Damage Index (CADI) but neither CADI in the 3 month biopsy nor other histological or clinical parameters.
We identifi ed a set of 13 genes that was independently predictive for the development of fi brosis at 1 year (ie, CADI-12 >=2). The gene set had high predictive capacity (area under the curve [AUC] 0·967), which was superior to that of baseline clinical variables (AUC 0·706) and clinical and pathological variables (AUC 0·806). Furthermore routine pathological variables were unable to identify which histologically normal allografts would progress to fi brosis (AUC 0·754), whereas the predictive gene set accurately discriminated between transplants at high and low risk of progression (AUC 0·916). The 13 genes also accurately predicted early allograft loss (AUC 0·842 at 2 years and 0·844 at 3 years). We validated the predictive value of this gene set in an independent cohort from the GoCAR study (n=45, AUC 0·866) and two independent, publically available expression datasets (n=282, AUC 0·831 and n=24, AUC 0·972).

overall_design: Biopsies obtained prospectively 3 months after transplantation from renal allograft recipients (n=159) with stable renal function were analyzed for gene expression by Affymetrix exon arrays. Genes that  were specifically correlated with 12-month Chronic Allograft Damage Index (CADI) but neither CADI in the 3 month biopsy nor other histological or clinical parameters were identified by correlation analysis. The minimal geneset was further identified to predict the progressors/non progressors and validated by qPCR in an independent cohort and two public datasets.

first: Philip

middle: J

last: O’Connell

first: Madhav

last: Menon

first: Zhengzi

last: Yi

first: Bernd

last: Schroppel

first: Lorenzo

last: Gallon

first: Yi

last: Luan

first: Ivy

last: Rosales

first: Yongchao

last: Ge

first: Bojan

last: Losic

first: Caixia

last: Xi

first: Christopher

last: Woytovich

first: Karen

last: Keung

first: Chengguo

last: Wei

first: Ilana

last: Greene

first: Jessica

last: Overbey

first: Emilia

last: Bagiella

first: Nader

last: Najafi an

first: Milagros

last: Samaniego

first: Arjang

last: Djamali

first: Stephen

last: Alexander

last: Nankivell

first: Jeremy

last: Chapman

first: Rex

middle: N

last: Smith

first: Robert

last: Colvin

first: Barbara

last: Murphy