title: RNA-Seq analysis of NKX2.2 knockdown in human pancreatic islets

last: Sussel

summary:
Aim:Transcriptional analysis of NKX2.2 knockdown versus control in human pancreatic islets
Methods:Pancreatic islets from 3 human donors  were transduced with an adenovirus encoding an shRNA directed against human NKX2.2 or a scrambled shRNA control.  Total RNA was extracted.Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the human genome (Human: NCBI/build37.2)) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq.
Results: Among the dysregulated genes with a p-value=0.05 are important genes for the maintenance of  beta cell function and idenity.
Conclusion: Nkx2.2 is a critical regulator of beta cell function and identity

overall_design: mRNA profiles of the pancreatic islets from 3 human donors transduced with Ad.sh-NKX2.2 or scramble sh-RNA control vector were generated by deep sequencing ,  using Illumina HiSeq2000.

last: Dominguez Gutierrez


title: Global transcriptional profiling confirmed failed decidualization of human Endometrial Stromal Cells (hESCs) obtained from non-pregnant women with a previous pregnancy complicated by severe preeclampsia (sPE).

status: Public on Dec 16 2016

city: Valencia

first: Tamara

last: Garrido-Gomez

address: Parc tecnologic

country: Spain

institute: Fundación IGENOMIX

summary: The data presented here suggested that sPE is associated with impaired decidualization. Initial experiments involved an in vitro approach. hESCs were isolated from patients who developed sPE in a previous pregnancy or control women who had normal obstetric outcomes. Function was tested by comparing the ability of hESCs in the two groups to decidualize in culture. By morphological criteria and marker expression (PRL and IGFBP1), the cells in the formerly sPE group were decidualization resistant, which was confirmed by microarray analyses showing that they were transcriptionally inert.

overall_design: Decidualized and non-decidualized hESCs from donors who had sPE (n=5) or normal pregnancies (n=7) were collected after 5 days in culture and total RNA was extracted into Trizol according to the manufacturer's instructions (Life Technologies). The RNA quality was assessed by using an RNA LabChip and an A2100 Bioanalyzer (Agilent Technologies). Samples with an RNA integrity >7 were selected for microarray analyses. Sample preparation and hybridization was accomplished using Agilent 2100 Bioanalyzer technology according to the manufacturer's guidelines. Hybridized microarrays were imaged with an Axon 4100A scanner (Molecular Devices) and the data were extracted with the GenePix Pro 6.0 software (Molecular Devices).

first: T

first: F

last: Dominguez

first: A

last: Quiñonero

first: P

last: Diaz-Gimeno

first: M

last: Kapidzic

last: Gormley

first: K

last: Ona

last: Padilla

first: O

last: Genbacev

last: Perales

first: S

middle: J

last: Fisher

first: C

last: Simón


title: Severe Preeclampsia is Associated with Alterations in Cytotrophoblasts of the Smooth Chorion

status: Public on Dec 10 2016

city: SAN FRANCISCO

first: Susan

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

country: USA

institute: UCSF

summary: Preeclampsia (PE), which affects ~8% of first pregnancies, is associated with faulty placentation. Extravillous cytotrophoblasts (CTBs) fail to differentiate properly, contributing to shallow uterine invasion and deficient spiral artery remodeling. We studied the effects of severe PE (sPE) on the smooth chorion portion of the fetal membranes. The results showed a significant expansion of the CTB layer. The cells displayed enhanced expression of stage-specific antigens that extravillous CTBs normally up regulate as they exit the placenta. Transcriptomics revealed the dysregulated expression of many genes (e.g., placental proteins, markers of oxidative stress). We confirmed a sPE-related increase in production of PAPPA1, which releases IGF-1 from its binding protein. IGF1 enhanced proliferation of smooth chorion CTBs (schCTB), a possible explanation for expansion of this layer, which may partially compensate for the placental deficits.

overall_design: To gain a better understanding of the molecular mechanisms behind the observed schCTB alterations in sPE, we used a laser capture microdissection approach to isolate this population of cells from the fetal membranes of sPE, nPTB, and second trimester (STM) pregnancies (n=4/group) and performed whole-transcipt genome-wide profiling of total RNA using the Affymetrix GeneChip Human Gene ST 2.0


title: RNA-Seq analysis of the pancreatic islets of beta cell specific adult Nkx2.2 mutant mice

status: Public on Dec 20 2016

city: Aurora

first: Lori

state: CO

address: 1775 Aurora Ct.

institute: University of Colorado

type: Expression profiling by high throughput sequencing

summary:
Aim:Transcriptional analysis of the pancreatic islets of adult Nkx2.2 flox/flox; RipCre mice versus control
Methods:Pancreatic islets from 4week old Nkx2.2 mutant mice and controls were isolated and total RNA was extracted.Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq.
Results: Among the downregulated genes with a p-value=0.05 are important genes for beta cell function and idenity.Among the upregulated genes with a p-value=0.05 are non beta endocrine hormones.
Conclusion: Nkx2.2 activates important beta cell genes and actively represses non beta cell genes

overall_design: mRNA profiles of the pancreatic islets of 4 week old control and Nkx2.2 mutant mice were generated by deep sequencing , in triplicate, using Illumina HiSeq2000.

first: Giselle


title: Genome-wide analysis of trehalose-responsive gene expression in control or JNCL human fibroblasts.

status: Public on Dec 13 2016

city: Houston

first: Marco

last: Sardiello

state: Texas

address: 1250 Moursund St.

department: Molecular and Human Genetics

institute: Baylor College of Medicine at Neurological Research Institute Texas Children Hospital

summary: Analysis of changes in gene expression induced by trehalose administration in fibroblasts derived from JNCL patients and control fibroblasts.

overall_design:
Total RNA obtained from control or JNCL fibroblasts treated with 100 mM of trehalose for 4 days was compared to untreated control or JNCL fibroblasts. Experiments were performed in triplicates.
The microarray analysis was performed at The Microarray Core Lab, UTHSC, under the supervision of Dr David S. Loose and Tuan M. Tran.

first: Michela

last: Palmieri


title: Alfa2-COP is involved in early secretory traffic in Arabidopsis and it is required for plant growth

status: Public on Dec 01 2016

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

institute: IBMCP (UPV-CSIC)

summary: The loss-of-function mutants of alfa1-COP (alfa1-COP-1) and alfa2-COP (alfa2-COP1), the two alfa-COP isoforms of Arabidopsis. Unlike in alfa1-COP mutant, the alfa2-COP mutant displays defects in plant growth, including small rosettes, stems and roots and mislocalization of p24a5, a protein containing a C-terminal dylisine motif involved in COPI binding. In addition, it exhibited abnormal morphology of the Golgi apparatus. Global expression analyses of the alfa2-COP mutant versus wild-type Arabidopsis plants reveal altered expression of plant cell wall-associated genes. A high expression of the COPII sec31A isoform was observed in the alfa2-COP mutant that also occurs in a mutant of an upstream gene of COPI assembly, the ARF-GEF GNL1

overall_design: Four biological replicates were generated. The goal of this experiment is to compared the α2-COP-3 mutant against a Col-0 wild type line. In the comparison  2 of the replicates were reversed-labeled.

first: Fatima

last: Gimeno-Ferrer

first: Noelia

last: Pastor-Cantizano

first: Cesar

last: Bernat-Silvestre

first: Pilar

last: Selvi-Martinez

first: Caiji

last: Gao

first: Miguel

middle: A

last: Perez-Amador

first: Liwen

last: Jiang

first: Fernando

last: Aniento

first: María

last: Marcote


title: Skin Transcriptomics of Common Bottlenose Dolphins (Tursiops truncatus) from the Northern Gulf of Mexico and Southeastern U.S. Atlantic Coasts

status: Public on Dec 06 2016

city: Charleston

first: Marion

last: Neely

state: SC

address: 331 Ft. Johnson Rd

department: NCCOS

institute: National Ocean Services

summary: Common bottlenose dolphins serve as sentinels for the health of their coastal environments as they are susceptible to health impacts from anthropogenic inputs through both direct exposure and food web magnification.  Remote biopsy samples have been widely used to reveal contaminant burdens in free-ranging bottlenose dolphins, but do not address the health consequences of this exposure.  To gain insight into whether remote biopsies can also identify health impacts associated with contaminant burdens, we employed RNA sequencing (RNA-seq) to interrogate the transcriptomes of remote skin biopsies from 116 bottlenose dolphins from the northern Gulf of Mexico and southeastern U.S. Atlantic coasts.  Gene expression was analyzed using principal component analysis, differential expression testing, and gene co-expression networks, and the results correlated to season, location, and contaminant burden.  Season had a significant impact, with over 30% of genes differentially expressed between spring/summer and winter months.  Geographic location exhibited lesser effects on the transcriptome, with 15% of genes differentially expressed between the northern Gulf of Mexico and the southeastern U.S. Atlantic locations.  Despite a large overlap between the seasonal and geographical gene sets, the pathways altered in the observed gene expression profiles were somewhat distinct.  Co-regulated gene modules and differential expression analysis both identified epidermal development and cellular architecture pathways to be expressed at lower levels in animals from the northern Gulf of Mexico.  Although contaminant burdens measured were not significantly different between regions, some correlation with contaminant loads in individuals was observed among co-expressed gene modules, but these did not include classical detoxification pathways.  Instead, this study identified other, possibly downstream pathways, including those involved in cellular architecture, immune response, and oxidative stress, that may prove to be contaminant responsive markers in bottlenose dolphin skin.

overall_design: RNA-seq of skin from 116 common bottlenose dolphins.

middle: G

first: Jeanine

middle: S

last: Morey

first: Paul

middle: E

last: Anderson

first: Brian

middle: C

last: Balmer

first: Gina

middle: M

last: Ylitalo

first: Eric

last: Zolman

first: Todd

middle: R

last: Speakman

first: Carrie

last: Sinclair

first: Melannie

last: Bachman

first: Kevin

last: Huncik

first: John

last: Kucklick

first: Patricia

last: Rosel

first: Keith

middle: D

last: Mullin

first: Teri

middle: K

last: Rowles

middle: H

last: Schwacke

first: Frances

last: VanDolah


title: Expression data of multi regional colorectal carcinoma

city: FUKUOKA

first: RYUTARO

last: UCHI

state: FUKUOKA

country: Japan

institute: KYUSHUUNIVERSItY

summary: Understanding intratumor heterogeneity is clinically important because it could cause therapeutic failure by fostering evolutionary adaptation. To this end, we profiled the genome and epigenome in multiple regions within each of nine colorectal tumors. Extensive intertumor heterogeneity is observed, from which we inferred the evolutionary history of the tumors. First, clonally shared alterations appeared, in which C>T transitions at CpG site and CpG island hypermethylation were relatively enriched. Correlation between mutation counts and patients’ ages suggests that the early-acquired alterations resulted from aging. In the late phase, a parental clone was branched into numerous subclones. Known driver alterations were observed frequently in the early-acquired alterations, but rarely in the late-acquired alterations. Consistently, our computational simulation of the branching evolution suggests that extensive intratumor heterogeneity could be generated by neutral evolution. Collectively, we propose a new model of colorectal cancer evolution, which is useful for understanding and confronting this heterogeneous disease.

overall_design: We isolated total RNA from geographically separated samples of one of eight series (case3) of colorectal carcinoma and matched normal mucosa and hybridised to the Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray

first: Ryutaro

last: Uchi

first: Yusuke

last: Takahashi

first: Atsushi

last: Niida

first: Teppei

last: Shimamura

first: Hidenari

last: Hirata

first: Keishi

last: Sugimachi

first: Genta

last: Sawada

first: Takeshi

last: Iwaya

first: Junji

last: Kurashige

first: Yoshiaki

last: Shinden


title: Identification of miRNAs and their targets in tomato at moderately and acutely elevated temperatures by high-throughput sequencing and degradome analysis

city: Nanjing

first: zhou

last: rong

address: Nanjing

country: China

institute: Nanjing Agricultural University (NAU)

summary: MicroRNAs (miRNAs) are 19-24 nucleotide (nt) noncoding RNAs that play important roles in abiotic stress responses in plants. High temperatures have been the subject of considerable attention due to their negative effects on plant growth and development. Heat-responsive miRNAs have been identified in some plants. However, there have been no reports on the global identification of miRNAs and their targets in tomato at high temperatures, especially at different elevated temperatures. Here, three small-RNA libraries and three degradome libraries were constructed from the leaves of the heat-tolerant tomato at normal, moderately and acutely elevated temperatures (26/18°C, 33/33°C and 40/40°C, respectively). Following high-throughput sequencing, 662 conserved and 97 novel miRNAs were identified. Of these miRNAs, 96 and 150 miRNAs were responsive to the moderately and acutely elevated temperature, respectively. Following degradome sequencing, 349 sequences were identified as targets of 138 conserved miRNAs, and 13 sequences were identified as targets of eight novel miRNAs. The expression levels of four miRNAs and five target genes obtained by quantitative real-time PCR (qRT-PCR) were largely consistent with the sequencing results. This study enriches the number of heat-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in tomatoes at elevated temperatures.

overall_design: The seedlings were randomly divided into three groups for temperature treatments on the seventh day after transfer. The first group was kept at a normal temperature and used as a control (26/18°C, NT); the second group was exposed to a moderately elevated temperature (33/33°C, MET); and the third group was exposed to an acutely elevated temperature (40/40°C, AET). The temperature reached 33°C in half an hour and 40°C in an hour in the climate chamber. All of them was used to do examination of small RNA and degradome RNA.

first: Rong

last: Zhou


title: M.tuberculosis H37Rv: Control vs. anti-TB compound treated

city: Beijing

first: Liyan

last: Yu

address: 1# Tian Tan Xi Li, Chongwen district

department: Institute of Medicinal Biotechnology

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

summary: To monitor the anti-tuberculosis compound IMB-YH-8 induced gene response profile at an early stage, we treated logarithmically growing M. tuberculosis with IMB-YH-8 at the concentration of 2.5 μg/ml throughout the first 4 hr.

overall_design: There four samples are analyzed and two replicates are included. The drug-treated (2.5 μg/ml IMB-YH-8), together with control (DMSO) mycobacterial cultures, were incubated at 37℃for 4 h.

first: Jian

last: Xu


title: Microarray analysis reveals the molecular foundation of the brown planthopper(BPH) resistance of rice variety Rathu Heenati

status: Public on Dec 05 2016

city: Wuhan

first: Li

last: Changyan

address: Shizishan Road NO.1

institute: Huazhong Agricultural University

summary: In order to reveal the molecular foundation of BPH resistance of RH, the whole genome expressional profiles of RH together with the control TN1 under BPH infestation were determined using cDNA microarray analysis.

overall_design: The experiment design included two rice varieties (RH and TN1), three treatments (natural growth, needle puncturing and BPH infestation) and two sampling time-points (6 and 24 h after BPH infestation). There were 12 samples in total, with three biological replicates per sample.The abbreviations of R6C, R24C, R6N, R24N, R6P, R24P, T6C, T24C, T6N, T24N, T6P and T24P were used to represent these 12 samples. The first letter R or T indicates the rice varieties RH or TN1, respectively; the Arabic numbers in the middle of the abbreviation 6 or 12 indicate the collection time-points 6 or 24 h after the treatment, respectively. The last letter C, N or P indicates the three different treatments: control, needle puncturing or BPH infestation, respectively.

first: Changyan

last: Li

first: Yongjun

last: Lin

first: Hao

last: Chen


title: Integrin-α10-dependency defines a novel therapeutic strategy targeting RAC and mTORC2 for metastatic myxofibrosarcoma

status: Public on Nov 29 2016

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary:
Analysis of U133A microarray data from 64 primary high-grade myxofibrosarcoma tumors identified ITGA10 as the gene most significantly associated with distant metastasis and poor disease-specific survival.
Further investigation using shRNA knockdown identifies the TRIO-RAC-PAK and RICTOR-mTORC2 pathways as important downstream signaling pathways for ITGA10.

overall_design: RNA samples were prepared from 64 primary high-grade myxofibrosarcoma tumors previously frozen in liquid nitrogen.  A portion of each tumor was placed in a cryomold and slides were cut for review by our pathologist to confirm the diagnosis in each case.  Areas of normal tissue and necrotic tumor were macrodissected based on slide review.  Only areas of viable tumor were included for RNA extraction.

first: Ann

middle: Y

last: Lee

first: Tomoyo

last: Okada

first: Narasimhan

last: Agaram

first: Li-Xuan

last: Qin

first: Nicholas

last: Socci

first: Martin

last: Miller

first: Phaedra

last: Agius

first: Evan

last: Molinelli

first: William

last: Tap

first: Aimee

last: Crago

first: Chris

last: Sander

first: Penelope

last: Decarolis

first: Yawei

last: Shen

first: Rachael

last: O'Connor

first: Samuel

last: Singer


title: The SWI/SNF chromatin remodeling complex is required for lineage specific enhancer activity [MEF_RNA-seq]

status: Public on Nov 21 2016

city: Boston

first: Peter

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: Genes encoding subunits of SWI/SNF (BAF) chromatin remodeling complexes are collectively altered in over 20% of all human malignancies, but the mechanisms by which these complexes alter chromatin to modulate transcription and control cell fate are poorly understood.  Utilizing both loss-of-function and gain-of-function approaches, here we show that SWI/SNF complexes are preferentially targeted to distal enhancers and interact with p300 to regulate transcription via modulation of histone H3 lysine 27 acetylation. We identify a greater requirement for SWI/SNF at typical enhancers than at most super-enhancers and at enhancers in untranscribed regions than in transcribed regions. Our data further demonstrate that SWI/SNF-dependent distal enhancers are essential for controlling expression of genes linked to developmental processes.  Our findings thus establish SWI/SNF complexes as regulators of the enhancer landscape and provide insight into the roles of SWI/SNF in cellular fate control.

overall_design: RNA-seq in Mouse Embryonic Fibroblasts in WT condition and for knockouts of different SWI/SNF complex subunits.

first: Kimberly

last: Kim

first: Burak

last: Alver

first: Ping

last: Lu

first: Charles

middle: W

last: Roberts


title: A model system to study secondary growth and bast fibre development: the hemp hypocotyl peeks behind the wall

status: Public on Nov 18 2016

city: Esch/Alzette

first: Marc

last: BEHR

address: 5, avenue des Hauts-Fourneaux

department: ERIN

country: Luxembourg

institute: LIST

summary: Cannabis sativa L. is an annual herbaceous crop grown for the production of long extraxylary fibers, the bast fibers, rich in cellulose and used both in the textile and biocomposite sectors. Despite being herbaceous, hemp undergoes secondary growth and this is well exemplified by the hypocotyl. The hypocotyl was already shown to be a suitable model to study secondary growth in other herbaceous species, namely Arabidopsis thaliana and it shows an important practical advantage, i.e. elongation and radial thickening are temporally separated. This study focuses on the mechanisms marking the transition from primary to secondary growth in the hemp hypocotyl by analysing the suite of events accompanying vascular tissue and bast fiber development. RNA-Seq transcriptomics, imaging and quantification of phytohormones were carried out on four representative developmental stages (i.e. 6-9-15-20 days after sowing) to provide a first comprehensive profiling of the events associated with primary and secondary growth in hemp. This multidisciplinary approach provides cell wall-related snapshots of the growing hemp hypocotyl and identifies marker genes associated with the young (expansins, β-galactosidases and transcription factors involved in light-related processes) and the older hypocotyl (secondary cell wall biosynthetic genes and transcription factors).

overall_design: Time-course analysis of hemp hypocotyl transcriptome (6, 9, 15 and 20 days after sowing) with 3 biological replicates for each time point.

last: Behr

first: Sylvain

last: Legay

first: Eva

last: Žizkova

first: Václav

last: Motyka

first: Petre

middle: I

last: Dobrev

first: Jean-Francois

last: Hausman

first: Stanley

last: Lutts

first: Gea

last: Guerriero


title: BCAS2 is involved in alternative mRNA splicing in spermatogonia and the transition to meiosis and male fertility

status: Public on Nov 15 2016

first: Wenbo

last: Liu

address: 1 Beichen West Road, Chaoyang District

institute: Institute of zoology

summary: BCAS2 (Breast cancer amplified sequence 2) is involved in multiple biological processes, including pre-mRNA splicing. However, the physiological roles of BCAS2 are still largely unclear. Here we report that BCAS2 is specifically enriched in spermatogonia of mouse testes. Conditional disruption of Bcas2 in male germ cells impairs spermatogenesis and leads to male mouse infertility. Although the spermatogonia appear grossly normal, spermatocytes in meiosis prophase I and meiosis events (recombination and synapsis) are rarely observed in the BCAS2-depleted testis. In BCAS2 null testis, 245 genes are altered in alternative splicing forms; at least three spermatogenesis-related genes (Dazl, Ehmt2 and Hmga1) can be verified. In addition, disruption of Bcas2 results in a significant decrease of the full-length form and an increase of the short form (lacking exon 8) of DAZL protein. Altogether, our results suggest that BCAS2 regulates alternative splicing in spermatogonia and the transition to meiosis initiation, and male fertility.

overall_design: Transcriptional profiles of P9 testes from Control and Bcas2F/-;V-cre males

first: Lei

last: Li


title: The SWI/SNF chromatin remodeling complex is required for lineage specific enhancer activity [MEF_ChIP]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq of three histone modifications (H3K27ac, H3K4m3, H3K4me1) and two SWI/SNF complex subunits SMARCC1 and SMARCC4) in WT, Smarcb1-KO and Smarca4-KO Mouse Embryonic Fibroblasts.


title: Histone methyltransferase SMYD3 knockdown effects in MCF7 breast cancer cell line

status: Public on Nov 17 2016

city: Taipei

first: Shu-Chun

last: Teng

address: No.1 Jen Ai Road Section 1

department: Department of Microbiology

country: Taiwan

institute: National Taiwan University

summary: The study aims to elucidate the effect of histone methyltransferase SMYD3 on gene expression in MCF-7 breast cancer cell line. Knockdown luciferase control v.s. knockdown SMYD3 in MCF-7 breast cancer cell line were conducted.  Results identify a large proportion of cell cycle-related genes regulated by SMYD3.

overall_design: SMYD3 was knockdowned in MCF-7 cells and shLuc was used as control. Their total RNA were isolated for genomic expression profiling with Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.

first: Cheng-Hui

last: Tsai

first: Yun-Ju

last: Chen

first: Chia-Jung

last: Yu

first: Wen-Hong

last: Kuo

first: Ming-Chieh

last: Lin

first: Nei-Li

last: Chan

first: Kou-Juey

last: Wu


title: The SWI/SNF chromatin remodeling complex is required for lineage specific enhancer activity

first: Peter

last: Park

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

overall_design: Refer to individual Series


title: Re-programming of low-grade inflammatory monocytes

status: Public on Oct 28 2016

city: Blacksburg

first: Liwu

state: VA

address: 970 Washington Street

institute: Virginia Tech

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose:   The goals of this study are to compare the mircoRNA expression profiles from monocytes challegned with subclinical low dosage of LPS
Methods: Primary murine bone marrow derived monocytes treated with or without 5 pg/ml LPS in complete culture medium.  Harvested mircoRNAs were  used to prepare libaray for subsequent sequencing, in triplicate, using HiSeq 1000. Sequences were assayed to ensure high quality for all samples using a custom R script. Reads were first trimmed for adaptor and quality using a combination of custom perl scripts and Btrim64.  After trimming, trimmed fastq sequences were imported into mirAnalyzer for mapping, miRNA assembly and prediction, quantitation and differential expression. qRT–PCR validation was performed to validate selected microRNAs.
Results:   miRNA-seq data confirmed selective induction of a limited set of mircoRNAs in monocytes treated with subclinical super-low dose LPS.
Conclusions: Our study revealed that there are selected miroRNAs preferentially induced in monocytes challenged with subclinical low dosage of LPS.

overall_design: microRNAs from monocytes  cultured with or without 5 pg/ml LPS were harvested, prepared for sequencing, in triplicate, using HiSeq 1000.


title: Merkel cell polyomavirus small T antigen promotes pro-glycolytic metabolic perturbations required for transformation

city: Tucson

first: Megha

last: Padi

state: AZ

address: 1071 East Lowell St.

department: Molecular and Cellular Biology

institute: University of Arizona

summary: Merkel cell polyomavirus (MCPyV) is an etiological agent of Merkel cell carcinoma (MCC), a highly aggressive skin cancer. The MCPyV small tumor antigen (ST) is required for maintenance of MCC and can transform normal cells. To gain insight into cellular perturbations induced by MCPyV ST, we performed transcriptome analysis of normal human fibroblasts with inducible expression of ST. MCPyV ST dynamically alters the cellular transcriptome with increased levels of glycolytic genes, including the monocarboxylate lactate transporter SLC16A1 (MCT1). Extracellular flux analysis revealed increased lactate export reflecting elevated aerobic glycolysis in ST expressing cells. Inhibition of MCT1 activity suppressed the growth of MCC cell lines and impaired MCPyV-dependent transformation of IMR90 cells. Both NF-κB and MYC have been shown to regulate MCT1 expression. While MYC was required for MCT1 induction, MCPyV-induced MCT1 levels decreased following knockdown of the NF-κB subunit RelA, supporting a synergistic activity between MCPyV and MYC in regulating MCT1 levels. Several MCC lines had high levels of MYCL and MYCN but not MYC. Increased levels of MYCL was more effective than MYC or MYCN in increasing extracellular acidification in MCC cells. Our results demonstrate the effects of MCPyV ST on the cellular transcriptome and reveal that transformation is dependent, at least in part, on elevated aerobic glycolysis.

overall_design: Expression of MCPyV ST or GFP was induced in IMR90 fibroblasts, and triplicate RNA samples were extracted and sequenced every 8 hours for a total of 96 hours

first: Christian

last: Berrios


title: Expression data from gastrocnemius of wild type and transgenic mice

status: Public on Oct 27 2016

city: wuhan

first: fei

last: ying

address: shizishan street

institute: hzau

summary:
We want to find differential expressed  genes of gastrocnemius from transgenic mice of knockout DGAT1 and WT mice.
We used microarrays to detail the global programme of differential expressed  genes of gastrocnemius from transgenic mice of konckout DGAT1 and WT mice.

overall_design: gastrocnemius were selected at three month of mice for RNA extraction and hybridization on Affymetrix microarrays. Transgenic mice1,Transgenic mice2,Transgenic mice3,WT mice1,WT mice2,WT mice3

first: Fei

last: Ying


title: Potential regulatory role of microRNAs in the development of bovine gastrointestinal tract during early life

status: Public on Oct 29 2016

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

summary:
Purpose: The aims of this study were to profile miRNAs throughout the GIT during the early life of dairy calves and to investigate their potential regulatory roles in the development of bovine GIT.
Results: The expression of miR-143 was abundant in all three gut regions and under all the time points and it targets genes involved primarily in the proliferation of connective tissue cells and muscle cells, suggesting its association with rapid tissue development during the early life of calves. The expression of miR-10, miR-146, miR-191, miR-33, miR-7, miR-96, miR-99/100, miR-486, miR-145, and miR-211 displayed significant temporal differences (FDR < 0.05), while miR-192/215, miR-194, miR-196,miR-205 and miR-31 revealed significant regional differences (FDR<0.05) throughout the GIT. Expression levels of miR-15/16, miR-29 and miR-196 were positively correlated with copy numbers of 16S rRNA gene of Bifidobacterium or Lactobacillus species or both of them (P < 0.05). Functional analysis using Ingenuity Pathway Analysis identified above mentioned differentially expressed miRNAs as potential regulators of gut tissue cells proliferation and differentiation, and bacterial density-associated miRNAs as modulators of development of lymphoid tissues (miR-196), maturation of dendritic cells (miR-29) and development of immune cells (miR-15/16).
Conclusion: This present study revealed temporal and regional changes in miRNA expression, correlation between miRNA expression and microbial population during early life suggest their potential roles in host-microbial interactions during the gut development.

overall_design: Small intestine (mid-jejunum and ileum) and rumen samples were collected from on newborn (30 min after birth; n = 3), 7-day-old (n = 6), 21-day-old (n = 6), and  42-day-old (n = 6) dairy calves. The miRNA profiling was performed using high-throughput miRNA sequencing (illumina HiScanSQ platform).


title: Transcript expression data from Populus euphratica shoots subjected to salt stress

status: Public on Nov 12 2016

city: Haidian

first: Mengzhu

last: Lu

state: Beijing

address: 1# Dongxiaofu,Xiangshan Road

department: Research Institute of Forestry

institute: Chinese Academy of Forestry

summary:
Populus euphratica is a medium-sized deciduous tree naturally grown in high saline condition, however, the molecular response of the poplar to salinity at global genome level maintain to be elucidated.
We used Affymetrix poplar genome microarrays to investigate the full transcript expression exposed to different salt intensities and identified significantly changed transcripts within the 24 hours after exposed to salt stress.

overall_design: Uniformly developed seedlings without salt treatment were sampled as control, and two salt intensities (400 mM and 600 mM NaCl solution) were employed to irrigate the seedlings. Samples were collected at 6, 12, and 24 hours after salt-irrigation. Shoots (terminal bud with 3 to 4 expanding leaves) of uniformly developed seedlings were choosed as samples.Affymetrix poplar genechip was introduced to analyze the full transcripts change of the poplar response to varying intensities within the 24 hour after exposed to NaCl solution.

first: Jiafei


title: Expression data from patients with different stages of clear cell renal cell carcinoma

status: Public on Nov 05 2016

city: Kraków

first: Paulina

last: Marona

state: Lesser

address: Gronostajowa 7

department: Department of General Biochemistry

country: Poland

institute: Jagiellonian University

summary: Clear cell renal cell carcinoma is the most common type of renal cancers, which forms tumors strongly supplied with blood vessels, here we wanted to check the exprresion of genes on different stages of tumor progression, and find which of them changes significantly with increased grade.

overall_design: Tumor samples from patients were divided into four grades by hospital pathologists. I- grade refers to the first stage of disease, II- grade to second, III- grade to third and IV- grade to fourth. Each patient received unrepeatable number. RNA extraction were performed using Eurx kit, and then microarrays were performed using Affymetrix GeneChip WT PLUS Reagent Kit.

first: Katarzyna

last: Miekus


title: Effects of methotrexate treatment on hepatic metabolism in obesity

status: Public on Oct 07 2016

city: Scottsdale

first: Cheryl

last: Myers

address: 13400 E Shea Blvd

department: Immunology

institute: Mayo Clinic College of Medicine

summary: Analysis of metabolic changes in liver from obese mice fed on 60% high fat diet and treated with chemotherapeutic agent methotrexate (50 mg/kg) with a minimum of .

overall_design: One color experiment. Our conditions: 1) Low fat diet, No treatment, 2) Low fat diet, Methotrexate 50 mg/kg treatment, 3) High fat diet, No treatment, 4) High fat diet, Methotrexate 50mg/kg treatment. A minimum of 3 replicates (3-5) for each condition.

last: Cohen


title: Simultaneous microRNA and mRNA expression profiling on mammary epithelial cells isolated from mice at pregnancy day 14 and lactation day 2

status: Public on Oct 05 2016

city: Silverthorne

first: Margaret

last: Neville

address: 712 Eveningstar Rd

department: OB/GYN

institute: UC Denver

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

platform_organism:
Mus musculus
synthetic construct


title: Methylation dataset of multi regional colorectal carcinoma.

status: Public on Oct 18 2016

first: RYUTARO

last: UCHI

institute: KYUSHUUNIVERSItY

type: Methylation profiling by genome tiling array

summary: Understanding intratumor heterogeneity is clinically important because it could cause therapeutic failure by fostering evolutionary adaptation. To this end, we profiled the genome and epigenome in multiple regions within each of eight colorectal tumors. Extensive intertumor heterogeneity is observed, from which we inferred the evolutionary history of the tumors. First, clonally shared alterations appeared, in which C>T transitions at CpG site and CpG island hypermethylation were relatively enriched. Correlation between mutation counts and patients’ ages suggests that the early-acquired alterations resulted from aging. In the late phase, a parental clone was branched into numerous subclones. Known driver alterations were observed frequently in the early-acquired alterations, but rarely in the late-acquired alterations. Consistently, our computational simulation of the branching evolution suggests that extensive intratumor heterogeneity could be generated by neutral evolution. Collectively, we propose a new model of colorectal cancer evolution, which is useful for understanding and confronting this heterogeneous disease.

overall_design: We isolated genomic DNA from geographically separated samples of eight series of colorectal carcinoma and matched normal mucosa to bisulphite and hybridise to the llumina HumanMethylation450 BeadChip

first: Ryutaro

last: Uchi

first: Yusuke

last: Takahashi

first: Atsushi

last: Niida

first: Teppei

last: Shimamura

first: Hidenari

last: Hirata

first: Keishi

last: Sugimachi

first: Genta

last: Sawada

first: Takeshi

last: Iwaya

first: Junji

last: Kurashige

first: Yoshiaki

last: Shinden

first: Tomohiro

last: Iguchi

first: Hidetoshi

last: Eguchi

first: Kenichi

last: Chiba

first: Yuichi

last: Shiraishi

last: Nagae

last: Yoshida

first: Yasunobu

last: Nagata

first: Hiroshi

last: Haeno

first: Hirofumi

last: Yamamoto

first: Hideshi

last: Ishii

first: Yuichiro

last: Doki

first: Hisae

last: Iinuma

first: Shin

last: Sasaki

first: Satoshi

last: Nagayama

first: Kazutaka

last: Yamada

first: Shinichi

last: Yachida

first: Mamoru

last: Kato

first: Tatsuhiro

last: Shibata

first: Eiji

last: Oki

last: Saeki

first: Ken

last: Shirabe

first: Yoshinao

last: Oda

first: Yoshihiko

last: Maehara

first: Shizuo

last: Komune

first: Masaki

last: Mori

first: Yutaka

last: Suzuki

first: Hiroyuki

last: Aburatani

first: Seishi

last: Ogawa

first: Satoru

last: Miyano

first: Koshi

last: Mimori


title: microRNA expression in postnatal mammary gland development -Pregnancy Day14 and Lactation day 2

first: Margaret

last: Neville

summary:
Previoulsly miRNA expression profiling of the whole mammary gland across different stages of pregnancy and lactation has been performed in mice. Since mammary gland has both epithelial and stromal compartments, to specifically identify the miRNAs involved in the transition from pregnancy to lactation a process termed as secretory activation, expression  profiling of isolated mammary epithelial cells (MECs) from four CD1 mice each at Pregnancy day 14 (P14) and Lactation day 2 (L2) was performed in the current study.
Statistical analysis of the miRNA changes between P14 and L2 identified 32 miRNAs to be differentially expressed with a fold change greater than or equal to 2, of which, the majority of them declinied at the onset of lactation.

overall_design: 4 replicates each from Pregnancy day 14 and Lactation day 2 were hybridized onto Affymetrix GeneChip® miRNA 1.0 ST Array (7,625 probesets)

first: Palaniappan

last: Ramanathan

first: Patricia

last: Webb

first: Jennifer

last: Richer


title: Gene expression in postnatal mammary gland development -pregnancy day 14 and lactation day 2

summary:
Previoulsly expression profiling of the whole mammary gland across different stages of pregnancy and lactation has been performed on different strains of mice. Since mammary gland has both epithelial and stromal compartments, to specifically identify the genes involved in the transition from pregnancy to lactation a process termed as secretory activation, expression  profiling of isolated mammary epithelial cells (MECs) from four CD1 mice each at Pregnancy day 14 (P14) and Lactation day 2 (L2) was performed in the current study.
Statistical analysis of the mRNA changes between P14 and L2 identified 5,499 unique genes as being differentially expressed (5% FDR), of which, 2,902 genes and 2,604 genes were higher in P14 or L2 stages, respectively.

overall_design: 4 replicates each from Pregnancy day 14 and Lactation day 2 were hybridized onto Affymetrix GeneChip® Mouse Gene 1.0 ST Array (28,853 genes)


title: DNA methylation alters transcriptional rates of differentially expressed genes and contributes to pathophysiology in mice fed a high fat diet

status: Public on Oct 01 2016

city: Pittsburgh

first: David Peter

middle: G.

last: Peters

state: PA

address: 204 Craft Avenue

department: Department of Obstetrics, Gynecology and Reproductive Sciences

institute: University of Pittsburgh/Magee-Womens Research Institute

type: Methylation profiling by high throughput sequencing


title: The effects of a phage protein gp70.1 on Pseudomonas aerugonosa

city: ChongQing

first: Xia

last: Zhao

address: Shapingba

institute: Third military medical school

summary: The phage protein gp70.1 encoded by Pseudomonas aerugonosa phage PaP3 was toxic to both P. aerugonosa and E. coli, microarry analysis was used to investigate the effects of gp70.1 on P. aerugonosa with three periods of bacterial growth.

overall_design: Samples were taken from the PA3/pUCP24 (control) and PA3/pUCP24-orf70.1 lysates at lag, logarithmic and stable phase. Three independent experiments were performed at each time point.

first: Yinling

last: Tan


title: Expression profiling of control and Yap/Taz conditional knockout mouse incisor labial cervical loops

status: Public on Sep 21 2016

city: Los Angeles

first: Jimmy

last: Hu

address: 10833 Le Conte Ave.

institute: UCLA

summary: To understand expression changes caused by deletion of Yap and Taz in the mouse incisor labial cervical loops, we performed microarray analysis. As 100% CreER recombination was not possible, mutant samples would have contained some wild type cells. Nonetheless, these results identified genes that are up- or down-regulated in the absence of Yap and Taz and led us to uncover changes in cell differentiation, as well as mTOR signaling.

overall_design: Total RNA extracted from isolated labial cervical loops of 8 weeks old Yap/TazcKO mice were compared with control samples.

first: Ophir

last: Klein


title: Transcriptome analysis of T. reesei upon growth on different carbon sources in light and darkness

status: Public on Oct 03 2016

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

summary: The aim of this study was to evaluate changes in the transcriptome upon growth on different carbon sources in light or darkness.

overall_design: Strains of this study were grown on Mandels Andreotti Minimal Medium with 1 % w/v microcrystalline cellulose, glucose, glycerol or lactose as carbon source in constant light or constant darkness or pregrown for 24 hours on glycerol and then replaced to 1.5 mM Sophorose for cellulase induction and harvested after 5 hours; 2 biological replicates were included

first: Doris

last: Tisch


title: Deep sequencing of mycovirus-derived small RNAs from the fungi Botrytis spp.

status: Public on Sep 15 2016

city: Murcia

first: Livia

last: Donaire

state: Murcia

address: Campus de Espinardo

department: Plant Pathology

institute: Centro de Edafología y Biología Aplicada del Segura

summary: In this work, we have used deep sequencing to study the viral small RNA (vsiRNA) populations from different mycoviruses infecting field isolates of Botrytis spp. The mycoviruses under study belong to different genera and species and have different type of genome (dsRNA, (+)ssRNA, and (-)ssRNA). In general, vsiRNAs derived from mycoviruses are mostly of 21, 20 and 22 nucleotides in length, possess sense or antisense orientation either in a similar ratio or with a predominance of sense polarity depending on the virus species, have predominantly U at their 5' end, and are unevenly distributed along the viral genome showing conspicuous hotspots of vsiRNA accumulation. These characteristics reveal striking concomitances with vsiRNAs produced by plant viruses suggesting similar pathways of viral targeting in plants and fungi

sample_organism:
Botrytis cinerea
Botrytis paeoniae

platform_organism:
Botrytis cinerea
Botrytis paeoniae

overall_design: sRNA sequencing of two isolates of Botrytis cinerea (Pi285.8 and V448) and one isolate of Botrytis paeoniae (V446) infected with different mycoviruses

first: María

last: Ayllón


title: RNA sequencing of mice fed a high fat/high sucrose diet or a low fat/low sucrose diet

summary: Publication Title: DNA methylation alters transcriptional rates of differentially expressed genes and contributes to pathophysiology in mice fed a high fat diet. It is now well established that an intrauterine environment altered by overnutrition or malnutrition can change gene expression patterns through epigenetic mechanisms that may persist through generations.  However, it is less clear if overnutrition alters epigenetic control of gene expression in adults, or if whether such mechanisms contribute to the pathology of obesity. Here we test the hypothesis that exposure to a high fat diet alters hepatic DNA methylation and gene expression patterns, and explore the contribution of such changes to the pathophysiology of overnutrition. RNA-seq and targeted high-throughput bisulfite DNA sequencing were used to undertake a systematic analysis of the hepatic response to a high fat diet. A subset of genes was found whose expression levels were altered in concert with DNA methylation changes.  Using chromatin immunoprecipitation of RNA polymerase, we determined that hypermethylation correlated with decreased transcription of two of the genes, Phlda1 and Onecut1. A subnetwork of these genes and their nearest neighbors was generated from an existing Bayesian gene network that contained numerous hepatic regulatory genes involved in lipid and body weight homeostasis. Hepatic-specific depletion of Phlda1 in mice decreased the genes in the subnetwork, and led to increased oil droplet size in standard chow-fed mice, an early indicator of steatosis, validating the contribution of this gene to the phenotype.

overall_design: 14 mice fed either a high fat/high sucrose (n=7) or low fat/low sucrose (n=7) diet.

first: Pili

last: Zhang

first: Carmen

last: Argmann

first: Jacob

last: Hagen

first: Tianjiao

last: Chu

first: N

last: Dedousis

first: Benjamin

last: Mantell

first: Ian

last: Sipula

first: Lucy

last: Li

first: Kimberly

last: Bunce

last: Shaw

first: Robert

last: O'Doherty

first: David

first: Donald

last: Scott


title: Targeted bisulfite sequencing of mice fed a high fat/high sucrose diet or a low fat/low sucrose diet

first: David Peter

last: Peters

overall_design: 13 mice fed either a high fat/high sucrose (n=6) or low fat/low sucrose (n=7) diet.

first: Patricia


title: Regulation of the biofilm-specific genes circuitry in Candida albicans by a novel histone H3 variant

status: Public on Sep 08 2016

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To understand the biological relevance of the role played by the HHT1 histone H3 variant in C. albicans, we performed a transcriptome analysis of the mutant by global gene expression array analysis. We analyzed gene expression profile of the mutant in strains LR107 and LR108 (hht1∆/hht1∆) and the parent wild type (SC5314) strain grown in YPD liquid medium at 30°C. In the microarray analysis, a total of 1222 genes were found to be expressed significantly different (fold change < 1.5 at p-value < 0.05) between wild type and two hht1 null mutants. Out of the 1222 differentially expressed genes, 670 genes were up-regulated whereas 552 genes were down-regulated. Gene ontology (GO) analysis of up-regulated and down-regulated genes suggests that biofilm, Hap43, transcription, filamentation, white-opaque/mating and invasive growth are the major pathways altered in minor H3 null mutant. Transcription profiling in planktonic YPD condition suggests that minor H3 represses biofilm genes in the planktonic mode of growth. Therefore we performed a genome-wide expression array study after growing the wild type strain and hht1/hht1 mutant strains in Spider induced biofilm condition. This experiment was carried out with two biological replicates of hht1 null mutants. The biofilm induced microarray data revealed that a total of 1010 genes were differentially expressed (at p-value <0.05 and fold change <1.5) between the wild type and hht1 mutants. Out of 1016 differentially expressed genes, 572 genes were up-regulated whereas 444 genes were down-regulated.

overall_design: Agilent custom one-color experiment,Organism:Candida albicans, Whole Genome Candida albicans 8x15K (AMADID: 026377) designed  by Genotypic Technology Private Limited.

first: Rai

last: Laxmi

first: Sanyal

last: Kaustuv


title: Differentially expressed genes in certinib-resistant NB-1 xenografts

status: Public on Sep 01 2016

city: Cambridge

first: Fang

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research, Inc.

summary: The goal of this study is to elucidate the molecular mechanism that allowed NB-1 xenograft tumors to grow out in the presence of continued ALK inhibition.  Poly(A)-selected RNA was extracted from tissues of NB-1 tumors that progressed on ceritinib treatment and those treated with a vehicle to identify differentially expressed genes between these two groups.

overall_design: mRNA profiles of NB-1 xenograft tumors that progressed on ceritinib treatment and those treated with a vehicle were generated by RNA sequencing, in duplicate, using Illumina HiSeq 2500.

last: Ruddy

first: Daniel

middle: P

last: Rakiec


title: Antibody profile in patients with mild and severe leptospirosis

status: Public on Sep 10 2016

city: Irvine

first: Carolina

last: Lessa Aquino

address: 302 MedSurge II

institute: University of California Irvine

summary: Leptospirosis is zoonotic disease of global importance, with over a million cases andnearly 60,000 deaths annually. Symptomatic disease presentation ranges from a mildfebrile disease with non-specific symptoms to severe forms, characterized by multi-organ failure, lung hemorrhage, and death. Factors governing severe outcomes remainunclear, but the host immune response likely plays an important role. In the presentstudy, we applied high throughput techniques to identify the antibody profiles ofpatients with severe and mild leptospirosis. We discovered a limited number ofimmunodominant antigens, specific to patients. Surprisingly, we found the antibodyrepertoire varies in patients with different clinical outcomes and hypothesized thatpatients with mild symptoms were protected from severe disease due to pre-existingantibodies, while the profile of patients with severe outcomes was representative of afirst exposure. These findings represent a substantial step forward in the knowledge ofthe humoral immune response to Leptospira infection, and we have identified newtargets for vaccine and diagnostic test development.

overall_design: We used protein microarray chip to profile theantibody responses of patients with severe and mild leptospirosis against the completeLeptospira interrogans serovar Copenhageni predicted ORFeome. Serum samplesfrom patients with mild or severe leptospirosis were collected twice: (i) acute sample,collected at patient admittance at the health care unit and (ii) convalescent sample,collected 5-276 days after the first sampling. Controls consisted of (i) 37 sera fromhealthy Leptospira-unexposed (naïve) volunteers from California/US and (ii) 37 serafrom healthy participants enrolled in a cohort study in a high risk urban slumcommunity in Salvador, endemic for leptospirosis.

last: Lessa-Aquino

first: Janet

last: Lindow

first: Arlo

last: Randall

first: Elsio

last: Wunder

first: Jozelyn

last: Pablo

first: Rie

last: Nakajima

first: Algis

last: Jasinskas

first: Jaqueline

last: Cruz

first: Alcineia

middle: O

last: Damião

first: Nívison

last: Nery

first: Guilherme

last: Ribeiro

first: Federico

last: Costa

first: José

last: Hagan

first: Mitermayer

last: Reis

first: Albert

last: Ko

first: Marco

last: Medeiros

first: Philip

middle: L

last: Felgner


title: Addiction to the IGF2-ID1-IGF2 circuit for maintenance of the breast cancer stem-like cells.

status: Public on Sep 05 2016

city: Shirokanedai Minato-ku

first: Kana

last: Tominaga

state: Tokyo

department: Molecular therapy

institute: Insutitute of Medical Science, University of Tokyo

summary: The transcription factor nuclear factor-κB (NF-κB) has important roles for tumorigenesis, but how it regulates cancer stem cells (CSCs) remains largely unclear. We identified insulin-like growth factor 2 (IGF2) is a key target of NF-κB activated by HER2/HER3 signaling to form tumor spheres in breast cancer cells. The IGF2 receptor, IGF1 R, was expressed at high levels in CSC-enriched populations in primary breast cancer cells. Moreover, IGF2-PI3K (IGF2-phosphatidyl inositol 3 kinase) signaling induced expression of a stemness transcription factor, inhibitor of DNA-binding 1 (ID1), and IGF2 itself. ID1 knockdown greatly reduced IGF2 expression, and tumor sphere formation. Finally, treatment with anti-IGF1/2 antibodies blocked tumorigenesis derived from the IGF1Rhigh CSC-enriched population in a patient-derived xenograft model. Thus, NF-κB may trigger IGF2-ID1-IGF2-positive feedback circuits that allow cancer stem-like cells to appear. Then, they may become addicted to the circuits. As the circuits are the Achilles' heels of CSCs, it will be critical to break them for eradication of CSCs.

overall_design: MCF7 cells were serum-starved for 16 hours prior to stimulation with HRG (100 ng/ml). DHMEQ (1 μg/ml) or LY294002 (1 μg/ml) was added 2 hours prior to HRG stimulation.

first: Teppei

last: Shimamura

first: Natsuko

last: Kimura

first: Takahiko

last: Murayama

first: Daisuke

last: Matsubara

first: Hajime

last: Kanauchi

first: Atsushi

last: Niida

first: Seiichiro

last: Shimizu

first: Kotoe

last: Nishioka

first: Ei-ichi

last: Tsuji

first: Masao

last: Yano

first: Sumio

last: Sugano

first: Yohei

last: Shimono

first: Hideshi

last: Ishii

first: Hideyuki

last: Saya

first: Masaki

last: Mori

first: Koichi

last: Akashi

first: Kei-ichiro

last: Tada

first: Toshihisa

last: Ogawa

first: Arinobu

last: Tojo

first: Satoru

last: Miyano

first: Noriko

last: Gotoh


title: Effect of SWELL1 gene deletion on gene expression in adipocytes

city: Boston

first: William

middle: James

last: Gibson

state: Massachusetts

address: 34 Fairfield St #1

institute: Harvard Medical School

summary: We used RNA-Seq to detail the global expression changes induced when SWELL1 is genetically deleted from adipocytes.

overall_design: We generated isogenic SWELL1 KO adipocyte cell lines from 3T3-F442A cells. CRISR/Cas9 was used to knockout the SWELL1 gene in the parental 3T3-F442A line. These cell lines were grown in culture and RNA was extracted for sequencing. RNA was sequenced on an Illumina Hi-Seq at the University of Iowa Core Facility.

first: Rajan

last: Sah

middle: J


title: Small RNA and mRNA transcriptome profiling in wildtype mice at multiple stages of spermatogenesis, from whole testis at day 1 postpartum (pp), day 3 pp, and day 7 pp and purified leptotene/zygotene and pachytene spermatocytes.

city: Ithaca

first: Andrew

last: Grimson

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

summary: MicroRNAs are essential for spermatogenesis. However, the stage‑specific requirements for specific miRNAs in the male mammalian germ line remain largely uncharacterized. The miR‑34 family is, to date, the only miRNA proven to be necessary for the production of sperm in mice, though its germline roles are poorly understood. Here, we generate and analyze paired small RNA and mRNA profiles across different stages of germline development in male mice, focusing on time points shortly before and during meiotic prophase I.

overall_design: Testes from mice at day 1 pp, day 3 pp, day 7 pp, or from adult mice (day 70-80 pp) were removed, weighed and decapsulated. Mixed leptotene/zygotene or pachytene spermatocytes were isolated from the testis of adult mice.  RNA was isolated from either the whole testis or from purified spermatocytes using TRIzol.  Small RNA or RNA-Seq libraries were prepped using Illumina's sequencing library preparation kits. Libraries were genereated from two biological replicates per sample.

first: Stephanie

last: Hilz

last: Modzelewski

first: Paula

last: Cohen


title: Gene expression profiling of TH-MYCN mouse neuroblastoma sphere cells and their parental primary tumor cells

status: Public on Aug 24 2016

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

summary: We performed microarray gene expression profiling to identify genes essential for the growth and tumorigenicity of mouse neuroblastoma stem-like cells

overall_design: Affymetrix microarray assays were performed according to the manufacturer's directions on total RNA isolated from three independent lines of mouse neuroblastoma sphere cells and their parental primary tumor cells

first: Han-Fei

last: Ding

first: Jane


title: microRNA suppresses prostate cancer stem cells and metastasis by inhibiting a cohort of pro-metastasis targets including CD44, Rho GTPases and EZH2

status: Public on Aug 15 2016

city: Smithville

first: Liu

last: Can

address: 1808 Park Road 1C

department: Department of Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: microRNA plays important roles in tumor initiation and progression. Here we showed that, one of the miR-200 family member, miR-141 is drastically under-expressed in several prostate cancer stem cell populations in both xenograft and primary patient samples. Enforced expression of miR-141 in CD44+ PCa cells suppressed tumor initation and metastasis. Cancer stem cell related properties including clonal and sphere formation ability as well as migration and invasion abilites were blocked by miR-141. Moreover, under-expression of miR-141 in prostate cancer stem cells is important in maintaining a partial mesenchymal status. Whole genome sequencing revealed novel pathways that are regulated by miR-141 including Rho GTPase signaling pathway. Stem cell related molecules including CD44 and EZH2 are also validated as direct targets of miR-141 mediating the tumor and metastasis suppressive function. Altogether, these data suggests that on e signal miRNA, miR-141 could utilize multiple mechanisms to obstruct tumor progression and metstasiss.

overall_design: Total transcriptome profiles of prostate cancer cells Du145 and LAPC9 transfected with 30nM miR-141 mimicking oligonucleotides or negative control (NC) oligonucleotides were generated by deep sequencing, in duplicates, using Illumina HiSeq 2000.

first: Can

last: Liu

first: Yue

last: Lu

first: Dean

last: Tang


title: Comparative genomic, transcriptomic and secretomic profilings of Penicillium oxalicum HP7-1 and its cellulase and xylanase hyper-producing mutant EU2106, and identification of two novel regulators for cellulase and xylanase gene expression

status: Public on Aug 31 2016

city: ShenZhen

first: Shangbo

last: Xie

address: BeiShanDao

institute: BGI

summary: In this study,comparative genomic, transcriptomic and secretomic profilings of Penicillium oxalicum HP7-1 and its cellulase and xylanase hyper-producing mutant EU2106 were employed to screen for novel regulators for cellulase and xylanase gene expression.

overall_design: mRNA profiles of P. oxalicum wild-type strain HP7-1 and its mutant EU2106 were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000

first: Jia

middle: X

last: Feng


title: m6A sequencing of HIV viral genomic RNA and infected host cell samples

status: Public on Aug 18 2016

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: The internal N6-methyladenosine (m6A) methylation of eukaryotic nuclear RNA controls post-transcriptional gene expression, which is regulated by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers) in cells. The YTH domain family proteins (YTHDF1–3) bind to m6A-modified cellular RNAs and affect RNA metabolism and processing. Here, we show that YTHDF1–3 proteins recognize m6A-modified HIV-1 RNA and inhibit HIV-1 infection in cell lines and primary CD4+ T-cells. We further mapped the YTHDF1–3 binding sites in HIV-1 RNA from infected cells. We found that the overexpression of YTHDF proteins in cells inhibited HIV-1 infection mainly by decreasing HIV-1 reverse transcription, while knockdown of YTHDF1–3 in cells had the opposite effects. Moreover, silencing the m6A writers decreased HIV-1 Gag protein expression in virus-producing cells, while silencing the m6A erasers increased Gag expression. Our findings suggest an important role of m6A modification of HIV-1 RNA in viral infection and HIV-1 protein synthesis.

overall_design: m6A-seq of vgRNA from virions and mRNA from infected host cells

first: Boxuan

middle: S

last: Zhao

first: Zhike

first: Chuan

last: He


title: Expression data from Rattus norvegicus cornea

city: Linkoping

first: Neil

last: Lagali

address: sandbacksgatan 7

department: Ophthalmology

country: Sweden

institute: linkoping University

summary:
Inflammation is a key component of pathological angiogenesis. Here we induce cornea neovascularisation using sutures placed into the cornea, and sutures are removed to induce a regression phase.
We used whole transcriptome microarray to monitor gene expression profies of several genes

overall_design: This was a time course study conprising two arms. In the suture IN arm, sutures were maintained in the cornea after the 0h time point, while suture OUT arm is where both sutures were removed from the cornea at the 0h timpoint. 0h timepoint is when sprouts were 3/4 the distance from the pre-existing limbal vessels towards the sutures. Microarrays were performed at 0h, 24h suture IN and 24h suture OUT. Non sutured eyes from separate animals were used as controls. At each time point except for 0h=3 rats, the rest of the timepoints had four rats each.

first: Anthony

last: Mukwaya

first: Beatrice

middle: B

last: Peebo

first: Maria

last: Xeroudaki

first: Jessica

last: Lindvall

first: Zaheer

last: Ali

first: Lasse

last: Jensen

first: Anton

last: Lennikov


title: Identification of novel ovarian predominant miRNAs in medaka

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

summary: The involvement of miRNAs during vertebrate oogenesis is poorly documented. Based on the assumption that ovarian-specific or ovarian-predominant genes usually play important roles during oogenesis, we searched for ovarian-predominant miRNAs in the medaka (Oryzias latipes) ovary. 10 tissus were collected from adult medaka (intestine, ovary, testis, liver, heart, gills, kidney, brain, muscle and bone) and RNAs were hybridized on a designed agilent microarray displaying 3800 distinct miRNAs from different teleost and vertebrate species.  We identified 66 miRNAs sequences predominantly expressed in the ovary that had never been previously described in medaka.

overall_design: miRNAs expression was mesured in 10 different medaka tissus (intestinee, ovary, testis, liver, heart, gills, kidney, brain, muscle and bone). Four biological replicates were used for each tissue.

first: Amine

last: Bouchareb

first: Aurélie

last: Le Cam

first: Jérôme

last: Montfort

first: Stéphanie

last: Gay

first: Thao

last: Nguyen

first: Violette

last: Thermes


title: Fibroblast transcription pattern in Salmonella infected Vs uninfected cells

status: Public on Aug 04 2016

city: Madrid

first: Francisco

last: García-del Portillo

address: Darwin 3

institute: Centro Nacional de Biotecnología (CNB-CSIC)

summary: Human fibroblasts were infected with GFP-expressing Salmonella enterica serovar Typmimurium and further separated by Fluorescence Activated Cell Sorting. RNA from infected and uninfected cells sub-populations were used for genome-wide expression studies

overall_design: 3 independent experiments enabled us to obtain 3 infected and 3 uninfected sub-populations.

first: Estel

last: Ramos-Marquès


title: Axonal mRNA in human embryonic stem cell derived neurons

status: Public on Jul 29 2016

city: Chapel Hill

first: Anne

middle: Marion

last: Taylor

state: North Carolina

address: 152 MacNider, CB 7575

department: Biomedical Engineering

institute: UNC-Chapel Hill

summary: The identification of axonal mRNAs in model organisms has led to the discovery of many axonally translated proteins required for axon guidance and injury response. The extent to which these axonal mRNAs are conserved in humans is unknown. Here we report on the axonal transcriptome of glutamatergic neurons derived from human embryonic stem cells (hESC-neurons) grown in axon isolating microfluidic chambers. We identified mRNAs enriched in axons, representing a functionally unique local transcriptome as compared to the whole neuron transcriptome. Further, we found that the enriched functional categories within high confidence axonal transcripts resemble those in the axonal transcriptome of rat cortical neurons. Comparing our list of human axonal transcripts to similar datasets generated from embryonic and adult rat dorsal root ganglia and rat cortical neurons we found 60 mRNAs common to all four neuron types. We found that over half of these genes are associated with neurological phenotypes or diseases in model organisms and human. This data provides an important resource for studying local mRNA translation in human axons and has the potential to reveal both conserved and unique axonal mechanisms across species and neuronal types.

overall_design: We analyzed the axonal and whole hESC-neuron transcriptome in triplicate using the Affymetrix Human Gene 2.0 ST Array platform.

first: Rebecca

last: Bigler

first: Joyce

last: Kamande

first: Raluca

last: Dumitru

first: Mark

last: Neidringhaus

middle: M


title: White adipose tissue browning in the R6/2 mouse model of Huntington's disease

status: Public on Jul 28 2016

city: Lund

first: Maria

last: Björkqvist

state: Skåne

address: Sölvegatan 17

department: Experimental Medical Sciences

institute: Lund University

summary:
We investigated gene expression signatures in subcutaneous inguinal adipose tissue obtained from wild type and R6/2 mice with the aim to identify gene expression changes and signalling pathway alterations in adipose tissue relevant to HD.
Gene expression was assessed using Affymetrix GeneChip® Mouse Gene 2.0 ST Array. Target genes were technically validated using real-time quantitative PCR.

overall_design: 12 subcutaneous inguinal white adipose tissue samples were analyzed by affymetrix: 6 wild-type samples; 6 R6/2 mouse samples.

first: Andrew

middle: C

last: McCourt

first: Lovisa

last: Jakobsson

first: Sara

last: Larsson

first: Cecilia

last: Holm

first: Sarah

last: Piel

first: Eskil

last: Elmér


title: BCL6 enforces human glioblastoma growth and serves as a novel therapeutic target (expression)

status: Public on Aug 01 2016

city: Singapore

first: Phillip

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

summary: This study uncovers a novel growth-promoting role of BCL6 in GBM, and provide the rationale of targeting BCL6 as a potential therapeutic approach for this deadly malignancy.

overall_design: cDNA microarray analysis was performed in U87 cells transfected with either non-targeting siRNAs or BCL6 siRNAs. All experiments were carried out in duplicates.

first: Xu

last: Liang

first: Chen

last: Ye

first: Marina

last: Dutra-Clarke

first: Anand

last: Mayakonda

first: Masaharu

last: Hazawa

first: Ngan

last: Doan

first: Jonathan

last: Said

first: William

last: Yong

first: Henry

last: Yang

first: Ling-Wen

last: Ding

first: Yan-Yi

last: Jiayng

first: Jeffrey

last: Tyner

first: Jianhong

last: Ching

first: Jean-Paul

last: Kovalik

first: Markus

last: Müschen

first: Joshua

last: Breunig

first: De-Chen

last: Lin


title: Characterization of peroxisome-associated transcriptome

first: Arsen

last: Batagov

address: 30 Biopolis St, Matrix, 07-1

institute: Bioinformatics Institute

summary:
This is a pioneer genome-wide study of localization of mRNAs to peroxisomes. The findings suggest that translation of a subset of peroxiomal proteins and other cellular metabolic enzymes may be spatially regulated by directing their encoding mRNAs to the surface of peroxisomes. The study provides foundation for more detailed dissection of mechanisms of RNA targeting to subcellular compartments.
In this study we performed the genome-wide transcriptome analysis of peroxisome preparations from the mouse liver using microarrays. We demonstrate that RNA is absent inside peroxisomes, however it is associated at their exterior via the noncovalent contacts with the membrane proteins. We detect enrichment of specific sets of transcripts in two preparations of peroxisomes, purified with different degrees of stringency. Importantly, among these were mRNAs encoding bona fide peroxisomal proteins, such as peroxins and peroxisomal matrix enzymes involved in beta-oxidation of fatty acids and bile acid biosynthesis.

overall_design: Two subcellular fractions were obtained from the mouse liver by centrifugation in iodixanol density gradient: 1) Peroxisomal (PX), 2) Mitochondrial/Lysosomal (ML). The membrane-enclosed peroxisomal fraction (PX-IP) was obtained by immuno-precispitation of the PX fraction with the PMP70-specific antibodies. RNA was extracted from each fraction. Additionally, the total cellular RNA was obtained from the whole cell extracts (T). Thus, four RNA sample types were obtained for gene expression analysis: T, ML, PX, PI. Three technical replicates of each sample ware analyzed with Illumina microarrays.

first: Aliaksandr

middle: A

last: Yarmishyn

last: O Batagov

first: Maksym

last: Kremenskoy

first: Igor

middle: V

last: Kurochkin


title: Subcutaneous adipose tissue and visceral adipose tissue gene expression profiles in Mexican patients with obesity

status: Public on Jul 20 2016

city: Mexico City

first: Esau

middle: Floriano

last: Sanchez

address: Cerrada de Palomas SN

department: Military School of Graduate of Health

country: Mexico

institute: SEDENA

summary: Using RNA isolated from subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) samples obtained from control and class I, II and III obese patients undergoing inguinal hernia repair and laparoscopic cholecystectomy, we compared the gene expression profiles between SAT and VAT using microarrays and validated the findings by real-time quantitative PCR.

overall_design: Two-condition experiment, SAT vs. VAT tissue. Biological replicates: 8 SAT replicates, 8 VAT replicates.

first: M

middle: D

last: Ronquillo Sanchez

first: A

last: Mellnyk

first: E

last: Lara Padilla

last: Martinez Lara

first: D

last: Comoto Santacruz

first: N

middle: E

last: Herrera Gonzalez

last: Pereyra Talamantes

last: Cardenas Rodriguez

last: Floriano Sanchez


title: Global Transcriptional profiling of bone marrow derived hepatocytes

status: Public on Jul 01 2016

city: Bangalore

first: Genotypic

last: technology

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: Whole genome expression of bone marrow deived hepatocytes after 1 and 5 months of transplantation are compared with that of primary hepatocytes and Lin- BM cells

overall_design: Agilent one-color experiment,Organism:Mouse, Agilent Whole Genome Mouse 8x60k (AMADID: 028005 & 026986)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Asok

last: Mukhopadhyay

first: Veena

last: Kochat


title: Gene expression in inflammatory macrophages, tissue resident macrophages and neutrophils

city: Shenzhen

first: Yaojiong

last: Wu

state: Guangzhou

address: Xili unversity town, Nanshan

department: Graduate school at shenzhen

institute: Tsinghua university

summary: Genes expression in Ly6C+/F4/80+ inflammatory macrophages, CX3CR1+/F4/80+ tissue resident macrophages and Ly6G+/F4/80- neutrophils which were isolated from day 3 wounds in C57/B6 mice aged 8 weeks by cell sorting

overall_design: Ly6C+ macrophages expressed higher (over 5 folds) levels of 241 genes compared to CX3CR1+ macrophages, and 3382 genes compared to neutrophils


title: Transcriptional and translational analysis of wild-type and Mincle-KO macrophages

status: Public on Jul 10 2016

city: Seoul

first: Wook-Bin

last: Lee

address: Shinchon-dong Seodeamun-gu

department: Biochemistry

country: South Korea

institute: Yonsei University

summary: Analysis of total RNAs from wild-type and Mincle-KO macrophages stimulated with TLR2 ligand and co-stimulated with TLR2 ligand and Mincle ligand. And analysis of total and polysomal RNAs from wild-type macrophages co-stimulated with TLR2 ligand and Mincle ligand in the presence or absence of DHS inhibitor (GC7). Mincle is a C-type lectin receptor for trehalose dimycolate, a mycobacterial cell wall component. And results provide insight into the crosstalk between the TLR2 and Mincle signaling pathways by RNA-seq assay and identifying potential targets of Mincle-mediated translational control by polysome profiling assay.

overall_design: Bone marrow derived macrophage mRNA profiles of wild type (WT) and Mincle-KO mice were generated by deep sequencing, using Illumina HiSeq-2000.

first: Young-Joon

last: Kim

first: Won

middle: Y

last: Choi


title: Unique inflammatory transcriptome profiles at the maternal fetal interface and onset of human preterm and term birth

status: Public on Jun 30 2016

city: Newtown Square

first: Don

middle: A.

last: Baldwin

address: 4240 Fairview Ave

institute: Signal Biology Inc

summary: Preterm birth is a main determinant of neonatal mortality and morbidity and a major contributor to the overall mortality and burden of disease. However, precise phenotyping of the preterm birth is hampered by the imprecise definition of the clinical phenotype and complexity of the molecular phenotype due to multiple pregnancy tissue types and molecular processes that may contribute to the preterm birth. The study’s aim was to comprehensively evaluate the mRNA transcriptome that characterizes preterm and term labor using precisely phenotyped samples. Expression profiles of 73 genes and non-coding RNA sequences uniquely identified the four groups of patients: delivering preterm with (PL) and without labor (PNL), term with (TL) and without labor (TNL).  The largest differences in gene expression among the four groups occurred in decidua, chorion and amnion. The gene expression profiles showed suppression of chemokines expression in TNL, withdrawal of this suppression in TL, activation of multiple pathways of inflammation in PL, and an immune rejection profile in PNL. The genes constituting expression signatures showed over-representation of three putative regulatory elements in their 5’ and 3’UTR regions. The results suggest that pregnancy is maintained by downregulation of chemokines at the maternal-fetal interface. Withdrawal of this downregulation results in the term birth and its overriding by the activation of multiple pathways of the immune system in the preterm birth. Complications of the pregnancy associated with impairment of placental function, which necessitated premature delivery of the fetus in the absence of labor, show gene expression patterns associated with immune rejection.

overall_design:
183 total RNA samples from 8 tissue types collected from 35 women grouped into six categories of pregnancy outcome. One microarray replicate per sample.

Other Contributors:
Radek Bukowski, Sam Parry and the NICHD Genomic and Proteomic Network for Preterm Birth Research


title: T cells from paroxysmal nocturnal hemoglobinuria patients show an altered TNFR signaling pathway

status: Public on Jun 29 2016

first: Wangmin

last: Qiao

address: Building NO.7, BGI Park, No.21 Hongan 3rd Street, Yantian District

summary: In order to identify aberrant molecular mechanisms involved in immune targeting of HSCs in bone marrow, RNA-seq was applied to examine the transcriptome of T cell subsets from PNH patients and healthy controls.

overall_design: RNA seq , 3 PNH patient's T cell subsets (CD4Naive, CD4Memory,CD8Naive, CD8Memory), 3 Healthy T cell subsets (CD4Naive,CD4Memory, CD8Naive, CD8memory)

first: Kohei

last: Hosokawa

first: Sachiko

last: Kajigaya

first: Keyvan

last: Keyvanfar

first: Yanling

last: Xie

first: Danielle

last: Townsley

first: Xingmin

last: Feng

first: Neal

last: Young


title: Expression data from Aspergillus nidulans FGSCA26 and SirAdelta grown for 24,48, and 72h

status: Public on Aug 09 2016

city: tsukuba

first: Eriko

last: Itoh

address: 1-1-1 tennodai

institute: university of tsukuba

summary: The sirA gene encodes a member of sirtuin protein that is NAD(+)-dependent histone deacetylase (HDAC) and ubiquitous in eukaryote. DNA microarray analyses for Aspergillus nidulans FGSCA26 (WT) strain and Gene disruptant of sirA (SirAd) indicated that genes for synthesizing secondary metabolic products such as sterigmatocystin, penicillin G, emericellamide, aspernidine A, xanthone, austinol, and siderophores are down-regulated by SirA.

overall_design: Aspergillus nidulans WT and SirAd strains were cultured in 200 ml of GMM at 30°C for 24, 48, and 72 h, and their total RNA was purified as described above.

first: Naoki

last: Takaya


title: Transcriptional profile of mice with good and poor spatial learning during West Nile virus recovery

status: Public on Jun 27 2016

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Greater than 50% of patients who survive neuroinvasive West Nile virus (WNV), a mosquito-borne, positive-sense strand flavivirus, exhibit cognitive sequelae including memory impairments which may last several years. High survival rates from WNV neuroinvasive disease (WNND) (>90%) have led to hundreds to thousands of cases of WNV-mediated neurologic impairment accruing annually, yet underlying mechanisms responsible for these impairments have not been investigated. Here, we established a novel murine model of recovery from WNND in which intracranial inoculation of a mutant WNV (WNV-NS5-E218A) leads to rates of survival and cognitive dysfunction that mirror human WNND. WNV-NS5-E218A-recovered mice exhibit impaired spatial learning and persistently phagocytic microglia without significant loss of hippocampal neurons or brain volume. Whole transcriptome analysis of hippocampi from WNV-NS5-E218A-recovered mice with poor spatial learning was performed in order to identify target pathways and molecules underlying cognitive impairments during WNND recovery.

overall_design: Total RNA obtained from isolated murine hippocampus at 25 days post-mock or WNV-NS5-E218A intracranial infection.

first: Michael

last: Vasek

first: Robyn

last: Klein


title: Tacrolimus in diabetic nephropathy

city: Vienna

first: Constantin

last: Aschauer

address: Waehringer Gürtel 18-20, 1090 Wien

institute: Medical University of Vienna

summary:
Validation of predicted gene expression of human mesangial cells after 24h Tacrolimus stimulus
Objective:
To evaluate tacrolimus as therapeutic option for diabetic nephropathy (DN) based on molecular profile and network-based molecular model comparisons.
Materials and Methods:
We generated molecular models representing pathophysiological mechanisms of DN and tacrolimus mechanism of action (MoA) based on literature derived data and transcriptomics datasets. Shared enriched molecular pathways were identified based on both model datasets. A newly generated transcriptomics dataset studying the effect of tacrolimus on mesangial cells in vitro was added to identify mechanisms in DN pathophysiology. We searched for features in interference between the DN molecular model and the tacrolimus MoA molecular model already holding annotation evidence as diagnostic or prognostic biomarker in the context of DN.
Results:
Thirty nine molecular features were shared between the DN molecular model, holding 252 molecular features and the tacrolimus MoA molecular model, holding 209 molecular features, with six additional molecular features affected by tacrolimus in mesangial cells. Significantly affected molecular pathways by both molecular model sets included cytokine-cytokine receptor interactions, adherens junctions, TGF-beta signaling, MAPK signaling, and calcium signaling. Molecular features involved in inflammation and immune response contributing to DN progression were significantly downregulated by tacrolimus (e.g. the tumor necrosis factor alpha (TNF), interleukin 4, or interleukin 10). On the other hand, pro-fibrotic stimuli being detrimental to renal function were induced by tacrolimus like the transforming growth factor beta 1 (TGFB1), endothelin 1 (EDN1), or type IV collagen alpha 1 (COL4A1).
Conclusion:
Patients with DN and elevated TNF levels might benefit from tacrolimus treatment regarding maintaining GFR and reducing inflammation. TGFB1 and EDN1 are proposed as monitoring markers to assess degree of renal damage. Next to this stratification approach, the use of drug combinations consisting of tacrolimus in addition to ACE inhibitors, angiotensin receptor blockers, TGFB1- or EDN1-receptor antagonists might warrant further studies.

overall_design: comparison of gene expression of human mesangial cells after 24h Tacrolimus vs. Ctrl; 4 independent experiments were conducted (4xTacrolimus 24h and 4x ctrl. 24h with Drug solvent (DMSO))

first: Paul

last: Perco

first: Andreas

last: Heinzel

first: Judith

last: Sunzenauer

first: Rainer

last: Oberbauer


title: fe-fit-diff_6d-Differential gene expression in A. thaliana roots depending on iron supply and FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) abundance

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: au15-01_iron-fit - fe-fit-diff_6d - Changes in gene expression profiles between fit knock-out, wild-type and FIT overexpressor seedlings under sufficient iron supply and under iron deficiency. - Col-0, HA-FIT and fit-3.

overall_design: 21 dye-swap - gene knock in (transgenic),gene knock out,treated vs untreated comparison

first: Petra-

last: Bauer

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Gene expression of Lymphoblastoid Cell Lines (LCLs) from Depressed Patients after in-vitro treatment with fluoxetine

status: Public on Jun 15 2016

city: Bonn

first: Julia

middle: Carolin

last: Stingl

address: Kurt-Georg-Kiesinger Allee 3

department: Research

country: Germany

institute: Federal Institute for Drugs and Medical Devices

summary: We used whole gene gene expression profiling to identify potential gene expression biomarkers associated for the treatment individualization of depressive disorders.

overall_design: Gene expression was measured after 21 days of in-vitro treatment with therapeutical concentrations of fluoxetine in n=10 LCLs derived from depressed patients with documented clinical treatment outcome.

first: Jörg

last: Breitfeld

first: Catharina

last: Scholl

last: Steffens


title: Gene expression data from 4T1 cells stably transduced with lentiviral vectors encoding a control shRNA (shscramble) or two shRNAs targeting TM4SF1 (shTM4SF1-1 and shTM4SF1-5) and from 4TO7 cells stably expressing with or without TM4SF1

status: Public on Jun 11 2016

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Compare the gene expression profile between shscramble with shTM4SF1 knockingdown 4T1 cells and between 4TO7 cells stably expressing with or without TM4SF1

first: Hua

last: Gao

first: Goutam

last: Chakraborty

first: Filippo

middle: G

last: Giancotti


title: Expression data from RAD21 knockdown in MCF7 cells

status: Public on Jun 01 2016

first: Jiyeon

last: YUN

address: 317,Cancer research institute, Seoul Nat. Univ. Youngondong, Jongnogu, Seoul

institute: Cancer research institute

summary:
RAD21 plays multi-functional roles in cell. We explored which genes are target of RAD21 in the cell.
We used microarray to find out the target of RAD21 comparing between shGFP(control) and shRAD21 expressing MCF7 cells.

overall_design: we stably expressed shGFP or shRAD21 in each MCF7 cell and selected single cells having high transfection efficiency of shRNAs. And then we had cultured the single cells for 30 days to harvest sufficient cells.

first: Tae-You

last: Kim

last: Yun


title: Transcriptome of K14 V12 Rac1 mice

status: Public on Jun 13 2016

city: Stanford

first: Marten

middle: CG

last: Winge

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford University

summary: Wholeskin from transgenic mice overexpressing epidermal specific (K14) activated mutant (V12) Rac1 analyzed with Illumina MouseRef8 v2 Gene Expression arrays

overall_design: Three V12 Rac1 7 day old pups compared to three 7 day old litter-mate controls

first: Mårten

first: Matt

middle: P

last: Marinkovich


title: Clostridium beijerinckii NCIMB8052 wild-type cells vs.Clostridium beijerinckii NCIMB8052 degenerated strain cells

city: Wooster

first: Yan

last: Zhang

state: OH

address: 1680 Madison Avenue

department: Animal Sciences

institute: The Ohio State University

summary: The transcriptome analysis by microarray was applied on wild-type and degenerated strains of C. beijerinckii NCIMB8052 (WT-8052 and DG-8052, respectively) to elucidate its mechanism of degeneration during solvent fermentation. The comparison of gene expression pattern in relation to ABE production is expected to provide insights toward metabolically engineering of C. beijerinckii NCIMB8052 with prevention of degeneration and eventually enhancement of ABE production.

overall_design: Two-fermentation time points (12h and 24h) experiments (wild-type cells vs.degenerated strain cells);Biological replicates: 3 replicates of wild-type cells at 12h;3 replicates of wild-type cells at 24h;3 replicates of degenerated cells at 12h;3 replicates of degenerated cells at 24h  .

first: Bei

last: Han


title: Gene Expression from hair cells and supporting cells in chick utricle

status: Public on May 17 2016

city: Fukuoka

first: Takahiro

last: Wakasaki

state: Fukuoka

address: 3-1-1 Notame

institute: National Kyushu Cancer Center

summary:
In adult mammals, hair cell loss is irreversible and may result in hearing and balance deficits. In contrast, birds can regenerate hair cells through differentiation of supporting cells and restore inner ear function, suggesting that hair cell progenitors are present in the population of supporting cells.
We used microarrays to identify novel genes related to the regeneration in the chicken utricle.

overall_design: Supporting cell and hair cell populations of chicken utricle obtained by laser capture microdissection, following to do RNA extraction and hybridization on Affymetrix microarrays.


title: Association of Multiparametric MRI Quantitative Imaging Features with Prostate Cancer Gene Expression in MRI-targeted Prostate Biopsies

status: Public on Jun 07 2016

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

institute: GenomeDx

summary: Standard clinicopathological variables are inadequate for optimal management of prostate cancer patients. While genomic classifiers have improved patient risk classification, the multifocality and heterogeneity of prostate cancer can confound pre-treatment assessment. The objective is to investigate the association of multiparametric (mp)MRI quantitative features with prostate cancer risk gene expression profiles in mpMRI-guided biopsies tissues.

overall_design: Global gene expression profiles were generated from 17 mpMRI-directed diagnostic prostate biopsies using an Affymetrix platform. Spatially distinct imaging areas (‘habitats’) were targeted following MRI/3D-Ultrasound fusion. Radiomic features were extracted from biopsy regions and normal appearing tissues

first: Radka

last: Stoyanova

first: Alan

last: Pollack

first: Mandeep

last: Takhar

first: Charles

last: Lynne

first: Nestor

last: Parra

first: Lucia

middle: L

last: Lam

first: Mohammed

last: Alshalalfa

first: Christine

last: Buerki

first: Rosa

last: Castillo

first: Merce

last: Jorda

first: Hussam

last: Al-deen Ashab

first: Oleksandr

middle: N

last: Kryvenko

first: Sanoj

last: Punnen

first: Dipen

middle: J

last: Parekh

first: Matthew

last: Abramowitz

first: Robert

last: Gillies

first: Nicholas

last: Erho

first: Adrian

last: Ishkanian


title: Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma

status: Public on May 07 2016

city: Tarrytown

first: Ruoyu

last: Zhang

address: 777 Old Saw Mill River Road

institute: Regeneron

summary: Background: Cell free DNA (cfDNA) in plasma has received increasing attention and has been studied in a broad range of clinical conditions implicating inflammation, cancer, and aging. However, few studies have focused on mitochondrial DNA (mtDNA) in the cell free form. This study characterized the size distribution and sequence characteristics of plasma cell free mtDNA (cf mtDNA) in humans.Methods and Results: We optimized DNA isolation and next-generation sequencing library preparation protocols to better retain short DNA fragments from plasma, and applied these optimized methods to plasma samples from patients with sepsis. After massive parallel sequencing, we verified that our methods can retain substantially shorter DNA fragments than the standard isolation method, resulting in an average of 11.5 fold increase in short DNA fragments yield (DNA < 100bp). We report that cf mtDNA in plasma is highly enriched in short-size cfDNA (30 ~ 60 bp), which is much shorter than the value previously reported (~140 bp). Motivated by this unique size distribution, we size-selected short cfDNA fragments from the sequencing library, which further increased the mtDNA recovery rate by an average of 10.4 fold. Using this approach we detected mixtures of different mtDNA sequences, termed heteroplasmy, in plasma from 3 patients. In one patient who previously received bone marrow transplantation, different minor allele frequencies were observed between plasma and white blood cells (WBC) at heteroplasmic mtDNA sites, consistent with mixed-tissue origin for plasma DNA.Conclusion: mtDNA in plasma exists as very short fragments that exhibit mtDNA heteroplasmy distribution differences from that found in a single organ/tissue. This study is the first report of genome wide identification of mtDNA heteroplasmy in human plasma. Our optimized method can be used to investigate the potential utility of cf mtDNA fragments and heteroplasmy as biomarkers in various diseases.

overall_design: Examine plasma mtDNA of 7 individuals by 3 different protocols

first: Kiichi

last: Nakahira

first: Xiaoxian

last: Guo

first: Augustine

last: Choi

first: Zhenglong

last: Gu


title: Expression data from porcine mandibular- and tibial-derived bone marrow mesenchymal stem cells.

status: Public on May 14 2016

city: Columbus

first: Zongyang

last: Sun

state: Ohio

address: 305 W 12th Ave

department: Orthodontics

summary: Objective: Craniofacial bone defects caused by injuries and congenital diseases are a formidable challenge to clinicians. Research has shown promise in using bone marrow mesenchymal stem cells (BM-MSCs) from limb bones for craniofacial bone regeneration; yet little is known about the potential of BM-MSCs from craniofacial bones. This study compared BM-MSCs isolated from limb and craniofacial bones in pigs, a preclinical model closely resembling humans.   Design: Bone marrow was aspirated from the tibia and mandible of four-month-old pigs (n=4), followed by BM-MSC isolation, culture-expansion and confirmation by flow cytometry. Proliferation rates were compared using population doubling times. Osteogenic differentiation was evaluated by quantifying alkaline phosphatase (ALP) activity. Total mRNA was extracted from freshly isolated BM-MSCs and analyzed to compare gene expressions of tibial and mandibular BM-MSCs using an Affymetrix GeneChip porcine genome array, followed by real-time RT-PCR evaluation of two neural crest markers.   Results: BM-MSCs from both locations expressed MSC markers without expression of hematopoietic markers. Mandibular BM-MSCs proliferated significantly faster than tibial BM-MSCs. Without osteogenic inducers, mandibular BM-MSC alkaline phosphatase activities were 3.3-fold greater than those of tibial origin. Microarray analysis identified 383 differentially expressed genes in mandibular and tibial BM-MSCs, including higher expression of cranial neural crest-related genes nestin and BMP-4 in mandibular BM-MSCs, a trend also confirmed by real-time RT-PCR. Among differently expressed genes, only 47 showed greater than 1.5-fold differences in expression.    Conclusions: These data indicate that despite many similarities in gene expression, mandibular BM-MSCs express of number of genes differently than tibial BM-MSCs and have a phenotypic profile that may make them advantageous for craniofacial bone regeneration.

overall_design: Bone marrow was aspirated from the mandibular symphyseal region and the tibia of 3 pigs. Mesenchymal stem cells were isolated from the bone marrow and cultured to 80% confluence. Cells were harvested for total RNA extraction and the RNA was analyzed by Affymetrix GeneChip porcine genome array.

first: B

last: Lloyd

last: Tee

first: C

last: Headley

first: H

last: Emam

first: S

last: Mallery

first: Z


title: Gene expression study of blood monocytes in pre- and postmenopausal females with low or high bone mineral density (HG-U133A)

city: New Orleans

first: Yao-Zhong

last: Liu

state: LA

address: 1440 Canal Street, Suite 2001

department: Dept. of Biostatistics and Bioinformatics

institute: Tulane University School of Public Health

summary:
Comparison of circulating monocytes from pre- and postmanopausal females with low or high bone mineral density (BMD). Circulating monocytes are progenitors of osteoclasts, and produce factors important to bone metabolism. Results provide insight into the role of monocytes in osteoporosis.
We identify osteoporosis genes by microarray analyses of monocytes in high vs. low hip BMD (bone mineral density) subjects.

overall_design: Microarray analyses of monocytes were performed using Affymetrix HG-133A arrays in 80 Caucasian females, including 40 high (20 pre- and 20 postmanopausal) and 40 low hip BMD (20 pre- and 20 postmanopausal) subjects

first: Yu

last: Zhou

first: Yongjun

first: Lei

first: Jian

last: Li

first: Qing

last: Tian

first: Ji-Gang

first: Hong-Wen

last: Deng


title: Gene expression study of blood monocytes in pre- and postmenopausal females with low or high bone mineral density (HuEx-1_0-st-v2)

summary:
Comparison of circulating monocytes from pre- and postmenopausal females with low or high bone mineral density (BMD). Circulating monocytes are progenitors of osteoclasts, and produce factors important to bone metabolism. Results provide insight into the role of monocytes in osteoporosis.
We identify osteoporosis genes by microarray analyses of monocytes in high vs. low hip BMD (bone mineral density) subjects.

overall_design: Microarray analyses of monocytes were performed using Affymetrix 1.0 ST arrays in 73 Caucasian females (age: 47-56) with extremely high (mean ZBMD =1.38, n=42, 16 pre- and 26 postmenopausal subjects) or low hip BMD (mean ZBMD=-1.05, n=31, 15 pre- and 16 postmenopausal subjects). Differential gene expression analysis in high vs. low BMD subjects was conducted in the total cohort as well as pre- and post-menopausal subjects.


title: Gene expression study of blood monocytes in pre- and postmenopausal females with low or high bone mineral density

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

overall_design: Refer to individual Series